Structured Review

Collaborative Drug Discovery Inc carotenoid cleavage dioxygenase
The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid <t>dioxygenase</t> 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.
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Images

1) Product Images from "Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay"

Article Title: Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

Journal: BMC Genomics

doi: 10.1186/1471-2164-10-212

The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid dioxygenase 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.
Figure Legend Snippet: The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid dioxygenase 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.

Techniques Used: Quantitative RT-PCR

2) Product Images from "Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay"

Article Title: Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

Journal: BMC Genomics

doi: 10.1186/1471-2164-10-212

The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid dioxygenase 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.
Figure Legend Snippet: The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid dioxygenase 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.

Techniques Used: Quantitative RT-PCR

3) Product Images from "Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits"

Article Title: Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/err284

Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.
Figure Legend Snippet: Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.

Techniques Used: Expressing

4) Product Images from "Expression of MdCCD7 in the scion determines the extent of sylleptic branching and the primary shoot growth rate of apple trees"

Article Title: Expression of MdCCD7 in the scion determines the extent of sylleptic branching and the primary shoot growth rate of apple trees

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/erx404

Unrooted phylogenetic tree of the CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) gene family. Only full-length members of the family are included. The predicted sequences were aligned using ClustalW in Geneious (version 10). Phylogenetic relationships were calculated using the maximum-likelihood principle, and bootstrap values with 500 replicates were determined using Geneious. The scale bar is the number of substitutions per site. Accession numbers for the sequences are as follows: Actinidia chinensis AcCCD7 (ADP37985.1), AcCCD8 (ADP37984.1); Arabidopsis thaliana AtCCD1 (AT3G63520), AtCCD4 (AT4G19170), AtCCD7 (AT2G44990.1), AtCCD8 (AT4G32810); Brassica oleracea BoCCD7 (XP_013635602.1), BoCCD8 (XP_013589279.1); Fragaria vesca FvCCD7 (XP_004306976.2), FvCCD8 (XP_011458989.1); Malus×domestica MdCCD7 (MF034498), MdCCD8a (XP_008378214.1), MdCCD8b (XP_008352014.1); Oryza sativa OsCCD7 (LOC_Os04g46470.1), OsCCD8 (XP_015642760.1); Petunia×hybrida PhCCD7 (ACY01408.1), PhCCD8 (AAW33596.1); Pisum sativum PsCCD7 (ABD67496.2), PsCCD8 (AAS66906.1); Populus trichocarpa PtCCD7 (XP_006375244.1), PtCCD8 (XP_002324797.1); Prunus persica PpCCD7 (XP_007221108.1), PpCCD8 (XP_007222386.2); Pyrus communis PcCCD7 (PCP005718), PcCCD8 (PCP000841); Vitis vinifera VvCCD7 (XP_002274198.1), VvCCD8 (XP_002281239.2).
Figure Legend Snippet: Unrooted phylogenetic tree of the CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) gene family. Only full-length members of the family are included. The predicted sequences were aligned using ClustalW in Geneious (version 10). Phylogenetic relationships were calculated using the maximum-likelihood principle, and bootstrap values with 500 replicates were determined using Geneious. The scale bar is the number of substitutions per site. Accession numbers for the sequences are as follows: Actinidia chinensis AcCCD7 (ADP37985.1), AcCCD8 (ADP37984.1); Arabidopsis thaliana AtCCD1 (AT3G63520), AtCCD4 (AT4G19170), AtCCD7 (AT2G44990.1), AtCCD8 (AT4G32810); Brassica oleracea BoCCD7 (XP_013635602.1), BoCCD8 (XP_013589279.1); Fragaria vesca FvCCD7 (XP_004306976.2), FvCCD8 (XP_011458989.1); Malus×domestica MdCCD7 (MF034498), MdCCD8a (XP_008378214.1), MdCCD8b (XP_008352014.1); Oryza sativa OsCCD7 (LOC_Os04g46470.1), OsCCD8 (XP_015642760.1); Petunia×hybrida PhCCD7 (ACY01408.1), PhCCD8 (AAW33596.1); Pisum sativum PsCCD7 (ABD67496.2), PsCCD8 (AAS66906.1); Populus trichocarpa PtCCD7 (XP_006375244.1), PtCCD8 (XP_002324797.1); Prunus persica PpCCD7 (XP_007221108.1), PpCCD8 (XP_007222386.2); Pyrus communis PcCCD7 (PCP005718), PcCCD8 (PCP000841); Vitis vinifera VvCCD7 (XP_002274198.1), VvCCD8 (XP_002281239.2).

Techniques Used:

Expression of CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) genes in ‘Royal Gala’ apple. qRT-PCR expression of MdCCD7 and MdCCD8 in wild-type tissues. Values are means of three technical replicates ±SE, normalized to internal control genes and relative to MdCCD8 expression in roots. Tissues without bars had expression levels below the threshold of detection. The scale for MdCCD7 is on the right axis and for MdCCD8 is on the left.
Figure Legend Snippet: Expression of CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) genes in ‘Royal Gala’ apple. qRT-PCR expression of MdCCD7 and MdCCD8 in wild-type tissues. Values are means of three technical replicates ±SE, normalized to internal control genes and relative to MdCCD8 expression in roots. Tissues without bars had expression levels below the threshold of detection. The scale for MdCCD7 is on the right axis and for MdCCD8 is on the left.

Techniques Used: Expressing, Quantitative RT-PCR

5) Product Images from "Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis"

Article Title: Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis

Journal: Scientific Reports

doi: 10.1038/s41598-018-21225-z

Expression levels of differentially expressed unigenes assigned to the carotenoid and apocarotenoid biosynthetic pathways in C. sieberi . ( a ) An overview of the carotenoid and crocin biosynthesis pathway enzymes and metabolites. Homologues for the different enzymes (in italics) were identified in the transcriptome assembly and unigenes codes are located beside each enzyme name. Abbreviations are as follows: PDS (phytoene synthase), PSY (phytoene synthase), PDS (phytoene desaturase), Z-ISO (15- cis -ζ-carotene isomerase), ZDS (Z-carotene desaturase), CrtISO (carotene isomerase), LCYB (lycopene-β-cyclase), BCH (β-carotene hydroxylase), CCD2 (carotenoid cleavage dioxygenase 2), ALDH (aldehyde dehydrogenase), CsUGT2 ( Crocus sativus glucosyltransferase 2). ( b ) Differential expression analyses of carotenoid biosynthesis pathway genes identified in the pairwise comparisons of 6Y/6W and 8Y/8W. ( c ) Differential expression analyses of homologues to ALDH and UGT genes identified in the pair-wise comparisons of 6Y/6W and 8Y/8W. ( d ) Differential expression analyses of carotenoid cleavage dioxygenase genes homologues identified in the pair-wise comparisons of 6Y/6W and 8Y/8W.
Figure Legend Snippet: Expression levels of differentially expressed unigenes assigned to the carotenoid and apocarotenoid biosynthetic pathways in C. sieberi . ( a ) An overview of the carotenoid and crocin biosynthesis pathway enzymes and metabolites. Homologues for the different enzymes (in italics) were identified in the transcriptome assembly and unigenes codes are located beside each enzyme name. Abbreviations are as follows: PDS (phytoene synthase), PSY (phytoene synthase), PDS (phytoene desaturase), Z-ISO (15- cis -ζ-carotene isomerase), ZDS (Z-carotene desaturase), CrtISO (carotene isomerase), LCYB (lycopene-β-cyclase), BCH (β-carotene hydroxylase), CCD2 (carotenoid cleavage dioxygenase 2), ALDH (aldehyde dehydrogenase), CsUGT2 ( Crocus sativus glucosyltransferase 2). ( b ) Differential expression analyses of carotenoid biosynthesis pathway genes identified in the pairwise comparisons of 6Y/6W and 8Y/8W. ( c ) Differential expression analyses of homologues to ALDH and UGT genes identified in the pair-wise comparisons of 6Y/6W and 8Y/8W. ( d ) Differential expression analyses of carotenoid cleavage dioxygenase genes homologues identified in the pair-wise comparisons of 6Y/6W and 8Y/8W.

Techniques Used: Expressing

6) Product Images from "Heterologous expression of xanthophyll esterase genes affects carotenoid accumulation in petunia corollas"

Article Title: Heterologous expression of xanthophyll esterase genes affects carotenoid accumulation in petunia corollas

Journal: Scientific Reports

doi: 10.1038/s41598-020-58313-y

Typical putative carotenoid biosynthetic pathway in corollas of IoXES -OX, SlXES -OX, and TeXES -OX plants. GA3P, glyceraldehyde 3-phosphate; DXS, 1-deoxy- d -xylulose 5-phosphate synthase; DOXP, 1-deoxy- d -xylulose 5-phosphate; MEP, 2-C-methyl- d -erythritol-2,4-cyclodisphosphate; IPP, isopentenyl diphosphate; IPI, IPP isomerase; GGPP, geranylgeranyl diphosphate; GGPS, GGPP synthase; PSY, phytoene synthase; PDS, phytoene desaturase; Z-ISO, 15- cis -ζ-carotene isomerase; ZDS, ζ-carotene desaturase; CRTISO, carotenoid isomerase; LCYB, lycopene β-ring cyclase; LCYE, lycopene ε-ring cyclase; CHYB, β-ring hydroxylase; CHYE, ε-ring hydroxylase; CHYB/CYP97A, cytochrome P450-type β-ring hydroxylase; CHYE/CYP97C, cytochrome P450-type ε-ring hydroxylase; ZEP, zeaxanthin epoxidase; NCED2, 9- cis -epoxy carotenoid dioxygenase 2; ABA, abscisic acid; CCD1, carotenoid cleavage dioxygenase 1; PhXES, Petunia hybrida xanthophyll esterase; IoXES, Ipomoea obscura XES; SlXES, Solanum lycopersicum XES; TeXES, Tagetes erecta XES. Expression of genes in bold was enhanced when XES genes were exogenously introduced.
Figure Legend Snippet: Typical putative carotenoid biosynthetic pathway in corollas of IoXES -OX, SlXES -OX, and TeXES -OX plants. GA3P, glyceraldehyde 3-phosphate; DXS, 1-deoxy- d -xylulose 5-phosphate synthase; DOXP, 1-deoxy- d -xylulose 5-phosphate; MEP, 2-C-methyl- d -erythritol-2,4-cyclodisphosphate; IPP, isopentenyl diphosphate; IPI, IPP isomerase; GGPP, geranylgeranyl diphosphate; GGPS, GGPP synthase; PSY, phytoene synthase; PDS, phytoene desaturase; Z-ISO, 15- cis -ζ-carotene isomerase; ZDS, ζ-carotene desaturase; CRTISO, carotenoid isomerase; LCYB, lycopene β-ring cyclase; LCYE, lycopene ε-ring cyclase; CHYB, β-ring hydroxylase; CHYE, ε-ring hydroxylase; CHYB/CYP97A, cytochrome P450-type β-ring hydroxylase; CHYE/CYP97C, cytochrome P450-type ε-ring hydroxylase; ZEP, zeaxanthin epoxidase; NCED2, 9- cis -epoxy carotenoid dioxygenase 2; ABA, abscisic acid; CCD1, carotenoid cleavage dioxygenase 1; PhXES, Petunia hybrida xanthophyll esterase; IoXES, Ipomoea obscura XES; SlXES, Solanum lycopersicum XES; TeXES, Tagetes erecta XES. Expression of genes in bold was enhanced when XES genes were exogenously introduced.

Techniques Used: Expressing

7) Product Images from "Heterologous expression of xanthophyll esterase genes affects carotenoid accumulation in petunia corollas"

Article Title: Heterologous expression of xanthophyll esterase genes affects carotenoid accumulation in petunia corollas

Journal: Scientific Reports

doi: 10.1038/s41598-020-58313-y

Typical putative carotenoid biosynthetic pathway in corollas of IoXES -OX, SlXES -OX, and TeXES -OX plants. GA3P, glyceraldehyde 3-phosphate; DXS, 1-deoxy- d -xylulose 5-phosphate synthase; DOXP, 1-deoxy- d -xylulose 5-phosphate; MEP, 2-C-methyl- d -erythritol-2,4-cyclodisphosphate; IPP, isopentenyl diphosphate; IPI, IPP isomerase; GGPP, geranylgeranyl diphosphate; GGPS, GGPP synthase; PSY, phytoene synthase; PDS, phytoene desaturase; Z-ISO, 15- cis -ζ-carotene isomerase; ZDS, ζ-carotene desaturase; CRTISO, carotenoid isomerase; LCYB, lycopene β-ring cyclase; LCYE, lycopene ε-ring cyclase; CHYB, β-ring hydroxylase; CHYE, ε-ring hydroxylase; CHYB/CYP97A, cytochrome P450-type β-ring hydroxylase; CHYE/CYP97C, cytochrome P450-type ε-ring hydroxylase; ZEP, zeaxanthin epoxidase; NCED2, 9- cis -epoxy carotenoid dioxygenase 2; ABA, abscisic acid; CCD1, carotenoid cleavage dioxygenase 1; PhXES, Petunia hybrida xanthophyll esterase; IoXES, Ipomoea obscura XES; SlXES, Solanum lycopersicum XES; TeXES, Tagetes erecta XES. Expression of genes in bold was enhanced when XES genes were exogenously introduced.
Figure Legend Snippet: Typical putative carotenoid biosynthetic pathway in corollas of IoXES -OX, SlXES -OX, and TeXES -OX plants. GA3P, glyceraldehyde 3-phosphate; DXS, 1-deoxy- d -xylulose 5-phosphate synthase; DOXP, 1-deoxy- d -xylulose 5-phosphate; MEP, 2-C-methyl- d -erythritol-2,4-cyclodisphosphate; IPP, isopentenyl diphosphate; IPI, IPP isomerase; GGPP, geranylgeranyl diphosphate; GGPS, GGPP synthase; PSY, phytoene synthase; PDS, phytoene desaturase; Z-ISO, 15- cis -ζ-carotene isomerase; ZDS, ζ-carotene desaturase; CRTISO, carotenoid isomerase; LCYB, lycopene β-ring cyclase; LCYE, lycopene ε-ring cyclase; CHYB, β-ring hydroxylase; CHYE, ε-ring hydroxylase; CHYB/CYP97A, cytochrome P450-type β-ring hydroxylase; CHYE/CYP97C, cytochrome P450-type ε-ring hydroxylase; ZEP, zeaxanthin epoxidase; NCED2, 9- cis -epoxy carotenoid dioxygenase 2; ABA, abscisic acid; CCD1, carotenoid cleavage dioxygenase 1; PhXES, Petunia hybrida xanthophyll esterase; IoXES, Ipomoea obscura XES; SlXES, Solanum lycopersicum XES; TeXES, Tagetes erecta XES. Expression of genes in bold was enhanced when XES genes were exogenously introduced.

