Journal: Molecular microbiology

Article Title: Bactericidal peptidoglycan recognition protein induces oxidative stress in Escherichia coli through a block in respiratory chain and increase in central carbon catabolism

doi: 10.1111/mmi.13733

Figure Lengend Snippet: (A) Mutants with increased resistance to PGRP killing were identified by three-stage screening of the entire Keio collection of single gene deletion mutants (Fig. S1 and Table S1) and here the survival of the parental strain (BW25113) and mutants following 3-hr incubation with 200 µg/ml of BSA (as a control) or PGRP is shown. Gene products, their functions, and numerical data are shown in Table S1. (B) Mutants for the key genes for the respiratory chain and TCA cycle, and their regulators (cyaA and crp) were constructed in MG1655 and their sensitivity to killing by 100 µg/ml of PGRP was similarly tested. The results are means of 3 experiments, expressed as percent of initial inoculum (100%) + SEM; ^ P≤0.05, ^^ P<0.001, numbers of viable bacteria (colony forming units) of Δ mutants versus parental strain (t-test).

Article Snippet: Bacteria, growth, and media The entire Keio collection of 3884 E. coli K-12 in-frame single-gene knockout mutants was obtained from the National BioResource Project, National Institute of Genetics, Japan ( Baba et al ., 2006 ).

Techniques: Incubation, Control, Construct, Bacteria

Journal: Molecular microbiology

Article Title: Bactericidal peptidoglycan recognition protein induces oxidative stress in Escherichia coli through a block in respiratory chain and increase in central carbon catabolism

doi: 10.1111/mmi.13733

Figure Lengend Snippet: (A) Time kinetics of changes of H2O2 in E. coli MG1655 treated with 100 µg/ml BSA or PGRP, or with 100 µM paraquat. (B) H2O2 in E. coli BW25113 and in the indicated deletion mutants from Keio collection treated with 100 µg/ml BSA or PGRP for 15 min. (C) H2O2 in E. coli MG1655 and in the indicated deletion mutants constructed in our laboratory treated with 100 µg/ml BSA or PGRP for 15 min. The results are means of 3–4 experiments ± SEM (SEM were within symbols if not visible); * P<0.05, ** P<0.001, PGRP vs BSA; +P<0.05, ++P<0.001, paraquat vs BSA; ^ P<0.05, ^^ P<0.001, PGRP-treated mutant vs parental strain.

Article Snippet: Bacteria, growth, and media The entire Keio collection of 3884 E. coli K-12 in-frame single-gene knockout mutants was obtained from the National BioResource Project, National Institute of Genetics, Japan ( Baba et al ., 2006 ).

Techniques: Construct, Mutagenesis

Journal: Molecular microbiology

Article Title: Bactericidal peptidoglycan recognition protein induces oxidative stress in Escherichia coli through a block in respiratory chain and increase in central carbon catabolism

doi: 10.1111/mmi.13733

Figure Lengend Snippet: Parental E. coli or the indicated deletion mutants from Keio collection (BW25113) or from our laboratory (MG1655) were treated with 100 µg/ml BSA or PGRP for 15 min (A) or 5 min (B and C). The results are means of 3–4 experiments + SEM; * P<0.05, ** P<0.001, PGRP vs BSA; ^ P<0.05, ^^ P<0.001, mutant vs parental strain.

Article Snippet: Bacteria, growth, and media The entire Keio collection of 3884 E. coli K-12 in-frame single-gene knockout mutants was obtained from the National BioResource Project, National Institute of Genetics, Japan ( Baba et al ., 2006 ).

Techniques: Mutagenesis

Journal: Molecular microbiology

Article Title: Bactericidal peptidoglycan recognition protein induces oxidative stress in Escherichia coli through a block in respiratory chain and increase in central carbon catabolism

doi: 10.1111/mmi.13733

Figure Lengend Snippet: E. coli and the indicated deletion mutants from Keio collection (BW25113) or from our laboratory (MG1655) were treated with 100 µg/ml BSA or PGRP for 30 min. The results are means of 3 experiments + SEM; * P<0.05, ** P<0.001, PGRP vs BSA; ^ P<0.05, mutant vs parental strain.

