Journal: BMC Genomics

Article Title: The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida

doi: 10.1186/s12864-018-4583-3

Figure Lengend Snippet: Example excerpt sequence from a potential control region of Anodonta cygnea within a non-coding segment between trnF and nad5 . Potential secondary structures are shown, a star indicates a potential origin of replication based on structural similarities to the classic origin of replication in metazoan control regions. Note that not all secondary structures within this region are pictured. Image generated in VARNA

Article Snippet: NAD5’s protein features were assigned in our figures using the annotations reported for H. sapiens NAD5 (UniProtKB code: P03915) at the website InterPro (an EMBL-EBI online tool, [ ]).

Techniques: Sequencing, Control, Generated

Journal: BMC Genomics

Article Title: The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida

doi: 10.1186/s12864-018-4583-3

Figure Lengend Snippet: Analysis of translocated nad5 region in Anodonta cygnea . a Upper plot shows NAD5 protein alignment for members of family Unionoida ( Anodonta anatina ; KF030964), Mytiloida ( Modiolus modiolus ; KX821782) and Veneroida ( Meretrix lusoria ; ACV92129). Lower plot shows the same A. anatina sequence aligned to Homo sapiens and Bos taurus NAD5 sequences; UniProtKB code P03915 and PDB ID: 5LDW Chain L, respectively. In both upper and lower plots the region corresponding to the partial nad5 translocation in A. cygnea is annotated. Functional regions are coloured according to the legend and descriptions provided in InterPro for H. sapiens NAD5 (accession P03915). Amino acids in alignments are colour coded by similarity (black = 100% similar, dark gray = 80–100% similar, light grey = 60–80% similar, white = < 60% similar). Identity graphs were generated with a sliding-window size of 50 bp, furthermore red and purple colours along plots represent positions that have very low identities (30%), and less than complete identities (30% to < 100%), respectively. See methods for an explanation of how similarity was calculated. Images were generated in Geneious . b Partial nad5 translocation in A. cygnea relative to the 3-dimentional structure of Respiratory Complex 1 (PDB ID: 5LDW). In particular, NAD5 (amino acid Chain L) is coloured. Note that structures are based on work in

Article Snippet: NAD5’s protein features were assigned in our figures using the annotations reported for H. sapiens NAD5 (UniProtKB code: P03915) at the website InterPro (an EMBL-EBI online tool, [ ]).

Techniques: Sequencing, Translocation Assay, Functional Assay, Generated

Journal: BMC Genomics

Article Title: The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida

doi: 10.1186/s12864-018-4583-3

Figure Lengend Snippet: Z-test of selection results for purifying selection (H o : d n = d s , H a : d n < d s ) and positive selection (H o : d n = d s , H a : d n > d s ) on alignments of (A) complete nad5 from 12 species with 543 positions, and (B) nad5 sequences corresponding to a putative translocated portion of nad5 from Anodonta cygnea (MF781083) from 12 species with 45 positions in the analysis. Alignments by ClustalW [ 36 ] and Z-tests were conducted in MEGA7 [ 37 ] using the Kumar method, 1000 bootstraps, and pairwise deletion. Statistically significant results are highlighted in bold using α = 0.05

Article Snippet: NAD5’s protein features were assigned in our figures using the annotations reported for H. sapiens NAD5 (UniProtKB code: P03915) at the website InterPro (an EMBL-EBI online tool, [ ]).

Techniques: Selection

Journal: BMC Genomics

Article Title: The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida

doi: 10.1186/s12864-018-4583-3

Figure Lengend Snippet: Assessment of hermaphroditic (H-type) Unionoid URs for presence of typical control region properties

Article Snippet: NAD5’s protein features were assigned in our figures using the annotations reported for H. sapiens NAD5 (UniProtKB code: P03915) at the website InterPro (an EMBL-EBI online tool, [ ]).