Techniques Used: Expressing

8) Product Images from "Heterologous biosynthesis and manipulation of crocetin in Saccharomyces cerevisiae"

Article Title: Heterologous biosynthesis and manipulation of crocetin in Saccharomyces cerevisiae

Journal: Microbial Cell Factories

doi: 10.1186/s12934-017-0665-1

Crocetin biosynthesis pathway construction in S. cerevisiae . a The paradigm of crocetin biosynthetic pathway in S. cerevisiae . The synthetic pathway to crocetin from β-carotene consists of three enzymes: CrtZ, β-carotene hydroxylase; CCD, carotenoid cleavage dioxygenase and ALD, aldehyde dehydrogenase. b , c Schematic representation of the engineering strategies for CrtZ, CCD and ALD expression cassette. CrtZ expression cassette was integrated into the ho locus of the chromosome, while CCD or CCD/ALD was carried by centromeric plasmid pRS416. ho _L, ho locus left homologous arm; ho _R, ho locus right homologous arm. d , e The HPLC profile of the parent strain SyBE_Sc0014CY06 ( orange ), zeaxanthin producing strain SyBE_Sc0123Cz12 ( yellow ), crocetin producing strain SyBE_Sc0123C009 ( red ), and standard ( black ). The signals for zeaxanthin (I), β-carotene (II) and lycopene (IV) were detected at 450 nm, while crocetin (III) was at 430 nm. The retention time of the unidentified intermediates which were boxed was close to that of lycopene
Figure Legend Snippet: Crocetin biosynthesis pathway construction in S. cerevisiae . a The paradigm of crocetin biosynthetic pathway in S. cerevisiae . The synthetic pathway to crocetin from β-carotene consists of three enzymes: CrtZ, β-carotene hydroxylase; CCD, carotenoid cleavage dioxygenase and ALD, aldehyde dehydrogenase. b , c Schematic representation of the engineering strategies for CrtZ, CCD and ALD expression cassette. CrtZ expression cassette was integrated into the ho locus of the chromosome, while CCD or CCD/ALD was carried by centromeric plasmid pRS416. ho _L, ho locus left homologous arm; ho _R, ho locus right homologous arm. d , e The HPLC profile of the parent strain SyBE_Sc0014CY06 ( orange ), zeaxanthin producing strain SyBE_Sc0123Cz12 ( yellow ), crocetin producing strain SyBE_Sc0123C009 ( red ), and standard ( black ). The signals for zeaxanthin (I), β-carotene (II) and lycopene (IV) were detected at 450 nm, while crocetin (III) was at 430 nm. The retention time of the unidentified intermediates which were boxed was close to that of lycopene

Techniques Used: Expressing, Plasmid Preparation, High Performance Liquid Chromatography

9) Product Images from "Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits"

Article Title: Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/err284

Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.
Figure Legend Snippet: Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.

Techniques Used: Expressing

10) Product Images from "Comparison of transcriptional expression patterns of phenols and carotenoids in ‘Kyoho’ grapes under a two-crop-a-year cultivation system"

Article Title: Comparison of transcriptional expression patterns of phenols and carotenoids in ‘Kyoho’ grapes under a two-crop-a-year cultivation system

Journal: PLoS ONE

doi: 10.1371/journal.pone.0210322

Transcriptomic profile of the structural genes involved in phenolic biosynthesis in summer and winter grape berries. PAL, phenylalanine ammonia-lyase; C4H, trans -cinnamate 4-monooxygenase; COMT, caffeic acid 3- O -methyltransferase; F5H, ferulate-5-hydroxylase; 4CL, 4-coumarate: CoA ligase; STS, stilbene synthase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavonoid 3-hydroxylase; F3’H, flavonoid 3’-hydroxylase; F3’5’H, flavonoid 3’,5’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; LAR, leucoanthocyanidin reductase; LDOX, leucoanthocyanidin dioxygenase; ANR, anthocyanidin reductase; UFGT, UDP-glucose: flavonoid 3- O -glucosyltransferase; GST, glutathione S-transferase. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as shown in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.
Figure Legend Snippet: Transcriptomic profile of the structural genes involved in phenolic biosynthesis in summer and winter grape berries. PAL, phenylalanine ammonia-lyase; C4H, trans -cinnamate 4-monooxygenase; COMT, caffeic acid 3- O -methyltransferase; F5H, ferulate-5-hydroxylase; 4CL, 4-coumarate: CoA ligase; STS, stilbene synthase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavonoid 3-hydroxylase; F3’H, flavonoid 3’-hydroxylase; F3’5’H, flavonoid 3’,5’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; LAR, leucoanthocyanidin reductase; LDOX, leucoanthocyanidin dioxygenase; ANR, anthocyanidin reductase; UFGT, UDP-glucose: flavonoid 3- O -glucosyltransferase; GST, glutathione S-transferase. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as shown in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.

Techniques Used:

Transcriptomic profile of the structural genes involved in the carotenoid and ABA biosynthetic pathways in summer and winter grape berries. PSY, phytoene synthase; Z-ISO, zeta-carotene isomerase; PISO, prolycopene isomerase; LBCY, lycopene-beta-cyclase; LECY, lycopene epsilon-cyclase; CCD, carotenoid cleavage dioxygenase; ZEP, zeaxanthin epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase; BCH, beta-carotene 3-hydroxylase; XO, xanthosin dehydrogenase; ABA8ox, ABA 8’-hydroxylase; ABAO, abscisic-aldehyde oxidase; ABA-GE, ABA glucosyl-ester; ABA-GT, ABA glucosyltransferase; PA, phaseic acid. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as illustrated in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.
Figure Legend Snippet: Transcriptomic profile of the structural genes involved in the carotenoid and ABA biosynthetic pathways in summer and winter grape berries. PSY, phytoene synthase; Z-ISO, zeta-carotene isomerase; PISO, prolycopene isomerase; LBCY, lycopene-beta-cyclase; LECY, lycopene epsilon-cyclase; CCD, carotenoid cleavage dioxygenase; ZEP, zeaxanthin epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase; BCH, beta-carotene 3-hydroxylase; XO, xanthosin dehydrogenase; ABA8ox, ABA 8’-hydroxylase; ABAO, abscisic-aldehyde oxidase; ABA-GE, ABA glucosyl-ester; ABA-GT, ABA glucosyltransferase; PA, phaseic acid. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as illustrated in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.

Techniques Used:

11) Product Images from "Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis"

Article Title: Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

Journal: BMC Genomics

doi: 10.1186/s12864-019-6261-5

Expression of genes related to carotenoid biosynthesis in apricot fruit. a Carotenoid biosynthesis pathway in apricot fruit. IPI, isopentenyl diphosphate isomerase; GGPPS, geranylgeranyl diphosphate synthase; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, ζ-carotene desaturase; CRTISO, carotenoid isomerase; LCYE, lycopene ε-cyclase; LCYB, lycopene β-cyclase; CHYB, β-carotene hydroxylase; ZEP, zeaxanthin epoxidase; VDE, violaxanthin de-epoxidase; NXS, neoxanthin synthase; CCD, carotenoid cleavage dioxygenase; NCED, 9-cis-epoxycarotenoid dioxygenase. b Heatmap of the expression of genes related to carotenoid biosynthesis during fruit ripening. Columns and rows represent samples and gene names in the heatmap, respectively. Red, blue and white indicate high expression, low expression and the absence (or undetectable levels) of detectable transcripts at the corresponding stage, respectively. c The linear fitting equation and R squared values between the FPKM and qRT-PCR values
Figure Legend Snippet: Expression of genes related to carotenoid biosynthesis in apricot fruit. a Carotenoid biosynthesis pathway in apricot fruit. IPI, isopentenyl diphosphate isomerase; GGPPS, geranylgeranyl diphosphate synthase; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, ζ-carotene desaturase; CRTISO, carotenoid isomerase; LCYE, lycopene ε-cyclase; LCYB, lycopene β-cyclase; CHYB, β-carotene hydroxylase; ZEP, zeaxanthin epoxidase; VDE, violaxanthin de-epoxidase; NXS, neoxanthin synthase; CCD, carotenoid cleavage dioxygenase; NCED, 9-cis-epoxycarotenoid dioxygenase. b Heatmap of the expression of genes related to carotenoid biosynthesis during fruit ripening. Columns and rows represent samples and gene names in the heatmap, respectively. Red, blue and white indicate high expression, low expression and the absence (or undetectable levels) of detectable transcripts at the corresponding stage, respectively. c The linear fitting equation and R squared values between the FPKM and qRT-PCR values

Techniques Used: Expressing, Quantitative RT-PCR

12) Product Images from "The Sensory Significance of Apocarotenoids in Wine: Importance of Carotenoid Cleavage Dioxygenase 1 (CCD1) in the Production of β-Ionone"

Article Title: The Sensory Significance of Apocarotenoids in Wine: Importance of Carotenoid Cleavage Dioxygenase 1 (CCD1) in the Production of β-Ionone

Journal: Molecules

doi: 10.3390/molecules25122779

Typical structure of the carotenoid cleavage dioxygenase (CCD) family. The protein structure of the CCDs consists of seven β-sheets with a Fe 2+ molecule at the catalytic centre of the propeller-like structure [ 9 ]. The structure contains four highly-conserved histidine molecules, which bind the Fe 2+ molecule. While the propeller-like structure and histidine placements are conserved within the CCD family, the CCDs differ in their amino acid sequences.
Figure Legend Snippet: Typical structure of the carotenoid cleavage dioxygenase (CCD) family. The protein structure of the CCDs consists of seven β-sheets with a Fe 2+ molecule at the catalytic centre of the propeller-like structure [ 9 ]. The structure contains four highly-conserved histidine molecules, which bind the Fe 2+ molecule. While the propeller-like structure and histidine placements are conserved within the CCD family, the CCDs differ in their amino acid sequences.

Techniques Used:

The development of ‘yeast cell factories’ for the production of the apocarotenoid, β-ionone. One approach would be to incorporate and express three heterologous carotenogenic genes ( crtE , crtYB and crtI ) and the CCD1 carotenoid cleavage dioxygenase gene in Saccharomyces cerevisiae .
Figure Legend Snippet: The development of ‘yeast cell factories’ for the production of the apocarotenoid, β-ionone. One approach would be to incorporate and express three heterologous carotenogenic genes ( crtE , crtYB and crtI ) and the CCD1 carotenoid cleavage dioxygenase gene in Saccharomyces cerevisiae .

Techniques Used:

13) Product Images from "The Banana Genome Hub"

Article Title: The Banana Genome Hub

Journal: Database: The Journal of Biological Databases and Curation

doi: 10.1093/database/bat035

Analysis of the banana NCED gene duplication events. ( A ) The GreenPhylDB pre-computed polypeptide tree of the carotenoid dioxygenase family (GP000379 CCD) contains eight Musa 9-cis-epoxycarotenoid dioxygenase genes (GP069973 NCED Blue). CCDs are in cyan (Poaceae), purple (Arecaceae), green (Arabidopsis), magenta (moss). Green dots represent speciation events, whereas red dots represent duplication events. ( B ) The nucleotide tree of the six Musa NCED genes was performed after manual curation using an in-house Galaxy workflow. ( C ) Location of the NCED Musa genes on the Karyotype representation. Musa beta ancestral blocks are represented by the colored boxes within the chromosomes. ( D ) Clusters of Musa paralogous regions are represented on a PGDD dotplot. They are colored according to the beta ancestral blocks. ( E ) List of duplicated genes within the paralogous region containing GSMUA_Achr4G22870_001 and GSMUA_Achr7G01250_001 NCED genes.
Figure Legend Snippet: Analysis of the banana NCED gene duplication events. ( A ) The GreenPhylDB pre-computed polypeptide tree of the carotenoid dioxygenase family (GP000379 CCD) contains eight Musa 9-cis-epoxycarotenoid dioxygenase genes (GP069973 NCED Blue). CCDs are in cyan (Poaceae), purple (Arecaceae), green (Arabidopsis), magenta (moss). Green dots represent speciation events, whereas red dots represent duplication events. ( B ) The nucleotide tree of the six Musa NCED genes was performed after manual curation using an in-house Galaxy workflow. ( C ) Location of the NCED Musa genes on the Karyotype representation. Musa beta ancestral blocks are represented by the colored boxes within the chromosomes. ( D ) Clusters of Musa paralogous regions are represented on a PGDD dotplot. They are colored according to the beta ancestral blocks. ( E ) List of duplicated genes within the paralogous region containing GSMUA_Achr4G22870_001 and GSMUA_Achr7G01250_001 NCED genes.