Article Snippet: Bacteria, growth, and media The entire Keio collection of 3884 E. coli K-12 in-frame single-gene knockout mutants was obtained from the National BioResource Project, National Institute of Genetics, Japan ( Baba et al ., 2006 ).

Techniques: Mutagenesis

Journal: The Plant Cell

Article Title: Ethylene Responses in Rice Roots and Coleoptiles Are Differentially Regulated by a Carotenoid Isomerase-Mediated Abscisic Acid Pathway ^[OPEN]

doi: 10.1105/tpc.15.00080

Figure Lengend Snippet: Genetic Interactions between mhz5-1 and Ethylene Receptor Loss-of-Function Mutants through Double Mutant Analyses. (A) Comparison of the root ethylene response in Nipponbare (Nip), Dongjin (DJ), and the single and double mutants in the absence or presence of ethylene (1 ppm). Representative 2.5-d-old dark-grown seedlings are shown. Bars = 10 mm. (B) Ethylene dose–response curves for the root length of 2.5-d-old dark-grown seedlings of Nipponbare, Dongjin, mhz5-1, and double mutants (ers1 mhz5-1, ers2 mhz5-1, and etr2 mhz5-1). The values are the means ± sd of 20 to 30 seedlings per genotype at each dose. The experiment was repeated at least three times with similar results.

Article Snippet: The T-DNA knockout mutants ers1 , ers2 , and etr2 are in the DJ background and were obtained from the POSTECH Biotech Center ( Yi and An, 2013 ).

Techniques: Mutagenesis, Comparison

Journal: The Plant Cell

Article Title: The WRKY6 Transcription Factor Modulates PHOSPHATE1 Expression in Response to Low Pi Stress in Arabidopsis [W] [OA]

doi: 10.1105/tpc.108.064980

Figure Lengend Snippet: Repression of PHO1 Expression by WRKY6 Was Released in Response to Low Pi Stress.

Article Snippet: We thank Imre E. Somssich (Max-Planck-Institut für Züchtungsforschung, Abteilung Biochemie, Germany) for kindly providing At WRKY6 overexpression lines 35S: WRKY6-3 , 35S: WRKY6-5 , and 35S: WRKY6-9 and the At WRKY6 knockout mutant ( wrky6-1 ).

Techniques: Expressing

Journal: The Plant Cell

Article Title: The WRKY6 Transcription Factor Modulates PHOSPHATE1 Expression in Response to Low Pi Stress in Arabidopsis [W] [OA]

doi: 10.1105/tpc.108.064980

Figure Lengend Snippet: ChIP Assays for At WRKY6 Binding to the W-Box of the PHO1 Promoter in Vivo.

Article Snippet: We thank Imre E. Somssich (Max-Planck-Institut für Züchtungsforschung, Abteilung Biochemie, Germany) for kindly providing At WRKY6 overexpression lines 35S: WRKY6-3 , 35S: WRKY6-5 , and 35S: WRKY6-9 and the At WRKY6 knockout mutant ( wrky6-1 ).

Techniques: Binding Assay, In Vivo

Journal: The Plant Cell

Article Title: The WRKY6 Transcription Factor Modulates PHOSPHATE1 Expression in Response to Low Pi Stress in Arabidopsis [W] [OA]

doi: 10.1105/tpc.108.064980

Figure Lengend Snippet: Suppression of PHO1 Expression by WRKY6.

Article Snippet: We thank Imre E. Somssich (Max-Planck-Institut für Züchtungsforschung, Abteilung Biochemie, Germany) for kindly providing At WRKY6 overexpression lines 35S: WRKY6-3 , 35S: WRKY6-5 , and 35S: WRKY6-9 and the At WRKY6 knockout mutant ( wrky6-1 ).

Techniques: Expressing

Journal: The Plant Cell

Article Title: The WRKY6 Transcription Factor Modulates PHOSPHATE1 Expression in Response to Low Pi Stress in Arabidopsis [W] [OA]

doi: 10.1105/tpc.108.064980

Figure Lengend Snippet: ChIP-qPCR Assays to Detect the Association of WRKY6 and the PHO1 Promoter in the Tested Plants as Indicated under Pi-Sufficient (MS) and Pi-Deficient (LP) Conditions.