Techniques: Control

Journal: Nucleic Acids Research

Article Title: Hypertension-associated mitochondrial DNA 4401A>G mutation caused the aberrant processing of tRNA Met , all 8 tRNAs and ND6 mRNA in the light-strand transcript

doi: 10.1093/nar/gkz742

Figure Lengend Snippet: A schema of location of m.4401A>G mutation in the precursors of tRNA Met and tRNA Gln , genetic and transcription map of human mitochondria. ( A ) Cloverleaf structures of mitochondrial tRNA Met and tRNA Gln are derived from Florentz et al. . Processing sites in the tRNA Met and tRNA Gln precursors were determined for RNase P. Arrow indicates the position of the m.4401A>G mutation. ( B ) Genetic and transcription maps of mitochondrial genomes were derived from Guan et al. . The two inner circles show the positions of 12S and 16S rRNA (black bars), of the 13 reading frames (ND1, ND2, ND3, ND4, ND4L, ND5, and ND6, COI, COII, COIII, cytb, A6 and A8) (white bars) and of 22 tRNA (solid circles). ( C ) Three polycistronic RNA transcripts ( , ). The transcription of L-strand promoter (LSP) resulted in a near genomic length primary transcript encoding eight tRNAs including tRNA Gln , tRNA Ser(UCN) and ND6. The transcription of H-strand promoter 1 (HSP1) generated the short transcript containing tRNA Phe , tRNA Val , 12S rRNA and 16S rRNA, while the transcription from HSP2 produced an almost genome transcript consisting of 12S rRNA, 16S rRNA, 12 mRNAs and 14 tRNAs including tRNA Met , tRNA Lys and tRNA Gly . RNA sequences are represented as follows: rRNAs as hashed boxes, mRNAs as gray boxes and tRNAs as white boxes.

Article Snippet: The antibodies used for this investigation were from Abcam [ND1(ab74257), ND5 (ab92624), ND6 (ab81212), CO2 (ab110258), Tom20 (ab56783), p62 (ab56416) and Total OXPHOS Human WB Antibody Cocktail (ab110411)], Proteintech [(CYTB (55090-1-AP), ND2 (19704-1-AP), ATP8 (26723-1-AP), and β-actin (20536-1-AP)], Novus [ND4 (NBP2-47365)], Cell Signaling Technology [LC3A/B (CST,#4108)].

Techniques: Mutagenesis, Derivative Assay, Generated, Produced

Journal: Nucleic Acids Research

Article Title: Hypertension-associated mitochondrial DNA 4401A>G mutation caused the aberrant processing of tRNA Met , all 8 tRNAs and ND6 mRNA in the light-strand transcript

doi: 10.1093/nar/gkz742

Figure Lengend Snippet: Western blot analysis of mitochondrial proteins. ( A ) Analysis of mtDNA encoding proteins. Five micrograms of total mitochondrial proteins from various cell lines were electrophoresed through a denaturing polyacrylamide gel, electroblotted and hybridized with antibodies specific for ND1, ND2, ND4, ND5, ND6, CO2, CYTB and ATP8 and with Tom20 as a loading control, respectively. ( B ) Quantification of total mitochondrial protein levels. The average levels of 8 mitochondrial proteins in mutant and control cell lines were determined as described elsewhere ( , ). ( C ) Quantification of 8 polypeptides. The levels of ND1, ND2, ND4, ND5, ND6, CO2, CYTB and ATP8 in mutant and control cell lines were determined as described elsewhere ( , ). ( D ) Analysis of five OXPHOS subunits encoded by mtDNA and nuclear genes. Five micrograms of total mitochondrial proteins from various cell lines were electrophoresed through a denaturing polyacrylamide gel, electroblotted and hybridized with antibody cocktail specific for subunits (ATP5A, UQCRC2, SDHB, CO2 and NDUFB8) of each OXPHOS complex and with TOM20 as a loading control. Graph details and symbols are explained in the legend to Figure .