Techniques Used:

14) Product Images from "Heterologous biosynthesis and manipulation of crocetin in Saccharomyces cerevisiae"

Article Title: Heterologous biosynthesis and manipulation of crocetin in Saccharomyces cerevisiae

Journal: Microbial Cell Factories

doi: 10.1186/s12934-017-0665-1

Crocetin biosynthesis pathway construction in S. cerevisiae . a The paradigm of crocetin biosynthetic pathway in S. cerevisiae . The synthetic pathway to crocetin from β-carotene consists of three enzymes: CrtZ, β-carotene hydroxylase; CCD, carotenoid cleavage dioxygenase and ALD, aldehyde dehydrogenase. b , c Schematic representation of the engineering strategies for CrtZ, CCD and ALD expression cassette. CrtZ expression cassette was integrated into the ho locus of the chromosome, while CCD or CCD/ALD was carried by centromeric plasmid pRS416. ho _L, ho locus left homologous arm; ho _R, ho locus right homologous arm. d , e The HPLC profile of the parent strain SyBE_Sc0014CY06 ( orange ), zeaxanthin producing strain SyBE_Sc0123Cz12 ( yellow ), crocetin producing strain SyBE_Sc0123C009 ( red ), and standard ( black ). The signals for zeaxanthin (I), β-carotene (II) and lycopene (IV) were detected at 450 nm, while crocetin (III) was at 430 nm. The retention time of the unidentified intermediates which were boxed was close to that of lycopene
Figure Legend Snippet: Crocetin biosynthesis pathway construction in S. cerevisiae . a The paradigm of crocetin biosynthetic pathway in S. cerevisiae . The synthetic pathway to crocetin from β-carotene consists of three enzymes: CrtZ, β-carotene hydroxylase; CCD, carotenoid cleavage dioxygenase and ALD, aldehyde dehydrogenase. b , c Schematic representation of the engineering strategies for CrtZ, CCD and ALD expression cassette. CrtZ expression cassette was integrated into the ho locus of the chromosome, while CCD or CCD/ALD was carried by centromeric plasmid pRS416. ho _L, ho locus left homologous arm; ho _R, ho locus right homologous arm. d , e The HPLC profile of the parent strain SyBE_Sc0014CY06 ( orange ), zeaxanthin producing strain SyBE_Sc0123Cz12 ( yellow ), crocetin producing strain SyBE_Sc0123C009 ( red ), and standard ( black ). The signals for zeaxanthin (I), β-carotene (II) and lycopene (IV) were detected at 450 nm, while crocetin (III) was at 430 nm. The retention time of the unidentified intermediates which were boxed was close to that of lycopene

Techniques Used: Expressing, Plasmid Preparation, High Performance Liquid Chromatography

15) Product Images from "Biochemistry and Molecular Biology of Carotenoid Biosynthesis in Chili Peppers (Capsicum spp.)"

Article Title: Biochemistry and Molecular Biology of Carotenoid Biosynthesis in Chili Peppers (Capsicum spp.)

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms140919025

Carotenoid biosynthesis pathway in plants. IPI, isopentenyl pyrophosphate isomerase; GGPS, geranylgeranyl pyrophosphate synthase; PSY, phytoene synthase; PDS, phytoene desaturase; Z-ISO, ζ-carotene isomerase; ZDS, ζ-carotene desaturase; CRTISO, carotene or carotenoid isomerase; LCY-B, lycopene-β-cyclase; LCY-E, lycopene-ɛ-cyclase; BCH, β-carotene hydroxylase or carotene β-hydroxylase (non-heme di-iron type); CYP97A, β-carotene hydroxylase (cytochrome 450 type); CYP97C, ɛ-carotene hydroxylase (cytochrome 450 type); ZEP, zeaxanthin epoxidase; CCS, capsanthin-capsorubin synthase; VDE, violaxanthin de-epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase (a carotenoid cleavage dioxygenase; CCD); SDR, short-chain dehydrogenase/reductase; AO, aldehyde oxidase; ABA, abscisic acid; PTOX, plastid terminal oxidase; PQ, oxidized plastoquinone; PQH 2 , reduced plastoquinone. Adapted from [ 69 – 77 ].
Figure Legend Snippet: Carotenoid biosynthesis pathway in plants. IPI, isopentenyl pyrophosphate isomerase; GGPS, geranylgeranyl pyrophosphate synthase; PSY, phytoene synthase; PDS, phytoene desaturase; Z-ISO, ζ-carotene isomerase; ZDS, ζ-carotene desaturase; CRTISO, carotene or carotenoid isomerase; LCY-B, lycopene-β-cyclase; LCY-E, lycopene-ɛ-cyclase; BCH, β-carotene hydroxylase or carotene β-hydroxylase (non-heme di-iron type); CYP97A, β-carotene hydroxylase (cytochrome 450 type); CYP97C, ɛ-carotene hydroxylase (cytochrome 450 type); ZEP, zeaxanthin epoxidase; CCS, capsanthin-capsorubin synthase; VDE, violaxanthin de-epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase (a carotenoid cleavage dioxygenase; CCD); SDR, short-chain dehydrogenase/reductase; AO, aldehyde oxidase; ABA, abscisic acid; PTOX, plastid terminal oxidase; PQ, oxidized plastoquinone; PQH 2 , reduced plastoquinone. Adapted from [ 69 – 77 ].

Techniques Used:

16) Product Images from "Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis"

Article Title: Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis

Journal: Scientific Reports

doi: 10.1038/s41598-018-21225-z

Expression levels of differentially expressed unigenes assigned to the carotenoid and apocarotenoid biosynthetic pathways in C. sieberi . ( a ) An overview of the carotenoid and crocin biosynthesis pathway enzymes and metabolites. Homologues for the different enzymes (in italics) were identified in the transcriptome assembly and unigenes codes are located beside each enzyme name. Abbreviations are as follows: PDS (phytoene synthase), PSY (phytoene synthase), PDS (phytoene desaturase), Z-ISO (15- cis -ζ-carotene isomerase), ZDS (Z-carotene desaturase), CrtISO (carotene isomerase), LCYB (lycopene-β-cyclase), BCH (β-carotene hydroxylase), CCD2 (carotenoid cleavage dioxygenase 2), ALDH (aldehyde dehydrogenase), CsUGT2 ( Crocus sativus glucosyltransferase 2). ( b ) Differential expression analyses of carotenoid biosynthesis pathway genes identified in the pairwise comparisons of 6Y/6W and 8Y/8W. ( c ) Differential expression analyses of homologues to ALDH and UGT genes identified in the pair-wise comparisons of 6Y/6W and 8Y/8W. ( d ) Differential expression analyses of carotenoid cleavage dioxygenase genes homologues identified in the pair-wise comparisons of 6Y/6W and 8Y/8W.
Figure Legend Snippet: Expression levels of differentially expressed unigenes assigned to the carotenoid and apocarotenoid biosynthetic pathways in C. sieberi . ( a ) An overview of the carotenoid and crocin biosynthesis pathway enzymes and metabolites. Homologues for the different enzymes (in italics) were identified in the transcriptome assembly and unigenes codes are located beside each enzyme name. Abbreviations are as follows: PDS (phytoene synthase), PSY (phytoene synthase), PDS (phytoene desaturase), Z-ISO (15- cis -ζ-carotene isomerase), ZDS (Z-carotene desaturase), CrtISO (carotene isomerase), LCYB (lycopene-β-cyclase), BCH (β-carotene hydroxylase), CCD2 (carotenoid cleavage dioxygenase 2), ALDH (aldehyde dehydrogenase), CsUGT2 ( Crocus sativus glucosyltransferase 2). ( b ) Differential expression analyses of carotenoid biosynthesis pathway genes identified in the pairwise comparisons of 6Y/6W and 8Y/8W. ( c ) Differential expression analyses of homologues to ALDH and UGT genes identified in the pair-wise comparisons of 6Y/6W and 8Y/8W. ( d ) Differential expression analyses of carotenoid cleavage dioxygenase genes homologues identified in the pair-wise comparisons of 6Y/6W and 8Y/8W.

Techniques Used: Expressing

17) Product Images from "Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus"

Article Title: Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus

Journal: Computational and Structural Biotechnology Journal

doi: 10.1016/j.csbj.2020.03.022

Evolutionary relationships and expression patterns of the key genes involved in apocarotenoid biosynthesis. (a) Biosynthetic pathway for producing distinct apocarotenoids through the cleavage of zeaxanthin. CCD, UGT, ALDH and β-GS represented gene-encoding enzymes of carotenoid cleavage dioxygenase, UDP-glucosyl transferase, aldehyde dehydrogenase and β-glucosidase, respectively. The histogram next to each enzyme showed the distribution of corresponding gene members identified from C. sativus , A. officinalis , Z. mays , D. carota and S. lycopersicum . Only the number of CCD members in C. sativus was relatively higher than other species. Table in the left box denoted zeaxanthin with different cleavage sites that were available by the CCD enzymes in the five representative species. Three-letter acronym for the abbreviation of each species name. (b) Neighbor-joining (NJ) phylogenetic tree of 38 CCD proteins constructed from the five representative plant species. Four subfamilies were grouped according to the substrate preference and cleavage specificity. In C. sativus (Csa, red solid dots), 13 CCD members were clustered into CCD1 and CCD4. The putative member for cleaving zeaxanthin at 7,8/7′,8′ double bonds was identified by similarity search against CsCCD2 and intended to be Cs3t109488 (blue pentagram). The numeric values within each red solid dot corresponded to the serial number given in the subgraph C. (c) Expression patterns of 13 CCD gene members (rows) from C. sativus based on the SGS RNA-Seq reads from five different tissues (columns). The heatmap was drawn with log 2 transformation of gene expression data. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Figure Legend Snippet: Evolutionary relationships and expression patterns of the key genes involved in apocarotenoid biosynthesis. (a) Biosynthetic pathway for producing distinct apocarotenoids through the cleavage of zeaxanthin. CCD, UGT, ALDH and β-GS represented gene-encoding enzymes of carotenoid cleavage dioxygenase, UDP-glucosyl transferase, aldehyde dehydrogenase and β-glucosidase, respectively. The histogram next to each enzyme showed the distribution of corresponding gene members identified from C. sativus , A. officinalis , Z. mays , D. carota and S. lycopersicum . Only the number of CCD members in C. sativus was relatively higher than other species. Table in the left box denoted zeaxanthin with different cleavage sites that were available by the CCD enzymes in the five representative species. Three-letter acronym for the abbreviation of each species name. (b) Neighbor-joining (NJ) phylogenetic tree of 38 CCD proteins constructed from the five representative plant species. Four subfamilies were grouped according to the substrate preference and cleavage specificity. In C. sativus (Csa, red solid dots), 13 CCD members were clustered into CCD1 and CCD4. The putative member for cleaving zeaxanthin at 7,8/7′,8′ double bonds was identified by similarity search against CsCCD2 and intended to be Cs3t109488 (blue pentagram). The numeric values within each red solid dot corresponded to the serial number given in the subgraph C. (c) Expression patterns of 13 CCD gene members (rows) from C. sativus based on the SGS RNA-Seq reads from five different tissues (columns). The heatmap was drawn with log 2 transformation of gene expression data. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Techniques Used: Expressing, Construct, RNA Sequencing Assay, Transformation Assay

18) Product Images from "Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism"

Article Title: Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism

Journal: BMC Plant Biology

doi: 10.1186/1471-2229-11-24

Expression patterns of carotenoid-related genes during ripening of RHB and RH fruits . Relative average gene transcript levels ± SD are given, following normalization with rps28 values. A: isoprenoid genes [ cmk , 4-(cytidine 5'-diphospho)-2- C -methyl-d-erythritol kinase; dxs , 1-deoxy-d-xylulose 5-phosphate synthase; hdr , 4-hydroxy-3-methylbut-2-enyl diphosphate reductase]. B: early carotenoid genes ( pds , phytoene desaturase; psy , phytoene synthase; zds , ζ-carotene desaturase). C: other carotenoid genes ( chy-b , carotene β-hydroxylase; chy-e , carotene ε-hydroxylase; lcy-b , lycopene β-cyclase; lcy-e , lycopene-e-cyclase; zep , zeaxanthin epoxidase). D: dioxygenase-related genes ( ccd1 and ccd4 , carotenoid cleavage dioxygenases 1 and 4; nced1 and nced2 , 9- cis -epoxycarotenoid dioxygenases 1 and 2). For each gene, different letters indicate significant differences among mean values from different stages (*: p ≤ 0.05; **: p ≤ 0.01).
Figure Legend Snippet: Expression patterns of carotenoid-related genes during ripening of RHB and RH fruits . Relative average gene transcript levels ± SD are given, following normalization with rps28 values. A: isoprenoid genes [ cmk , 4-(cytidine 5'-diphospho)-2- C -methyl-d-erythritol kinase; dxs , 1-deoxy-d-xylulose 5-phosphate synthase; hdr , 4-hydroxy-3-methylbut-2-enyl diphosphate reductase]. B: early carotenoid genes ( pds , phytoene desaturase; psy , phytoene synthase; zds , ζ-carotene desaturase). C: other carotenoid genes ( chy-b , carotene β-hydroxylase; chy-e , carotene ε-hydroxylase; lcy-b , lycopene β-cyclase; lcy-e , lycopene-e-cyclase; zep , zeaxanthin epoxidase). D: dioxygenase-related genes ( ccd1 and ccd4 , carotenoid cleavage dioxygenases 1 and 4; nced1 and nced2 , 9- cis -epoxycarotenoid dioxygenases 1 and 2). For each gene, different letters indicate significant differences among mean values from different stages (*: p ≤ 0.05; **: p ≤ 0.01).