Article Snippet: We thank Imre E. Somssich (Max-Planck-Institut für Züchtungsforschung, Abteilung Biochemie, Germany) for kindly providing At WRKY6 overexpression lines 35S: WRKY6-3 , 35S: WRKY6-5 , and 35S: WRKY6-9 and the At WRKY6 knockout mutant ( wrky6-1 ).

Techniques: ChIP-qPCR

Journal: The Plant Cell

Article Title: The WRKY6 Transcription Factor Modulates PHOSPHATE1 Expression in Response to Low Pi Stress in Arabidopsis [W] [OA]

doi: 10.1105/tpc.108.064980

Figure Lengend Snippet: WRKY6 Protein Blot Analysis.

Article Snippet: We thank Imre E. Somssich (Max-Planck-Institut für Züchtungsforschung, Abteilung Biochemie, Germany) for kindly providing At WRKY6 overexpression lines 35S: WRKY6-3 , 35S: WRKY6-5 , and 35S: WRKY6-9 and the At WRKY6 knockout mutant ( wrky6-1 ).

Techniques:

Journal: Frontiers in Plant Science

Article Title: OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

doi: 10.3389/fpls.2018.01330

Figure Lengend Snippet: The expression of OsWRKY28 was responsive to arsenate and other oxidative stress. (A) Time course of the expression level of OsWRKY28 in roots. The plants were exposed to 1.5 μM As(V) without Pi supply for 24 h. (B) The transcript levels of OsWRKY28 exposed to other oxidative stresses for 12 h. The plants were exposed to 1.5 μM As 5+ , 20 μM As 3+ , 3 μM Cd, 2 μM Cu, 500 μM H 2 O 2 without Pi supply. The relative expression of OsWRKY28 were normalized to the expression level at 0 h (A) or without treatment, respectively. OsHistone3 was used as the reference gene. Data are means ± SE ( n = 3 biological replicates).

Article Snippet: Two T-DNA insertion mutants of OsWRKY28 were obtained in the present study, oswrky28-1 (PFG_1B-20614.L from Postech in the Dongjin (DJ) background) and oswrky28-2 [RMD_04Z11OD34 from Huazhong Agricultural University in the Zhonghua 11 (ZH11) background].

Techniques: Expressing

Journal: Frontiers in Plant Science

Article Title: OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

doi: 10.3389/fpls.2018.01330

Figure Lengend Snippet: Subcellular localization and expression pattern of OsWRKY28 . (A–D) Subcellular localization and expression pattern of OsWRKY28 . Confocal image of tobacco ( Nicotiana benthamiana ) epidermal cells expressing the OsWRKY28:eYFP fusion protein (A) . (B) Confocal images of epidermal cells stained by a nuclear specific dye 4,6-diamidino-2-phenylindole (DAPI). (C) Bright-field images. (D) The merged image of (A–C) . Bar = 20 μm. (E–J) Expression pattern of OsWRKY28 was revealed by GUS-staining. Primary root (E) , lateral root, (F) , leaf (G) , caryopsis at the flower development stage (H) , stamen (I) , stigma and ovary (J) . Four independent GUS lines were observed, and the same results were obtained. Bar = 1 mm.

Article Snippet: Two T-DNA insertion mutants of OsWRKY28 were obtained in the present study, oswrky28-1 (PFG_1B-20614.L from Postech in the Dongjin (DJ) background) and oswrky28-2 [RMD_04Z11OD34 from Huazhong Agricultural University in the Zhonghua 11 (ZH11) background].

Techniques: Expressing, Staining

Journal: Frontiers in Plant Science

Article Title: OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

doi: 10.3389/fpls.2018.01330

Figure Lengend Snippet: Arsenate and phosphate uptake and the expression levels of phosphate transporter genes in WT and oswrky28 mutants. (A) Arsenic concentrations in shoots and roots of WT and oswrky28 . (B,C) The concentrations of P (B) , and total phosphorus concentrations (C) in roots and shoots of WT and oswrky28. Plants were hydroponically cultivated in 1/2 kimura solution for 3 weeks and then exposed to 5 μM As(V) for 3 days. (D) The expression levels of different phosphate transporter genes in the roots of WT and oswrky28 without arsenate treatment. Data are means ± SE ( n = 4). FW, fresh weight, DW, dry weight. Asterisks indicate significantly different at P < 0.05 (Tukey’s test).