Article Snippet: The antibodies used for this investigation were from Abcam [ND1(ab74257), ND5 (ab92624), ND6 (ab81212), CO2 (ab110258), Tom20 (ab56783), p62 (ab56416) and Total OXPHOS Human WB Antibody Cocktail (ab110411)], Proteintech [(CYTB (55090-1-AP), ND2 (19704-1-AP), ATP8 (26723-1-AP), and β-actin (20536-1-AP)], Novus [ND4 (NBP2-47365)], Cell Signaling Technology [LC3A/B (CST,#4108)].

Techniques: Western Blot, Control, Mutagenesis

Journal: PLoS ONE

Article Title: Kidney-Specific Reduction of Oxidative Phosphorylation Genes Derived from Spontaneously Hypertensive Rat

doi: 10.1371/journal.pone.0136441

Figure Lengend Snippet: A: mt-ND1 was reduced ~3.7 fold in HT BN/SHR-mt SHR (*P<0.05). mt- ND3 was reduced ~2.6 fold in HT SHR/BN-mt SHR (**P<0.01). mt-ND4 was reduced ~10.8 fold in HT SHR/BN-mt SHR (*P<0.05). mt-ND4L was reduced ~7.7 fold in HT SHR/BN-mt SHR (P<0.05). mt-ND5 was reduced ~2.7 fold in HT SHR/BN-mt SHR (P<0.05). mt-ND6 was reduced ~1.7 fold in HT SHR/BN-mt SHR (P>0.05) . mt-ND2 was not different between the two phenotypes (P>0.05). B: mt-CYB was reduced ~5 fold in HT BN/SHR-mt SHR (*P<0.05). C: mt-CO1 was reduced ~3.2 fold in HT BN/SHR-mt SHR (*P<0.05), mt-CO2 was reduced ~3.6 fold in HT BN/SHR-mt SHR (P<0.05), and mt-CO3 was reduced 4.1 fold in HT BN/SHR-mt SHR (P<0.05). D: mt-ATP6 was reduced ~2.3 fold in HT BN/SHR—mt SHR (*P<0.05), while mt-ATP8 was reduced ~3.1 fold in HT BN/SHR-mt SHR (*P<0.05). (NT: open bars; HT: closed bars).

Article Snippet: Pre-designed TaqMan primers and hydrolysis probes for all genes of interest were purchased from Applied Biosystems ( mt-ND1 - Rn03296764_s1, mt-ND2 - Rn03296765_s1, mt-ND3 - Rn03296825_s1, mt-ND4 - Rn03296781_s1, mt-ND4L - Rn03296792_s1, mt-ND5 - Rn03296799_s1, mt-ND6 - Rn03296815_s1, mt-CO1 - Rn03296721_s1, mt-CO2 - Rn03296737_s1, mt-CO3 - Rn03296820_s1, mt-CYB - Rn03296746_s1, mt-ATP6 - Rn03296710_s1, mt-ATP8 - Rn03296716_s1, NRF1 - Rn01455958_m1, NRF2a - Rn01767215_m1, NRF2b -Rn01514289_g1, Pgc1α -Rn00598552_m1, Tfam -Rn00580051_m1, Cyc1 -Rn01504159_g1, Cox6c -Rn00820983_gH, GAPDH - Rn01775763_g1).

Techniques:

Journal: PLoS ONE

Article Title: Kidney-Specific Reduction of Oxidative Phosphorylation Genes Derived from Spontaneously Hypertensive Rat

doi: 10.1371/journal.pone.0136441

Figure Lengend Snippet: A: mt-CYB , B: mt-CO2 , C: mt-ND1 , and D: ATP6 were shown to be not different (P>0.05) between the HT and NT BN/SHR-mt SHR liver and heart compared with kidney tissue. (NT: open bars; HT: closed bars).