Techniques Used: Expressing

19) Product Images from "Heterologous biosynthesis and manipulation of crocetin in Saccharomyces cerevisiae"

Article Title: Heterologous biosynthesis and manipulation of crocetin in Saccharomyces cerevisiae

Journal: Microbial Cell Factories

doi: 10.1186/s12934-017-0665-1

Crocetin biosynthesis pathway construction in S. cerevisiae . a The paradigm of crocetin biosynthetic pathway in S. cerevisiae . The synthetic pathway to crocetin from β-carotene consists of three enzymes: CrtZ, β-carotene hydroxylase; CCD, carotenoid cleavage dioxygenase and ALD, aldehyde dehydrogenase. b , c Schematic representation of the engineering strategies for CrtZ, CCD and ALD expression cassette. CrtZ expression cassette was integrated into the ho locus of the chromosome, while CCD or CCD/ALD was carried by centromeric plasmid pRS416. ho _L, ho locus left homologous arm; ho _R, ho locus right homologous arm. d , e The HPLC profile of the parent strain SyBE_Sc0014CY06 ( orange ), zeaxanthin producing strain SyBE_Sc0123Cz12 ( yellow ), crocetin producing strain SyBE_Sc0123C009 ( red ), and standard ( black ). The signals for zeaxanthin (I), β-carotene (II) and lycopene (IV) were detected at 450 nm, while crocetin (III) was at 430 nm. The retention time of the unidentified intermediates which were boxed was close to that of lycopene
Figure Legend Snippet: Crocetin biosynthesis pathway construction in S. cerevisiae . a The paradigm of crocetin biosynthetic pathway in S. cerevisiae . The synthetic pathway to crocetin from β-carotene consists of three enzymes: CrtZ, β-carotene hydroxylase; CCD, carotenoid cleavage dioxygenase and ALD, aldehyde dehydrogenase. b , c Schematic representation of the engineering strategies for CrtZ, CCD and ALD expression cassette. CrtZ expression cassette was integrated into the ho locus of the chromosome, while CCD or CCD/ALD was carried by centromeric plasmid pRS416. ho _L, ho locus left homologous arm; ho _R, ho locus right homologous arm. d , e The HPLC profile of the parent strain SyBE_Sc0014CY06 ( orange ), zeaxanthin producing strain SyBE_Sc0123Cz12 ( yellow ), crocetin producing strain SyBE_Sc0123C009 ( red ), and standard ( black ). The signals for zeaxanthin (I), β-carotene (II) and lycopene (IV) were detected at 450 nm, while crocetin (III) was at 430 nm. The retention time of the unidentified intermediates which were boxed was close to that of lycopene

Techniques Used: Expressing, Plasmid Preparation, High Performance Liquid Chromatography

20) Product Images from "Photomodulation of strigolactone biosynthesis and accumulation during sunflower seedling growth"

Article Title: Photomodulation of strigolactone biosynthesis and accumulation during sunflower seedling growth

Journal: Plant Signaling & Behavior

doi: 10.1080/15592324.2015.1049792

Carotenoid cleavage dioxygenase (CCD) activity in roots and cotyledons from sunflower seedlings at different developmental stages (2, 4 and 6 d), grown in light and dark. Data represent mean specific activity ± SE from the respective tissue
Figure Legend Snippet: Carotenoid cleavage dioxygenase (CCD) activity in roots and cotyledons from sunflower seedlings at different developmental stages (2, 4 and 6 d), grown in light and dark. Data represent mean specific activity ± SE from the respective tissue

Techniques Used: Activity Assay

21) Product Images from "Photomodulation of strigolactone biosynthesis and accumulation during sunflower seedling growth"

Article Title: Photomodulation of strigolactone biosynthesis and accumulation during sunflower seedling growth

Journal: Plant Signaling & Behavior

doi: 10.1080/15592324.2015.1049792

Carotenoid cleavage dioxygenase (CCD) activity in roots and cotyledons from sunflower seedlings at different developmental stages (2, 4 and 6 d), grown in light and dark. Data represent mean specific activity ± SE from the respective tissue
Figure Legend Snippet: Carotenoid cleavage dioxygenase (CCD) activity in roots and cotyledons from sunflower seedlings at different developmental stages (2, 4 and 6 d), grown in light and dark. Data represent mean specific activity ± SE from the respective tissue

Techniques Used: Activity Assay

22) Product Images from "Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis"

Article Title: Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis

Journal: Scientific Reports

doi: 10.1038/s41598-018-21225-z

Expression levels of differentially expressed unigenes assigned to the carotenoid and apocarotenoid biosynthetic pathways in C. sieberi . ( a ) An overview of the carotenoid and crocin biosynthesis pathway enzymes and metabolites. Homologues for the different enzymes (in italics) were identified in the transcriptome assembly and unigenes codes are located beside each enzyme name. Abbreviations are as follows: PDS (phytoene synthase), PSY (phytoene synthase), PDS (phytoene desaturase), Z-ISO (15- cis -ζ-carotene isomerase), ZDS (Z-carotene desaturase), CrtISO (carotene isomerase), LCYB (lycopene-β-cyclase), BCH (β-carotene hydroxylase), CCD2 (carotenoid cleavage dioxygenase 2), ALDH (aldehyde dehydrogenase), CsUGT2 ( Crocus sativus glucosyltransferase 2). ( b ) Differential expression analyses of carotenoid biosynthesis pathway genes identified in the pairwise comparisons of 6Y/6W and 8Y/8W. ( c ) Differential expression analyses of homologues to ALDH and UGT genes identified in the pair-wise comparisons of 6Y/6W and 8Y/8W. ( d ) Differential expression analyses of carotenoid cleavage dioxygenase genes homologues identified in the pair-wise comparisons of 6Y/6W and 8Y/8W.
Figure Legend Snippet: Expression levels of differentially expressed unigenes assigned to the carotenoid and apocarotenoid biosynthetic pathways in C. sieberi . ( a ) An overview of the carotenoid and crocin biosynthesis pathway enzymes and metabolites. Homologues for the different enzymes (in italics) were identified in the transcriptome assembly and unigenes codes are located beside each enzyme name. Abbreviations are as follows: PDS (phytoene synthase), PSY (phytoene synthase), PDS (phytoene desaturase), Z-ISO (15- cis -ζ-carotene isomerase), ZDS (Z-carotene desaturase), CrtISO (carotene isomerase), LCYB (lycopene-β-cyclase), BCH (β-carotene hydroxylase), CCD2 (carotenoid cleavage dioxygenase 2), ALDH (aldehyde dehydrogenase), CsUGT2 ( Crocus sativus glucosyltransferase 2). ( b ) Differential expression analyses of carotenoid biosynthesis pathway genes identified in the pairwise comparisons of 6Y/6W and 8Y/8W. ( c ) Differential expression analyses of homologues to ALDH and UGT genes identified in the pair-wise comparisons of 6Y/6W and 8Y/8W. ( d ) Differential expression analyses of carotenoid cleavage dioxygenase genes homologues identified in the pair-wise comparisons of 6Y/6W and 8Y/8W.

Techniques Used: Expressing

23) Product Images from "Comparison of transcriptional expression patterns of phenols and carotenoids in ‘Kyoho’ grapes under a two-crop-a-year cultivation system"

Article Title: Comparison of transcriptional expression patterns of phenols and carotenoids in ‘Kyoho’ grapes under a two-crop-a-year cultivation system

Journal: PLoS ONE

doi: 10.1371/journal.pone.0210322

Transcriptomic profile of the structural genes involved in phenolic biosynthesis in summer and winter grape berries. PAL, phenylalanine ammonia-lyase; C4H, trans -cinnamate 4-monooxygenase; COMT, caffeic acid 3- O -methyltransferase; F5H, ferulate-5-hydroxylase; 4CL, 4-coumarate: CoA ligase; STS, stilbene synthase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavonoid 3-hydroxylase; F3’H, flavonoid 3’-hydroxylase; F3’5’H, flavonoid 3’,5’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; LAR, leucoanthocyanidin reductase; LDOX, leucoanthocyanidin dioxygenase; ANR, anthocyanidin reductase; UFGT, UDP-glucose: flavonoid 3- O -glucosyltransferase; GST, glutathione S-transferase. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as shown in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.
Figure Legend Snippet: Transcriptomic profile of the structural genes involved in phenolic biosynthesis in summer and winter grape berries. PAL, phenylalanine ammonia-lyase; C4H, trans -cinnamate 4-monooxygenase; COMT, caffeic acid 3- O -methyltransferase; F5H, ferulate-5-hydroxylase; 4CL, 4-coumarate: CoA ligase; STS, stilbene synthase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavonoid 3-hydroxylase; F3’H, flavonoid 3’-hydroxylase; F3’5’H, flavonoid 3’,5’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; LAR, leucoanthocyanidin reductase; LDOX, leucoanthocyanidin dioxygenase; ANR, anthocyanidin reductase; UFGT, UDP-glucose: flavonoid 3- O -glucosyltransferase; GST, glutathione S-transferase. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as shown in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.

Techniques Used:

Transcriptomic profile of the structural genes involved in the carotenoid and ABA biosynthetic pathways in summer and winter grape berries. PSY, phytoene synthase; Z-ISO, zeta-carotene isomerase; PISO, prolycopene isomerase; LBCY, lycopene-beta-cyclase; LECY, lycopene epsilon-cyclase; CCD, carotenoid cleavage dioxygenase; ZEP, zeaxanthin epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase; BCH, beta-carotene 3-hydroxylase; XO, xanthosin dehydrogenase; ABA8ox, ABA 8’-hydroxylase; ABAO, abscisic-aldehyde oxidase; ABA-GE, ABA glucosyl-ester; ABA-GT, ABA glucosyltransferase; PA, phaseic acid. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as illustrated in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.
Figure Legend Snippet: Transcriptomic profile of the structural genes involved in the carotenoid and ABA biosynthetic pathways in summer and winter grape berries. PSY, phytoene synthase; Z-ISO, zeta-carotene isomerase; PISO, prolycopene isomerase; LBCY, lycopene-beta-cyclase; LECY, lycopene epsilon-cyclase; CCD, carotenoid cleavage dioxygenase; ZEP, zeaxanthin epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase; BCH, beta-carotene 3-hydroxylase; XO, xanthosin dehydrogenase; ABA8ox, ABA 8’-hydroxylase; ABAO, abscisic-aldehyde oxidase; ABA-GE, ABA glucosyl-ester; ABA-GT, ABA glucosyltransferase; PA, phaseic acid. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as illustrated in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.

Techniques Used:

24) Product Images from "Regulation of the Rhythmic Emission of Plant Volatiles by the Circadian Clock"

Article Title: Regulation of the Rhythmic Emission of Plant Volatiles by the Circadian Clock

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms18112408

Known factors controlling the circadian rhythmic emission of plant volatiles. Blue text and clock labels indicate that the levels of volatiles emission, intermediate metabolites content, gene transcript, or enzyme activity are under circadian control. Solid arrow is representative of a known route, dotted arrow is representative of an unproven route, and two-way arrow is representative of multiple enzymatic steps. BA2H, benzoic acid-2 hydroxylase; BPBT, benzoyl-CoA:benzylalcohol/2-phenylethanol benzoyltransferase; BSMT, benzoic acid/salicylic acid carboxyl methyltransferase; CCD, carotenoid cleavage dioxygenase; DMAPP, dimethylallyl diphosphate; DXP, 1-deoxy- d -xylulose-5-phosphate; DXPS, 1-deoxy- d -xylulose-5-phosphate synthase; DXR, 1-deoxy- d -xylulose-5-phosphate reductoisomerase; GGPP, geranylgeranyl diphosphate; GGPPS, geranylgeranyl diphosphate synthase; GLVs, green leaf volatiles; GPP, geranyl diphosphate; GPPS, geranyl diphosphate synthase; 13-LOX, 13-lipoxygenase; MEP, methylerythritol phosphate; MVP, mevalonic acid; HPL, hydroperoxide layse; 13-HPOT, 13 S -hydroperoxy-( 9Z , 11E , 15Z )-octadecatrienoic; SAMT, salicylic acid carboxyl methyltransferase; IDI, isopentenyl diphosphate isomerase; IPP, isopentenyl diphosphate; ISPS, isoprene synthase; TPS, terpene synthase; PAL, phenylalanine ammonia lyase; PK, pyruvate kinase. The rhythmic emissions of methyl benzoate [ 36 ], benzyl alcohol [ 37 ], methyl salicylate [ 37 , 42 ], isoprene [ 38 , 39 ], β-ionone [ 40 ], mycrene [ 41 ], and ocimene [ 41 ], β-pinene [ 43 ], linalool [ 44 ], were under circadian control. The content of benzoic acid [ 36 ] and MEP [ 45 ] was under rhythmic change. ISPS [ 39 ], CCD [ 40 ], OH6 [ 43 ], SAMT [ 42 ], DXPS [ 45 ], 13-LOX [ 46 ] and were under circadian control.
Figure Legend Snippet: Known factors controlling the circadian rhythmic emission of plant volatiles. Blue text and clock labels indicate that the levels of volatiles emission, intermediate metabolites content, gene transcript, or enzyme activity are under circadian control. Solid arrow is representative of a known route, dotted arrow is representative of an unproven route, and two-way arrow is representative of multiple enzymatic steps. BA2H, benzoic acid-2 hydroxylase; BPBT, benzoyl-CoA:benzylalcohol/2-phenylethanol benzoyltransferase; BSMT, benzoic acid/salicylic acid carboxyl methyltransferase; CCD, carotenoid cleavage dioxygenase; DMAPP, dimethylallyl diphosphate; DXP, 1-deoxy- d -xylulose-5-phosphate; DXPS, 1-deoxy- d -xylulose-5-phosphate synthase; DXR, 1-deoxy- d -xylulose-5-phosphate reductoisomerase; GGPP, geranylgeranyl diphosphate; GGPPS, geranylgeranyl diphosphate synthase; GLVs, green leaf volatiles; GPP, geranyl diphosphate; GPPS, geranyl diphosphate synthase; 13-LOX, 13-lipoxygenase; MEP, methylerythritol phosphate; MVP, mevalonic acid; HPL, hydroperoxide layse; 13-HPOT, 13 S -hydroperoxy-( 9Z , 11E , 15Z )-octadecatrienoic; SAMT, salicylic acid carboxyl methyltransferase; IDI, isopentenyl diphosphate isomerase; IPP, isopentenyl diphosphate; ISPS, isoprene synthase; TPS, terpene synthase; PAL, phenylalanine ammonia lyase; PK, pyruvate kinase. The rhythmic emissions of methyl benzoate [ 36 ], benzyl alcohol [ 37 ], methyl salicylate [ 37 , 42 ], isoprene [ 38 , 39 ], β-ionone [ 40 ], mycrene [ 41 ], and ocimene [ 41 ], β-pinene [ 43 ], linalool [ 44 ], were under circadian control. The content of benzoic acid [ 36 ] and MEP [ 45 ] was under rhythmic change. ISPS [ 39 ], CCD [ 40 ], OH6 [ 43 ], SAMT [ 42 ], DXPS [ 45 ], 13-LOX [ 46 ] and were under circadian control.

Techniques Used: Activity Assay

25) Product Images from "Molecular Characterization of Carotenoid Biosynthetic Genes and Carotenoid Accumulation in Lycium chinense"

Article Title: Molecular Characterization of Carotenoid Biosynthetic Genes and Carotenoid Accumulation in Lycium chinense

Journal: Molecules

doi: 10.3390/molecules190811250

Carotenoid biosynthetic pathway in plants. GGDP, geranylgeranyl diphosphate; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, ξ-carotene desaturase; LCYB, lycopene β-cyclase; LCYE, lycopene ε-cyclase; CHXB, β-ring carotene hydroxylase; CHXE, ε-ring carotene hydroxylase; ZEP, zeaxanthin epoxidase; CCD, carotenoid cleavage dioxygenase; NCED, 9-cis epoxycarotenoid dioxygenase.
Figure Legend Snippet: Carotenoid biosynthetic pathway in plants. GGDP, geranylgeranyl diphosphate; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, ξ-carotene desaturase; LCYB, lycopene β-cyclase; LCYE, lycopene ε-cyclase; CHXB, β-ring carotene hydroxylase; CHXE, ε-ring carotene hydroxylase; ZEP, zeaxanthin epoxidase; CCD, carotenoid cleavage dioxygenase; NCED, 9-cis epoxycarotenoid dioxygenase.

Techniques Used:

26) Product Images from "Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development"

Article Title: Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development

Journal: PLoS ONE

doi: 10.1371/journal.pone.0130267

Expression profiles of carotenoid biosynthesis and metabolism genes during watermelon fruit development. PSY: phytoene synthase; CHYB: β-carotene hydroxylase; NCED: 9- cis -epoxy-carotenoid dioxygenase; CCD: carotenoid cleavage dioxygenase.
Figure Legend Snippet: Expression profiles of carotenoid biosynthesis and metabolism genes during watermelon fruit development. PSY: phytoene synthase; CHYB: β-carotene hydroxylase; NCED: 9- cis -epoxy-carotenoid dioxygenase; CCD: carotenoid cleavage dioxygenase.

Techniques Used: Expressing

27) Product Images from "Crocins with High Levels of Sugar Conjugation Contribute to the Yellow Colours of Early-Spring Flowering Crocus Tepals"

Article Title: Crocins with High Levels of Sugar Conjugation Contribute to the Yellow Colours of Early-Spring Flowering Crocus Tepals

Journal: PLoS ONE

doi: 10.1371/journal.pone.0071946

Expression analysis of selected genes involved in carotenoid metabolism. A. Schematic carotenoid and apocarotenoid biosynthetic pathway in Crocus . Enzymatic reactions are represented by arrows. GGPP, geranyl geranyl diphosphate; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, z-carotene desaturase; CRTISO, carotene isomerase; LCYe, lycopene e-cyclase; LCYb, lycopene b-cyclase; bCH, b-carotene hydroxylase; eCH, e-carotene hydroxylase; ZEP, zeaxanthin epoxidase; VDE, violaxanthin de-epoxidase; NXS, neoxanthin synthase; CCD, carotenoid cleavage dioxygenase. B. RT-PCR analysis for expression of selected candidate genes related to the carotenoid metabolism. Equal amounts of total RNA were used in each reaction. The levels of constitutively expressed RPS18 coding gene were assayed as controls. The PCR products were separated by 1.5% (w/v) agarose gel electrophoresis and visualized by ethidium bromide staining. C. Relative transcript levels in tepals of the genes analysed by RT-PCR in B.
Figure Legend Snippet: Expression analysis of selected genes involved in carotenoid metabolism. A. Schematic carotenoid and apocarotenoid biosynthetic pathway in Crocus . Enzymatic reactions are represented by arrows. GGPP, geranyl geranyl diphosphate; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, z-carotene desaturase; CRTISO, carotene isomerase; LCYe, lycopene e-cyclase; LCYb, lycopene b-cyclase; bCH, b-carotene hydroxylase; eCH, e-carotene hydroxylase; ZEP, zeaxanthin epoxidase; VDE, violaxanthin de-epoxidase; NXS, neoxanthin synthase; CCD, carotenoid cleavage dioxygenase. B. RT-PCR analysis for expression of selected candidate genes related to the carotenoid metabolism. Equal amounts of total RNA were used in each reaction. The levels of constitutively expressed RPS18 coding gene were assayed as controls. The PCR products were separated by 1.5% (w/v) agarose gel electrophoresis and visualized by ethidium bromide staining. C. Relative transcript levels in tepals of the genes analysed by RT-PCR in B.

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining

28) Product Images from "A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development"

Article Title: A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development

Journal: eLife

doi: 10.7554/eLife.45310

Altered plastid development in ccr2 is linked with cis -carotene accumulation and not to a perturbation in ABA or SL. ( A ) Mutants that perturb the levels of lutein, ABA, SL and accumulate cis -carotenes ( ccr2 , ccr1 and ziso ) were grown for two weeks under a 16 hr photoperiod and then shifted to a shorter 8 hr photoperiod for one week. Representative images showing newly emerged and expanding leaves from multiple experimental and biological repetitions (n > 20 plants per line) are displayed. Genetic alleles tested include Col-0 (WT), ccr2-1 ( carotenoid isomerase ), lut2-1 ( epsilon lycopene cyclase ), aba1-3 (Ler background) ( zeaxanthin epoxidase ), max4/ccd8 (carotenoid cleavage dioxygenase 8), ccr1-1/sdg8 ( set domain group 8 ) and ziso1-3 ( ζ-carotene isomerase ). ( B ) Carotenoid profiles in rosette leaves from three-week-old plants grown under a 16 hr photoperiod and subjected to 6-d of extended darkness. ( C ) Carotenoid profiles in three-week-old rosette leaves from plants grown under a constant 8 hr light photoperiod. Pigments were profiled in a yellow leaf (YL) and green leaf (GL) from WT and ccr2 . ( D ) Carotenoid profiles in newly emerged floral bud and rosette leaf tissues harvested from four-week-old plants growing under a 16 hr photoperiod. Carotenoid profile traces of various tissue extracts from wild type (WT) and ccr2 show pigments at wavelengths close to the absorption maxima of A 440nm (Neoxanthin; N, violaxanthin; V, antheraxanthin; A, lutein; L, zeaxanthin; Z, β-carotene isomers; β-C, chlorophyll a; Chl a, chlorophyll b; chl b, tetra- cis- lycopene; plyc, neurosporene isomers; neuro, and ζ-carotene; ζ-C), A 348nm (phytofluene; pflu) and A 286nm (phytoene; phyt). HPLC profile y-axis units are in milli-absorbance units (mAU). HPLC traces are representative of multiple leaves from multiple experimental repetitions and retention times vary due to using different columns.
Figure Legend Snippet: Altered plastid development in ccr2 is linked with cis -carotene accumulation and not to a perturbation in ABA or SL. ( A ) Mutants that perturb the levels of lutein, ABA, SL and accumulate cis -carotenes ( ccr2 , ccr1 and ziso ) were grown for two weeks under a 16 hr photoperiod and then shifted to a shorter 8 hr photoperiod for one week. Representative images showing newly emerged and expanding leaves from multiple experimental and biological repetitions (n > 20 plants per line) are displayed. Genetic alleles tested include Col-0 (WT), ccr2-1 ( carotenoid isomerase ), lut2-1 ( epsilon lycopene cyclase ), aba1-3 (Ler background) ( zeaxanthin epoxidase ), max4/ccd8 (carotenoid cleavage dioxygenase 8), ccr1-1/sdg8 ( set domain group 8 ) and ziso1-3 ( ζ-carotene isomerase ). ( B ) Carotenoid profiles in rosette leaves from three-week-old plants grown under a 16 hr photoperiod and subjected to 6-d of extended darkness. ( C ) Carotenoid profiles in three-week-old rosette leaves from plants grown under a constant 8 hr light photoperiod. Pigments were profiled in a yellow leaf (YL) and green leaf (GL) from WT and ccr2 . ( D ) Carotenoid profiles in newly emerged floral bud and rosette leaf tissues harvested from four-week-old plants growing under a 16 hr photoperiod. Carotenoid profile traces of various tissue extracts from wild type (WT) and ccr2 show pigments at wavelengths close to the absorption maxima of A 440nm (Neoxanthin; N, violaxanthin; V, antheraxanthin; A, lutein; L, zeaxanthin; Z, β-carotene isomers; β-C, chlorophyll a; Chl a, chlorophyll b; chl b, tetra- cis- lycopene; plyc, neurosporene isomers; neuro, and ζ-carotene; ζ-C), A 348nm (phytofluene; pflu) and A 286nm (phytoene; phyt). HPLC profile y-axis units are in milli-absorbance units (mAU). HPLC traces are representative of multiple leaves from multiple experimental repetitions and retention times vary due to using different columns.

Techniques Used: High Performance Liquid Chromatography

cis -carotene biosynthesis and regulation of PLB formation during skotomorphogenesis. ( A ) A pathway for cis -carotene and xanthophyll synthesis. Tri- cis -ζ-carotene and tetra- cis -lycopene are isomerised by ZISO and CRTISO to form di- cis -ζ-carotene and lycopene, respectively. ziso and ccr2 mutants accumulate cis -carotenes ( Park et al., 2002 ; Chen et al., 2010 ). In the light, photoisomerisation facilitates cis -carotene isomerisation. Norflurazon (NF) inhibits PDS activity. CAROTENOID CLEAVAGE DIOXYGENASE (CCD) activity may cleave cis -carotenes to generate an apocarotenoid signal (ACS) ( Kachanovsky et al., 2012 ; Fantini et al., 2013 ; Avendaño-Vázquez et al., 2014 ; Álvarez et al., 2016 ). Chemical treatment of seedlings with D15 can inhibit CCD activity and enhance carotenoid accumulation ( Van Norman et al., 2014 ). Mutants that block the production of lutein ( lut2; lutein-deficient 2 ), strigolactone ( max4-3; more axillary branching 4 ) and abscisic acid ( aba1-3; aba deficient 1 ) were utilised to interrogate the cause of the ccr2 leaf virescence phenotype. ( B ) Control of prolamellar body (PLB) formation and protein levels during skotomorphogenesis. DET1 acts as a repressor of photomorphogenesis in etiolated tissues to maintain high PIF3 and low HY5 protein levels, which reduce PHOTOSYNTHESIS ASSOCIATED NUCLEAR GENE ( PhANG ) expression. det1 mutants do not accumulate PORA and do not form a PLB within the etioplast. Upon de-etiolation, the protein levels DET1 and PIF3 decline and HY5 increases, which induces PhANG expression. Grey insert boxes digitally represent published western protein blots for PORA ( Lebedev et al., 1995 ), PIF3 ( Dong et al., 2014 ) and HY5 ( Osterlund et al., 2000 ) in WT and det1 mutant genotypes. Solid black and grey fills represents high and low protein expression, respectively. Green arrows and red lines represent positive and negative regulation, respectively. Abbreviations: GGPP, geranylgeranyl pyrophosphate; PSY, PHYTOENE SYNTHASE; PDS, PHYTOENE DESATURASE, ZDS, ζ-CAROTENE DESATURASE; ZISO, ζ-CAROTENE ISOMERASE; CRTISO, CAROTENOID ISOMERASE.
Figure Legend Snippet: cis -carotene biosynthesis and regulation of PLB formation during skotomorphogenesis. ( A ) A pathway for cis -carotene and xanthophyll synthesis. Tri- cis -ζ-carotene and tetra- cis -lycopene are isomerised by ZISO and CRTISO to form di- cis -ζ-carotene and lycopene, respectively. ziso and ccr2 mutants accumulate cis -carotenes ( Park et al., 2002 ; Chen et al., 2010 ). In the light, photoisomerisation facilitates cis -carotene isomerisation. Norflurazon (NF) inhibits PDS activity. CAROTENOID CLEAVAGE DIOXYGENASE (CCD) activity may cleave cis -carotenes to generate an apocarotenoid signal (ACS) ( Kachanovsky et al., 2012 ; Fantini et al., 2013 ; Avendaño-Vázquez et al., 2014 ; Álvarez et al., 2016 ). Chemical treatment of seedlings with D15 can inhibit CCD activity and enhance carotenoid accumulation ( Van Norman et al., 2014 ). Mutants that block the production of lutein ( lut2; lutein-deficient 2 ), strigolactone ( max4-3; more axillary branching 4 ) and abscisic acid ( aba1-3; aba deficient 1 ) were utilised to interrogate the cause of the ccr2 leaf virescence phenotype. ( B ) Control of prolamellar body (PLB) formation and protein levels during skotomorphogenesis. DET1 acts as a repressor of photomorphogenesis in etiolated tissues to maintain high PIF3 and low HY5 protein levels, which reduce PHOTOSYNTHESIS ASSOCIATED NUCLEAR GENE ( PhANG ) expression. det1 mutants do not accumulate PORA and do not form a PLB within the etioplast. Upon de-etiolation, the protein levels DET1 and PIF3 decline and HY5 increases, which induces PhANG expression. Grey insert boxes digitally represent published western protein blots for PORA ( Lebedev et al., 1995 ), PIF3 ( Dong et al., 2014 ) and HY5 ( Osterlund et al., 2000 ) in WT and det1 mutant genotypes. Solid black and grey fills represents high and low protein expression, respectively. Green arrows and red lines represent positive and negative regulation, respectively. Abbreviations: GGPP, geranylgeranyl pyrophosphate; PSY, PHYTOENE SYNTHASE; PDS, PHYTOENE DESATURASE, ZDS, ζ-CAROTENE DESATURASE; ZISO, ζ-CAROTENE ISOMERASE; CRTISO, CAROTENOID ISOMERASE.

Techniques Used: Activity Assay, Blocking Assay, Expressing, Western Blot, Mutagenesis

The loss-of-function in individual members of the carotenoid cleavage dioxygenase gene family cannot restore plastid development in ccr2 rosettes. Two-week-old WT, ccr2 , ccr2 ccd1, ccr2 ccd4, ccr2 ccd7, and ccr2 ccd8 (F 3 homozygous double mutant lines) plants were shifted from a 16 hr to 8 hr photoperiod until newly formed leaves in the ccr2 rosette displayed a virescent leaf phenotype. ( A ) Representative images of plants showing newly developed leaves in the rosette. ( B ) Quantification of yellow leaf virescence in individual rosettes from ccr2 ccd double mutants. Data is representative of multiple independent experiments. Statistical analysis by ANOVA with post-hoc Tukey test showed no significant difference in the number of ccr2 and ccr2 ccd plants displaying a virescent phenotype.
Figure Legend Snippet: The loss-of-function in individual members of the carotenoid cleavage dioxygenase gene family cannot restore plastid development in ccr2 rosettes. Two-week-old WT, ccr2 , ccr2 ccd1, ccr2 ccd4, ccr2 ccd7, and ccr2 ccd8 (F 3 homozygous double mutant lines) plants were shifted from a 16 hr to 8 hr photoperiod until newly formed leaves in the ccr2 rosette displayed a virescent leaf phenotype. ( A ) Representative images of plants showing newly developed leaves in the rosette. ( B ) Quantification of yellow leaf virescence in individual rosettes from ccr2 ccd double mutants. Data is representative of multiple independent experiments. Statistical analysis by ANOVA with post-hoc Tukey test showed no significant difference in the number of ccr2 and ccr2 ccd plants displaying a virescent phenotype.

Techniques Used: Mutagenesis

29) Product Images from "Expression of MdCCD7 in the scion determines the extent of sylleptic branching and the primary shoot growth rate of apple trees"

Article Title: Expression of MdCCD7 in the scion determines the extent of sylleptic branching and the primary shoot growth rate of apple trees

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/erx404

Unrooted phylogenetic tree of the CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) gene family. Only full-length members of the family are included. The predicted sequences were aligned using ClustalW in Geneious (version 10). Phylogenetic relationships were calculated using the maximum-likelihood principle, and bootstrap values with 500 replicates were determined using Geneious. The scale bar is the number of substitutions per site. Accession numbers for the sequences are as follows: Actinidia chinensis AcCCD7 (ADP37985.1), AcCCD8 (ADP37984.1); Arabidopsis thaliana AtCCD1 (AT3G63520), AtCCD4 (AT4G19170), AtCCD7 (AT2G44990.1), AtCCD8 (AT4G32810); Brassica oleracea BoCCD7 (XP_013635602.1), BoCCD8 (XP_013589279.1); Fragaria vesca FvCCD7 (XP_004306976.2), FvCCD8 (XP_011458989.1); Malus×domestica MdCCD7 (MF034498), MdCCD8a (XP_008378214.1), MdCCD8b (XP_008352014.1); Oryza sativa OsCCD7 (LOC_Os04g46470.1), OsCCD8 (XP_015642760.1); Petunia×hybrida PhCCD7 (ACY01408.1), PhCCD8 (AAW33596.1); Pisum sativum PsCCD7 (ABD67496.2), PsCCD8 (AAS66906.1); Populus trichocarpa PtCCD7 (XP_006375244.1), PtCCD8 (XP_002324797.1); Prunus persica PpCCD7 (XP_007221108.1), PpCCD8 (XP_007222386.2); Pyrus communis PcCCD7 (PCP005718), PcCCD8 (PCP000841); Vitis vinifera VvCCD7 (XP_002274198.1), VvCCD8 (XP_002281239.2).
Figure Legend Snippet: Unrooted phylogenetic tree of the CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) gene family. Only full-length members of the family are included. The predicted sequences were aligned using ClustalW in Geneious (version 10). Phylogenetic relationships were calculated using the maximum-likelihood principle, and bootstrap values with 500 replicates were determined using Geneious. The scale bar is the number of substitutions per site. Accession numbers for the sequences are as follows: Actinidia chinensis AcCCD7 (ADP37985.1), AcCCD8 (ADP37984.1); Arabidopsis thaliana AtCCD1 (AT3G63520), AtCCD4 (AT4G19170), AtCCD7 (AT2G44990.1), AtCCD8 (AT4G32810); Brassica oleracea BoCCD7 (XP_013635602.1), BoCCD8 (XP_013589279.1); Fragaria vesca FvCCD7 (XP_004306976.2), FvCCD8 (XP_011458989.1); Malus×domestica MdCCD7 (MF034498), MdCCD8a (XP_008378214.1), MdCCD8b (XP_008352014.1); Oryza sativa OsCCD7 (LOC_Os04g46470.1), OsCCD8 (XP_015642760.1); Petunia×hybrida PhCCD7 (ACY01408.1), PhCCD8 (AAW33596.1); Pisum sativum PsCCD7 (ABD67496.2), PsCCD8 (AAS66906.1); Populus trichocarpa PtCCD7 (XP_006375244.1), PtCCD8 (XP_002324797.1); Prunus persica PpCCD7 (XP_007221108.1), PpCCD8 (XP_007222386.2); Pyrus communis PcCCD7 (PCP005718), PcCCD8 (PCP000841); Vitis vinifera VvCCD7 (XP_002274198.1), VvCCD8 (XP_002281239.2).

Techniques Used:

Expression of CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) genes in ‘Royal Gala’ apple. qRT-PCR expression of MdCCD7 and MdCCD8 in wild-type tissues. Values are means of three technical replicates ±SE, normalized to internal control genes and relative to MdCCD8 expression in roots. Tissues without bars had expression levels below the threshold of detection. The scale for MdCCD7 is on the right axis and for MdCCD8 is on the left.
Figure Legend Snippet: Expression of CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) genes in ‘Royal Gala’ apple. qRT-PCR expression of MdCCD7 and MdCCD8 in wild-type tissues. Values are means of three technical replicates ±SE, normalized to internal control genes and relative to MdCCD8 expression in roots. Tissues without bars had expression levels below the threshold of detection. The scale for MdCCD7 is on the right axis and for MdCCD8 is on the left.

Techniques Used: Expressing, Quantitative RT-PCR

30) Product Images from "Comparison of transcriptional expression patterns of phenols and carotenoids in ‘Kyoho’ grapes under a two-crop-a-year cultivation system"

Article Title: Comparison of transcriptional expression patterns of phenols and carotenoids in ‘Kyoho’ grapes under a two-crop-a-year cultivation system

Journal: PLoS ONE

doi: 10.1371/journal.pone.0210322

Transcriptomic profile of the structural genes involved in phenolic biosynthesis in summer and winter grape berries. PAL, phenylalanine ammonia-lyase; C4H, trans -cinnamate 4-monooxygenase; COMT, caffeic acid 3- O -methyltransferase; F5H, ferulate-5-hydroxylase; 4CL, 4-coumarate: CoA ligase; STS, stilbene synthase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavonoid 3-hydroxylase; F3’H, flavonoid 3’-hydroxylase; F3’5’H, flavonoid 3’,5’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; LAR, leucoanthocyanidin reductase; LDOX, leucoanthocyanidin dioxygenase; ANR, anthocyanidin reductase; UFGT, UDP-glucose: flavonoid 3- O -glucosyltransferase; GST, glutathione S-transferase. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as shown in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.
Figure Legend Snippet: Transcriptomic profile of the structural genes involved in phenolic biosynthesis in summer and winter grape berries. PAL, phenylalanine ammonia-lyase; C4H, trans -cinnamate 4-monooxygenase; COMT, caffeic acid 3- O -methyltransferase; F5H, ferulate-5-hydroxylase; 4CL, 4-coumarate: CoA ligase; STS, stilbene synthase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavonoid 3-hydroxylase; F3’H, flavonoid 3’-hydroxylase; F3’5’H, flavonoid 3’,5’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; LAR, leucoanthocyanidin reductase; LDOX, leucoanthocyanidin dioxygenase; ANR, anthocyanidin reductase; UFGT, UDP-glucose: flavonoid 3- O -glucosyltransferase; GST, glutathione S-transferase. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as shown in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.

Techniques Used:

Transcriptomic profile of the structural genes involved in the carotenoid and ABA biosynthetic pathways in summer and winter grape berries. PSY, phytoene synthase; Z-ISO, zeta-carotene isomerase; PISO, prolycopene isomerase; LBCY, lycopene-beta-cyclase; LECY, lycopene epsilon-cyclase; CCD, carotenoid cleavage dioxygenase; ZEP, zeaxanthin epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase; BCH, beta-carotene 3-hydroxylase; XO, xanthosin dehydrogenase; ABA8ox, ABA 8’-hydroxylase; ABAO, abscisic-aldehyde oxidase; ABA-GE, ABA glucosyl-ester; ABA-GT, ABA glucosyltransferase; PA, phaseic acid. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as illustrated in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.
Figure Legend Snippet: Transcriptomic profile of the structural genes involved in the carotenoid and ABA biosynthetic pathways in summer and winter grape berries. PSY, phytoene synthase; Z-ISO, zeta-carotene isomerase; PISO, prolycopene isomerase; LBCY, lycopene-beta-cyclase; LECY, lycopene epsilon-cyclase; CCD, carotenoid cleavage dioxygenase; ZEP, zeaxanthin epoxidase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase; BCH, beta-carotene 3-hydroxylase; XO, xanthosin dehydrogenase; ABA8ox, ABA 8’-hydroxylase; ABAO, abscisic-aldehyde oxidase; ABA-GE, ABA glucosyl-ester; ABA-GT, ABA glucosyltransferase; PA, phaseic acid. Each square in the heatmap located beside its gene names corresponds to the average FPKM value of the gene in each sample, as illustrated in the legend. SK, summer ‘Kyoho’; WK, winter ‘Kyoho’.