Article Snippet: Two T-DNA insertion mutants of OsWRKY28 were obtained in the present study, oswrky28-1 (PFG_1B-20614.L from Postech in the Dongjin (DJ) background) and oswrky28-2 [RMD_04Z11OD34 from Huazhong Agricultural University in the Zhonghua 11 (ZH11) background].

Techniques: Expressing

Journal: Frontiers in Plant Science

Article Title: OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

doi: 10.3389/fpls.2018.01330

Figure Lengend Snippet: Root architecture of wild-type and oswrky28 plants. Two wild-types and oswrky28 T-DNA mutants were grown under 100 μM Pi conditions for 3 weeks. (A) Root architectural details. (B) Total root length. (C) Root surface area. (D) Total root tip number. Asterisks indicate statistically different at P < 0.05 (Tukey’s test). Values are means ± SE ( n = 4 per genotype).

Article Snippet: Two T-DNA insertion mutants of OsWRKY28 were obtained in the present study, oswrky28-1 (PFG_1B-20614.L from Postech in the Dongjin (DJ) background) and oswrky28-2 [RMD_04Z11OD34 from Huazhong Agricultural University in the Zhonghua 11 (ZH11) background].

Techniques:

Journal: Frontiers in Plant Science

Article Title: OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

doi: 10.3389/fpls.2018.01330

Figure Lengend Snippet: Agronomic trait comparison of the wild-type and oswrky28 mutants in the soil pot experiment. (A) Comparison of the spikelets of wild-type and oswrky28 plants. (B,C) Seed yield per plant of wild-type and oswrky28 . (D) Seed-setting rate; (E) Effective tiller number; (F) Thousand grain weight. Asterisks indicate significantly different at P < 0.05 (Tukey’s test, n = 4).

Article Snippet: Two T-DNA insertion mutants of OsWRKY28 were obtained in the present study, oswrky28-1 (PFG_1B-20614.L from Postech in the Dongjin (DJ) background) and oswrky28-2 [RMD_04Z11OD34 from Huazhong Agricultural University in the Zhonghua 11 (ZH11) background].

Techniques: Comparison

Journal: Frontiers in Plant Science

Article Title: OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

doi: 10.3389/fpls.2018.01330

Figure Lengend Snippet: Gene ontology (GO) enrichment analysis of differently expressed genes in roots (A) and shoots (B) of WT and oswrky28-1 mutant. GO categories are clustered by the biological processes. Red and blue colors represent the genes up- and down-regulated, respectively.

Article Snippet: Two T-DNA insertion mutants of OsWRKY28 were obtained in the present study, oswrky28-1 (PFG_1B-20614.L from Postech in the Dongjin (DJ) background) and oswrky28-2 [RMD_04Z11OD34 from Huazhong Agricultural University in the Zhonghua 11 (ZH11) background].

Techniques: Mutagenesis

Journal: Frontiers in Plant Science

Article Title: OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

doi: 10.3389/fpls.2018.01330

Figure Lengend Snippet: Expression profiling of genes involved in jasmonic acid (JA) and gibberellin (GA) synthesis. (A) Heat map comparison of genes involved in JA biosynthesis between oswrky28 mutant and WT. The main enzymes included extra glume 1 (EG1), defective in anther dehiscence1 (DAD1), 13-lipoxygenases (LOX), allene oxide synthase (AOS), allene oxide cyclase (AOC), OPDA reductase (OPR), acyl-CoA oxidase (ACX) and GH3 enzyme jasmonate resistant (JAR) . (B) Heat map comparison of genes involved in GA biosynthesis between oswrky28 mutant and WT. The main enzymes included Ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS) ent-kaurene oxidase 2 (KO2), gibberellin 20-oxidase gene (GA20ox) and gibberellins 3β-hydroxylase gene (GA3ox). The genes involved in GA synthesis process from trans-geranylgeranyl diphosphate (GGDP) were analyzed . Color scale represents log 2 (fold change in gene expression between mutant and WT).

Article Snippet: Two T-DNA insertion mutants of OsWRKY28 were obtained in the present study, oswrky28-1 (PFG_1B-20614.L from Postech in the Dongjin (DJ) background) and oswrky28-2 [RMD_04Z11OD34 from Huazhong Agricultural University in the Zhonghua 11 (ZH11) background].

Techniques: Expressing, Comparison, Mutagenesis, Gene Expression