Article Snippet: Pre-designed TaqMan primers and hydrolysis probes for all genes of interest were purchased from Applied Biosystems ( mt-ND1 - Rn03296764_s1, mt-ND2 - Rn03296765_s1, mt-ND3 - Rn03296825_s1, mt-ND4 - Rn03296781_s1, mt-ND4L - Rn03296792_s1, mt-ND5 - Rn03296799_s1, mt-ND6 - Rn03296815_s1, mt-CO1 - Rn03296721_s1, mt-CO2 - Rn03296737_s1, mt-CO3 - Rn03296820_s1, mt-CYB - Rn03296746_s1, mt-ATP6 - Rn03296710_s1, mt-ATP8 - Rn03296716_s1, NRF1 - Rn01455958_m1, NRF2a - Rn01767215_m1, NRF2b -Rn01514289_g1, Pgc1α -Rn00598552_m1, Tfam -Rn00580051_m1, Cyc1 -Rn01504159_g1, Cox6c -Rn00820983_gH, GAPDH - Rn01775763_g1).

Techniques:

Journal: BMC Genomics

Article Title: Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

doi: 10.1186/s12864-017-4080-0

Figure Lengend Snippet: The human mtDNA and its mRNAs. The double-stranded circular mtDNA of the human is linearly expressed and genes contained therein are shown as columns that do not accurately reflect their actual sizes. Gene abbreviations are the following: 12S and 16S, 12S and 16S rRNAs (green columns); ND1–6 and 4 L, NADH dehydrogenase subunits 1–6 and 4 L (blue columns); CO1–3, cytochrome oxidase subunits I-III (orange columns); ATP6 and ATP8, ATP synthase subunits 6 and 8 (violet columns); and CYTB, cytochrome b (red column). Transfer RNA genes are indicated as corresponding one-letter amino acids and the major non-coding region is abbreviated as MNCR. The arrows show the encoded direction of protein and rRNA genes. Transfer RNA genes over the column stand for H-strand-encoded ones, whereas those under the column show L-strand-encoded ones. Ranges for H-strand-transcribed mRNAs [ , ] are shown by horizontal arrows with numbers in the original literature. A range for non-polyadenylated ND6 mRNA is also shown by a reverse horizontal arrow

Article Snippet: Polyadenylation sites for the ND5 mRNAs of four bird species ( G. gallus, U. epops, F. tinnunculus and A. monachus ) occurred immediately after the ND5 stop codon in response to this gene rearrangement (Fig. ).

Techniques:

Journal: BMC Genomics

Article Title: Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

doi: 10.1186/s12864-017-4080-0

Figure Lengend Snippet: Characterization of Takydromus tachydromoides mt-mRNAs using RNA-Seq reads. a Gene organization of T. tachydromoides mtDNA with major polyadenylation sites. Major polyadenylation sites for H-strand-transcribed and L-strand-transcribed RNAs supported by 10 or more independent (forward and reverse paired-end reads derived from a common cDNA fragment were merged for the counting) polyA-containing reads are shown over and under the column, respectively, with the number of the supporting polyA-containing reads. Note that no major polyadenylation sites were found for L-strand transcripts of T. tachydromoides . Changes in mRNA polyadenylation sites as compared to the human are highlighted by a circle. Refer to the legend of Fig. for gene abbreviations and other details. b Mapping of RNA-Seq reads to T. tachydromoides mtDNA. At the bottom, frequency of the RNA-Seq reads covering each site of the 17,923-bp mtDNA sequence is plotted in the vertical direction. In the horizontal direction, ranges for protein (from a start codon to a stop codon) and rRNA genes are shown along with tRNA gene cluster regions (IQM, WANCY and HSL). A sharp decline of read frequencies, which corresponds to the new polyadenylation site for ND5 mRNA (see text), is indicated by a red arrow. At the top, the slope of the mapped read frequencies as measured by sliding a 10-nucleotide window is plotted in the vertical direction. Ranges for H-strand-transcribed mRNAs estimated are illustrated by horizontal arrows

Article Snippet: Polyadenylation sites for the ND5 mRNAs of four bird species ( G. gallus, U. epops, F. tinnunculus and A. monachus ) occurred immediately after the ND5 stop codon in response to this gene rearrangement (Fig. ).