Techniques Used:

31) Product Images from "Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism"

Article Title: Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism

Journal: BMC Plant Biology

doi: 10.1186/1471-2229-11-24

Expression patterns of carotenoid-related genes during ripening of RHB and RH fruits . Relative average gene transcript levels ± SD are given, following normalization with rps28 values. A: isoprenoid genes [ cmk , 4-(cytidine 5'-diphospho)-2- C -methyl-d-erythritol kinase; dxs , 1-deoxy-d-xylulose 5-phosphate synthase; hdr , 4-hydroxy-3-methylbut-2-enyl diphosphate reductase]. B: early carotenoid genes ( pds , phytoene desaturase; psy , phytoene synthase; zds , ζ-carotene desaturase). C: other carotenoid genes ( chy-b , carotene β-hydroxylase; chy-e , carotene ε-hydroxylase; lcy-b , lycopene β-cyclase; lcy-e , lycopene-e-cyclase; zep , zeaxanthin epoxidase). D: dioxygenase-related genes ( ccd1 and ccd4 , carotenoid cleavage dioxygenases 1 and 4; nced1 and nced2 , 9- cis -epoxycarotenoid dioxygenases 1 and 2). For each gene, different letters indicate significant differences among mean values from different stages (*: p ≤ 0.05; **: p ≤ 0.01).
Figure Legend Snippet: Expression patterns of carotenoid-related genes during ripening of RHB and RH fruits . Relative average gene transcript levels ± SD are given, following normalization with rps28 values. A: isoprenoid genes [ cmk , 4-(cytidine 5'-diphospho)-2- C -methyl-d-erythritol kinase; dxs , 1-deoxy-d-xylulose 5-phosphate synthase; hdr , 4-hydroxy-3-methylbut-2-enyl diphosphate reductase]. B: early carotenoid genes ( pds , phytoene desaturase; psy , phytoene synthase; zds , ζ-carotene desaturase). C: other carotenoid genes ( chy-b , carotene β-hydroxylase; chy-e , carotene ε-hydroxylase; lcy-b , lycopene β-cyclase; lcy-e , lycopene-e-cyclase; zep , zeaxanthin epoxidase). D: dioxygenase-related genes ( ccd1 and ccd4 , carotenoid cleavage dioxygenases 1 and 4; nced1 and nced2 , 9- cis -epoxycarotenoid dioxygenases 1 and 2). For each gene, different letters indicate significant differences among mean values from different stages (*: p ≤ 0.05; **: p ≤ 0.01).

Techniques Used: Expressing

32) Product Images from "Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology"

Article Title: Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology

Journal: BMC Genomics

doi: 10.1186/1471-2164-13-292

Distribution of carnation transcripts in the carotenoid biosynthesis pathway. Previously published sequences in GenBank belonging to the carotenoid biosynthesis pathway were used in BLAST searches to identify genes in the carnation EST database. Each enzyme name is followed in parentheses by the number of contigs homologous to gene families encoding this enzyme. IPI, isopentenyl pyrophosphate isomerase; GGDP, geranylgeranyl diphosphate synthase; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, ζ-carotene desaturase; LCYB, lycopene β-cyclase; LCYE, lycopene ϵ-cyclase; CHYB, β-ring hydroxylase; CHYE, ϵ-ring hydroxylase; ZEP, zeaxanthin epoxidase; VDE, violaxanthin de-epoxidase; CRTISO, carotenoid isomerase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase.
Figure Legend Snippet: Distribution of carnation transcripts in the carotenoid biosynthesis pathway. Previously published sequences in GenBank belonging to the carotenoid biosynthesis pathway were used in BLAST searches to identify genes in the carnation EST database. Each enzyme name is followed in parentheses by the number of contigs homologous to gene families encoding this enzyme. IPI, isopentenyl pyrophosphate isomerase; GGDP, geranylgeranyl diphosphate synthase; PSY, phytoene synthase; PDS, phytoene desaturase; ZDS, ζ-carotene desaturase; LCYB, lycopene β-cyclase; LCYE, lycopene ϵ-cyclase; CHYB, β-ring hydroxylase; CHYE, ϵ-ring hydroxylase; ZEP, zeaxanthin epoxidase; VDE, violaxanthin de-epoxidase; CRTISO, carotenoid isomerase; NSY, neoxanthin synthase; NCED, 9- cis -epoxycarotenoid dioxygenase.

Techniques Used:

33) Product Images from "A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development"

Article Title: A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development

Journal: bioRxiv

doi: 10.1101/528331

A model describing how a cis -carotene derived cleavage product controls POR and PLB formation during plastid development. (A) ccr2 can accumulate poly- cis -carotenes that undergo enzymatic cleavage via CCDs to generate an apocarotenoid signal (ACS). Norflurazon (NF) treatment of ccr2 etiolated seedlings or the loss-of-function in ziso-155 block the accumulation of downstream cis-carotenes required for the biosynthesis of ACS. Chemical treatment of etiolated seedlings with D15 inhibits CCD cleavage of pro-neurosporene and/or tetra- cis -lycopene isomers into ACS. (B) During skotomorphogenesis, ACS promotes “Factor X”. Factor X negatively affects PLB formation. Factor X could act to stabilise proteins by disrupting ubiquitination, de-ubiquitination, protease mediated protein degradation, heterodimerization of transcription factors, coactivator concentrations, and/or interact with ligand binding sites of receptors. DET1 is a repressor of photomorphogenesis that post-transcriptionally regulate PIF3 and HY5 protein levels, which control PhANG expression. det1 mutants lack POR and cannot make a PLB. ACS post-transcriptionally enhances POR protein levels, while det1 blocks Factor X, thereby allowing PLB formation in ccr2 det1-154 . det1 reduces cis -carotene accumulation, and downregulates pro-neurosporene and tetra- cis -lycopene to maintain a threshold level of ACS. (C) During photomorphogenesis, extended dark and/or shorter photoperiods, ACS manifests in newly emerged leaves from the ccr2 shoot meristem and perturbed chloroplast development and chlorophyll accumulation causing a leaf variegation phenotype. Green arrows and red lines represent positive and negative regulation, respectively. Abbreviations: PSY, phytoene synthase; PDS, phytoene desaturase, ZDS, ζ-carotene desaturase; Z1SO, ζ-carotene isomerase; CRTISO, carotenoid isomerase; det1-154 , DEETIOLATED1-154; D15, inhibitor of CCD activity; CCD, carotenoid cleavage dioxygenase; ccr2 , CRTISO mutant.
Figure Legend Snippet: A model describing how a cis -carotene derived cleavage product controls POR and PLB formation during plastid development. (A) ccr2 can accumulate poly- cis -carotenes that undergo enzymatic cleavage via CCDs to generate an apocarotenoid signal (ACS). Norflurazon (NF) treatment of ccr2 etiolated seedlings or the loss-of-function in ziso-155 block the accumulation of downstream cis-carotenes required for the biosynthesis of ACS. Chemical treatment of etiolated seedlings with D15 inhibits CCD cleavage of pro-neurosporene and/or tetra- cis -lycopene isomers into ACS. (B) During skotomorphogenesis, ACS promotes “Factor X”. Factor X negatively affects PLB formation. Factor X could act to stabilise proteins by disrupting ubiquitination, de-ubiquitination, protease mediated protein degradation, heterodimerization of transcription factors, coactivator concentrations, and/or interact with ligand binding sites of receptors. DET1 is a repressor of photomorphogenesis that post-transcriptionally regulate PIF3 and HY5 protein levels, which control PhANG expression. det1 mutants lack POR and cannot make a PLB. ACS post-transcriptionally enhances POR protein levels, while det1 blocks Factor X, thereby allowing PLB formation in ccr2 det1-154 . det1 reduces cis -carotene accumulation, and downregulates pro-neurosporene and tetra- cis -lycopene to maintain a threshold level of ACS. (C) During photomorphogenesis, extended dark and/or shorter photoperiods, ACS manifests in newly emerged leaves from the ccr2 shoot meristem and perturbed chloroplast development and chlorophyll accumulation causing a leaf variegation phenotype. Green arrows and red lines represent positive and negative regulation, respectively. Abbreviations: PSY, phytoene synthase; PDS, phytoene desaturase, ZDS, ζ-carotene desaturase; Z1SO, ζ-carotene isomerase; CRTISO, carotenoid isomerase; det1-154 , DEETIOLATED1-154; D15, inhibitor of CCD activity; CCD, carotenoid cleavage dioxygenase; ccr2 , CRTISO mutant.

Techniques Used: Derivative Assay, Blocking Assay, Ligand Binding Assay, Expressing, Activity Assay, Mutagenesis

Altered plastid development in ccr2 is linked with cis -carotene accumulation and not to a perturbation in ABA or SL. (A) Mutants that perturb the levels of lutein, ABA, SL and accumulate cis -carotenes ( ccr2 , ccr1 and ziso ) were grown for two weeks under a 16-h photoperiod and then shifted to a shorter 8-h photoperiod for one week. Representative images showing newly emerged and expanding leaves from multiple experimental and biological repetitions (n > 20 plants per line) are displayed. Genetic alleles tested include Col-0 (WT), ccr2.1 (carotenoid isomerase), lut2.1 (epsilon lycopene cyclase), aba1-3 (Ler background) (zeaxanthin epoxidase), max4/ccd8 (carotenoid cleavage dioxygenase 8), ccr1.1/sdg8 (set domain group 8) and ziso1-3 (ζ-carotene isomerase). (B) Carotenoid profiles in rosette leaves from three-week-old plants grown under a 16-h photoperiod and subjected to 6-d of extended darkness. (C) Carotenoid profiles in three-week-old rosette leaves from plants grown under a constant 8-h light photoperiod. Pigments were profiled in a yellow leaf (YL) and green leaf (GL) from WT and ccr2 . (D) Carotenoid profiles in newly emerged floral bud and rosette leaf tissues harvested from four-week-old plants growing under a 16-h photoperiod. Carotenoid profile traces of various tissue extracts from wild type (WT) and ccr2 show pigments at wavelengths close to the absorption maxima of A 440nm (Neoxanthin; N, violaxanthin; V, antheraxanthin; A, lutein; L, zeaxanthin; Z, β-carotene isomers; β-C, chlorophyll a; Chl a, chlorophyll b; chl b, tetra- cis- lycopene; plyc, neurosporene isomers; neuro, and ζ-carotene; ζ-C), A 348nm (phytofluene; pflu) and A 286nm (phytoene; phyt). HPLC profile y-axis units are in milli-absorbance units (mAU). HPLC traces are representative of multiple leaves from multiple experimental repetitions and retention times vary due to using different columns.
Figure Legend Snippet: Altered plastid development in ccr2 is linked with cis -carotene accumulation and not to a perturbation in ABA or SL. (A) Mutants that perturb the levels of lutein, ABA, SL and accumulate cis -carotenes ( ccr2 , ccr1 and ziso ) were grown for two weeks under a 16-h photoperiod and then shifted to a shorter 8-h photoperiod for one week. Representative images showing newly emerged and expanding leaves from multiple experimental and biological repetitions (n > 20 plants per line) are displayed. Genetic alleles tested include Col-0 (WT), ccr2.1 (carotenoid isomerase), lut2.1 (epsilon lycopene cyclase), aba1-3 (Ler background) (zeaxanthin epoxidase), max4/ccd8 (carotenoid cleavage dioxygenase 8), ccr1.1/sdg8 (set domain group 8) and ziso1-3 (ζ-carotene isomerase). (B) Carotenoid profiles in rosette leaves from three-week-old plants grown under a 16-h photoperiod and subjected to 6-d of extended darkness. (C) Carotenoid profiles in three-week-old rosette leaves from plants grown under a constant 8-h light photoperiod. Pigments were profiled in a yellow leaf (YL) and green leaf (GL) from WT and ccr2 . (D) Carotenoid profiles in newly emerged floral bud and rosette leaf tissues harvested from four-week-old plants growing under a 16-h photoperiod. Carotenoid profile traces of various tissue extracts from wild type (WT) and ccr2 show pigments at wavelengths close to the absorption maxima of A 440nm (Neoxanthin; N, violaxanthin; V, antheraxanthin; A, lutein; L, zeaxanthin; Z, β-carotene isomers; β-C, chlorophyll a; Chl a, chlorophyll b; chl b, tetra- cis- lycopene; plyc, neurosporene isomers; neuro, and ζ-carotene; ζ-C), A 348nm (phytofluene; pflu) and A 286nm (phytoene; phyt). HPLC profile y-axis units are in milli-absorbance units (mAU). HPLC traces are representative of multiple leaves from multiple experimental repetitions and retention times vary due to using different columns.

Techniques Used: High Performance Liquid Chromatography

The carotenoid cleavage dioxygenase (CCD) inhibitor, D15, restores PLB formation in etiolated ccr2 seedlings, cotyledon greening following de-etiolation and alters cis -carotene accumulation. (A) Transmission electron micrographs of a representative etioplast from 5-d-old dark grown cotyledons reveal a well-developed PLB in ccr2 treated with the D15, but not in ccr2 treated with ethanol only (control; ctrl). (B) Pchlide levels in Wild Type (WT) and ccr2 treated +/-D15. Fluorescence was measured at 638 nm and 675 nm with an excitation at 440 nm. Net fluorescence of Pchlide was calculated and normalised to protein content. (C) D15 restores chlorophyll accumulation in ccr2 de-etiolated seedlings exposed to continuous light. Twenty seedlings from each of three biological replicates were harvested for chlorophyll determination in every 24 h under continuous light. Statistical analysis was by ANOVA with a post-hoc Tukey test (n= 20 seedlings). (D) cis -carotene quantification in etiolated cotyledons of ccr2 treated with D15. phytoene (phyt), phytofluene (pflu), tri- cis -ζ-carotene (3ζ-C), di- cis -ζ-carotene (2ζ-C), pro-neurosporene (p-N), tetra- cis -lycopene (p-lyc) and total cis -carotenes were quantified at absorption wavelengths providing maximum detection. Star denotes significance (ANOVA, p
Figure Legend Snippet: The carotenoid cleavage dioxygenase (CCD) inhibitor, D15, restores PLB formation in etiolated ccr2 seedlings, cotyledon greening following de-etiolation and alters cis -carotene accumulation. (A) Transmission electron micrographs of a representative etioplast from 5-d-old dark grown cotyledons reveal a well-developed PLB in ccr2 treated with the D15, but not in ccr2 treated with ethanol only (control; ctrl). (B) Pchlide levels in Wild Type (WT) and ccr2 treated +/-D15. Fluorescence was measured at 638 nm and 675 nm with an excitation at 440 nm. Net fluorescence of Pchlide was calculated and normalised to protein content. (C) D15 restores chlorophyll accumulation in ccr2 de-etiolated seedlings exposed to continuous light. Twenty seedlings from each of three biological replicates were harvested for chlorophyll determination in every 24 h under continuous light. Statistical analysis was by ANOVA with a post-hoc Tukey test (n= 20 seedlings). (D) cis -carotene quantification in etiolated cotyledons of ccr2 treated with D15. phytoene (phyt), phytofluene (pflu), tri- cis -ζ-carotene (3ζ-C), di- cis -ζ-carotene (2ζ-C), pro-neurosporene (p-N), tetra- cis -lycopene (p-lyc) and total cis -carotenes were quantified at absorption wavelengths providing maximum detection. Star denotes significance (ANOVA, p

Techniques Used: Transmission Assay, Fluorescence

The loss-of-function in individual members of the carotenoid cleavage dioxygenase gene family cannot restore plastid development in ccr2 rosettes. Three-week-old WT, ccr2 , ccr2 ccd1, ccr2 ccd4, ccr2 ccd7 , and ccr2 ccd8 (F 3 homozygous double mutant lines) plants were shifted from a 16-h to 8-h photoperiod until newly formed leaves in the ccr2 rosette displayed a virescent leaf phenotype. (A) Representative images of plants showing newly developed leaves in the rosette. (B) Quantification of leaf variegation in individual rosettes from ccr2 ccd double mutants. Data is representative of multiple independent experiments. Statistical analysis by ANOVA with post-hoc Tukey test showed no significant difference in the number of ccr2 and ccr2 ccd plants displaying a virescent phenotype.
Figure Legend Snippet: The loss-of-function in individual members of the carotenoid cleavage dioxygenase gene family cannot restore plastid development in ccr2 rosettes. Three-week-old WT, ccr2 , ccr2 ccd1, ccr2 ccd4, ccr2 ccd7 , and ccr2 ccd8 (F 3 homozygous double mutant lines) plants were shifted from a 16-h to 8-h photoperiod until newly formed leaves in the ccr2 rosette displayed a virescent leaf phenotype. (A) Representative images of plants showing newly developed leaves in the rosette. (B) Quantification of leaf variegation in individual rosettes from ccr2 ccd double mutants. Data is representative of multiple independent experiments. Statistical analysis by ANOVA with post-hoc Tukey test showed no significant difference in the number of ccr2 and ccr2 ccd plants displaying a virescent phenotype.

Techniques Used: Mutagenesis

34) Product Images from "Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits"

Article Title: Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/err284

Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.
Figure Legend Snippet: Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.

Techniques Used: Expressing

35) Product Images from "Efficient production of saffron crocins and picrocrocin in Nicotiana benthamiana using a virus-driven system"

Article Title: Efficient production of saffron crocins and picrocrocin in Nicotiana benthamiana using a virus-driven system

Journal: bioRxiv

doi: 10.1101/2019.12.18.880765

Schematic overview of the crocins biosynthesis pathway in C. sativus and B. davidii . CrtB, phytoene synthase; PDS, phytoene desaturase; BCH2, carotene hydroxylase; CsCCD2L, C. sativus carotenoid cleavage dioxygenase 2L; BdCCD4.1 and 4.3, B. davidii carotenoid cleavage dioxygenase 4.1 and 4.3; ALDH, aldehyde dehydrogenase; UGT74AD1, UDP-glucosyltransferase 74AD1.
Figure Legend Snippet: Schematic overview of the crocins biosynthesis pathway in C. sativus and B. davidii . CrtB, phytoene synthase; PDS, phytoene desaturase; BCH2, carotene hydroxylase; CsCCD2L, C. sativus carotenoid cleavage dioxygenase 2L; BdCCD4.1 and 4.3, B. davidii carotenoid cleavage dioxygenase 4.1 and 4.3; ALDH, aldehyde dehydrogenase; UGT74AD1, UDP-glucosyltransferase 74AD1.

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Related Articles

other:

Article Title: Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits
Article Snippet: carotenoid cleavage dioxygenase

Article Title: Heterologous biosynthesis and manipulation of crocetin in Saccharomyces cerevisiae
Article Snippet: carotenoid cleavage dioxygenase

Article Title: Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay
Article Snippet: The transcript abundance of a terpenoid synthetase and a carotenoid cleavage dioxygenase was increased by water deficit in Chardonnay at maturity, but not in Cabernet Sauvignon (Fig. ).

Article Title: Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis
Article Snippet: Carotenoids are the substrates of carotenoid cleavage dioxygenase (CCD) enzymes, producing apocarotenoids that play diverse functions as bioactive molecules .

Article Title: Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay
Article Snippet: Downstream of BHASE, a carotenoid cleavage dioxygenase (CCD) known to increase at véraison [ ], cleaves zeaxanthin into a C13 -norisoprenoid and a C14 -dialdehyde, both volatile compounds.

Expressing:

Article Title: Heterologous expression of xanthophyll esterase genes affects carotenoid accumulation in petunia corollas
Article Snippet: .. Among the carotenoid catabolic genes, we analyzed expression of carotenoid cleavage dioxygenase (CCD ) 1 and 9- cis-epoxy carotenoid dioxygenase (NCED ) 2, but not CCD4a or CCD4b , because we have previously clarified that expression of CCD4a is not detected at all and expression of CCD4b is not associated with carotenoid accumulation in corollas of ‘California Girl’, the petunia cultivar used in this study (Kishimoto et al ., 2018). .. NCED2 expression was lower in all XES -OX plants than in WT plants; this trend was significant for all plants except IoXES -OX #1.

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    Collaborative Drug Discovery Inc carotenoid cleavage dioxygenase
    The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid <t>dioxygenase</t> 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.
    Carotenoid Cleavage Dioxygenase, supplied by Collaborative Drug Discovery Inc, used in various techniques. Bioz Stars score: 91/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid dioxygenase 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.

    Journal: BMC Genomics

    Article Title: Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

    doi: 10.1186/1471-2164-10-212

    Figure Lengend Snippet: The influence of water deficit on transcript abundance NCED1 and NCED2 using qRT-PCR and other ABA-related transcripts on the Vitis Genome Array . Data were normalized to the transcript abundance of an ankyrin-repeat protein (1612584_s_at) that did not change with developmental stage or stress treatment. The lines and symbols are the same as Figure 1; n = 3. NCED1 (nine-cis-epoxycarotenoid dioxygenase 1), 1608022_at, TC57089, AY337613; NCED2 (nine-cis-epoxycarotenoid dioxygenase 2), TC71235, AY337614; bZIP TF (homeobox-leucine zipper transcription factor), 1609295_at.

    Article Snippet: Downstream of BHASE, a carotenoid cleavage dioxygenase (CCD) known to increase at véraison [ ], cleaves zeaxanthin into a C13 -norisoprenoid and a C14 -dialdehyde, both volatile compounds.

    Techniques: Quantitative RT-PCR

    Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.

    Journal: Journal of Experimental Botany

    Article Title: Plastid structure and carotenogenic gene expression in red- and white-fleshed loquat (Eriobotrya japonica) fruits

    doi: 10.1093/jxb/err284

    Figure Lengend Snippet: Carotenoid biosynthetic pathway in higher plants. Genes with expression levels studied are in bold letters. GAP, D-glyceraldehyde 3-phosphate; DXS , 1-deoxy-D-xylulose 5-phosphate-synthase; DXR , DXP reductoisomerase; HMBPP, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate; IDS, isopentenyl pyrophosphate synthase; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl diphosphate; IDI , isopentenyl pyrophosphate isomerase; GGPS , geranylgeranyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; PSY1 , phytoene synthase; PDS , phytoene desaturase; ZDS , ζ-carotene desaturase; CRTISO , carotene isomerase; ZISO , ζ-carotene isomerase; LCYE , lycopene ε-cyclase; LCYB , lycopene β-cyclase; CYCB , chromoplast-specific lycopene β-cyclase; BCH , β-carotene hydroxylase; ECH , ε-carotene hydroxylase; ZEP , zeaxanthin epoxidase; VDE , violaxanthin de-epoxidase; NSY , neoxanthin synthase; NCED , 9- cis -epoxycarotenoid dioxygenase.

    Article Snippet: carotenoid cleavage dioxygenase

    Techniques: Expressing

    Unrooted phylogenetic tree of the CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) gene family. Only full-length members of the family are included. The predicted sequences were aligned using ClustalW in Geneious (version 10). Phylogenetic relationships were calculated using the maximum-likelihood principle, and bootstrap values with 500 replicates were determined using Geneious. The scale bar is the number of substitutions per site. Accession numbers for the sequences are as follows: Actinidia chinensis AcCCD7 (ADP37985.1), AcCCD8 (ADP37984.1); Arabidopsis thaliana AtCCD1 (AT3G63520), AtCCD4 (AT4G19170), AtCCD7 (AT2G44990.1), AtCCD8 (AT4G32810); Brassica oleracea BoCCD7 (XP_013635602.1), BoCCD8 (XP_013589279.1); Fragaria vesca FvCCD7 (XP_004306976.2), FvCCD8 (XP_011458989.1); Malus×domestica MdCCD7 (MF034498), MdCCD8a (XP_008378214.1), MdCCD8b (XP_008352014.1); Oryza sativa OsCCD7 (LOC_Os04g46470.1), OsCCD8 (XP_015642760.1); Petunia×hybrida PhCCD7 (ACY01408.1), PhCCD8 (AAW33596.1); Pisum sativum PsCCD7 (ABD67496.2), PsCCD8 (AAS66906.1); Populus trichocarpa PtCCD7 (XP_006375244.1), PtCCD8 (XP_002324797.1); Prunus persica PpCCD7 (XP_007221108.1), PpCCD8 (XP_007222386.2); Pyrus communis PcCCD7 (PCP005718), PcCCD8 (PCP000841); Vitis vinifera VvCCD7 (XP_002274198.1), VvCCD8 (XP_002281239.2).

    Journal: Journal of Experimental Botany

    Article Title: Expression of MdCCD7 in the scion determines the extent of sylleptic branching and the primary shoot growth rate of apple trees

    doi: 10.1093/jxb/erx404

    Figure Lengend Snippet: Unrooted phylogenetic tree of the CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) gene family. Only full-length members of the family are included. The predicted sequences were aligned using ClustalW in Geneious (version 10). Phylogenetic relationships were calculated using the maximum-likelihood principle, and bootstrap values with 500 replicates were determined using Geneious. The scale bar is the number of substitutions per site. Accession numbers for the sequences are as follows: Actinidia chinensis AcCCD7 (ADP37985.1), AcCCD8 (ADP37984.1); Arabidopsis thaliana AtCCD1 (AT3G63520), AtCCD4 (AT4G19170), AtCCD7 (AT2G44990.1), AtCCD8 (AT4G32810); Brassica oleracea BoCCD7 (XP_013635602.1), BoCCD8 (XP_013589279.1); Fragaria vesca FvCCD7 (XP_004306976.2), FvCCD8 (XP_011458989.1); Malus×domestica MdCCD7 (MF034498), MdCCD8a (XP_008378214.1), MdCCD8b (XP_008352014.1); Oryza sativa OsCCD7 (LOC_Os04g46470.1), OsCCD8 (XP_015642760.1); Petunia×hybrida PhCCD7 (ACY01408.1), PhCCD8 (AAW33596.1); Pisum sativum PsCCD7 (ABD67496.2), PsCCD8 (AAS66906.1); Populus trichocarpa PtCCD7 (XP_006375244.1), PtCCD8 (XP_002324797.1); Prunus persica PpCCD7 (XP_007221108.1), PpCCD8 (XP_007222386.2); Pyrus communis PcCCD7 (PCP005718), PcCCD8 (PCP000841); Vitis vinifera VvCCD7 (XP_002274198.1), VvCCD8 (XP_002281239.2).

    Article Snippet: CAROTENOID CLEAVAGE DIOXYGENASE (CCD ) genes are integral to the biosynthesis of SLs and are well characterized in annual plants, but their role in woody perennials is relatively unknown.

    Techniques:

    Expression of CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) genes in ‘Royal Gala’ apple. qRT-PCR expression of MdCCD7 and MdCCD8 in wild-type tissues. Values are means of three technical replicates ±SE, normalized to internal control genes and relative to MdCCD8 expression in roots. Tissues without bars had expression levels below the threshold of detection. The scale for MdCCD7 is on the right axis and for MdCCD8 is on the left.

    Journal: Journal of Experimental Botany

    Article Title: Expression of MdCCD7 in the scion determines the extent of sylleptic branching and the primary shoot growth rate of apple trees

    doi: 10.1093/jxb/erx404

    Figure Lengend Snippet: Expression of CAROTENOID CLEAVAGE DIOXYGENASE ( CCD ) genes in ‘Royal Gala’ apple. qRT-PCR expression of MdCCD7 and MdCCD8 in wild-type tissues. Values are means of three technical replicates ±SE, normalized to internal control genes and relative to MdCCD8 expression in roots. Tissues without bars had expression levels below the threshold of detection. The scale for MdCCD7 is on the right axis and for MdCCD8 is on the left.

    Article Snippet: CAROTENOID CLEAVAGE DIOXYGENASE (CCD ) genes are integral to the biosynthesis of SLs and are well characterized in annual plants, but their role in woody perennials is relatively unknown.

    Techniques: Expressing, Quantitative RT-PCR