Techniques: RNA Sequencing, Derivative Assay, Sequencing

Journal: BMC Genomics

Article Title: Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

doi: 10.1186/s12864-017-4080-0

Figure Lengend Snippet: Major polyadenylation sites for twelve tetrapod species in which the polyadenylation profile differed from that of the human. Refer to the legend of Fig. for gene abbreviations and the use of colors and that of Fig. for ways to show major polyadenylation sites with numbers of supportive polyA-containing reads. Asterisks in P. przewalskii show truncated major noncoding regions. Changes in mRNA polyadenylation sites as compared to the human noted in text are highlighted by a circle. Note that polyadenylation sites for P. vitticeps ND5 mRNA could not be surely identified due to the insertion of an extra copy of MNCR. Also note that there was a minor polyadenylation site 242 bp downstream of the ND5 stop codon as supported by 6 polyA-containing reads in A. mississippiensis (data not shown) and this site may function as a polyadenylation site for the ND5 mRNA

Article Snippet: Polyadenylation sites for the ND5 mRNAs of four bird species ( G. gallus, U. epops, F. tinnunculus and A. monachus ) occurred immediately after the ND5 stop codon in response to this gene rearrangement (Fig. ).

Techniques:

Journal: BMC Genomics

Article Title: Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

doi: 10.1186/s12864-017-4080-0

Figure Lengend Snippet: Evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs. Colored lineages show the presence of new polyadenylation sites as estimated by the parsimony criterion based on well-established phylogenetic relationships . Dotted lineages show the occurrence of new polyadenylation sites possibly linked with mtDNA gene rearrangements. New polyadenylation sites are considered in this figure when the number of polyA-containing reads that support them is more than a half of that supporting the polyadenylation sites found for the human. New polyadenylation sites for the ND1 mRNA have two states, which existed without gene rearrangement in the IQM tRNA gene cluster (state 1) and with the IQM-to-QIM gene rearrangement (state 2). New polyadenylation sites for the CYTB mRNA also have two states, which existed without gene rearrangement around the CYTB gene (state 1) and with a rearrangement of the tRNA Phe gene near the CYTB gene (state 2)

Article Snippet: Polyadenylation sites for the ND5 mRNAs of four bird species ( G. gallus, U. epops, F. tinnunculus and A. monachus ) occurred immediately after the ND5 stop codon in response to this gene rearrangement (Fig. ).

Techniques:

Journal: BMC Genomics

Article Title: Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

doi: 10.1186/s12864-017-4080-0

Figure Lengend Snippet: Nucleotide and amino acid sequences at the junction between ND1 and tRNA Ile genes in four birds a and between ATP6 and CO3 genes in four turtles b . The relevant mtDNA sequences deduced for the RNA-sequenced individual are shown together with translated amino acid sequences. An asterisk shows the position of a stop codon. In a , the ND1 and tRNA Ile genes of U. epops and A. monachus are overlapped without a polyadenylation site at the 5′ end of the tRNA Ile gene. In the other two birds, there is no gene overlap and the polyadenylation occurs at the 5′ end of the tRNA Ile gene. In b , ATP6 and CO3 genes of P. castaneus are overlapped without a polyadenylation site at this junction. In the other turtles, there is no gene overlap and the processing and subsequent polyadenylation at the junction can create stop codons for the ATP8/ATP6 mRNAs

Article Snippet: Polyadenylation sites for the ND5 mRNAs of four bird species ( G. gallus, U. epops, F. tinnunculus and A. monachus ) occurred immediately after the ND5 stop codon in response to this gene rearrangement (Fig. ).

Techniques: