ATP6 Gene Research Articles

Genetic variants in ATP6 and ND3 mitochondrial genes are not associated with aggressive prostate cancer in Mexican–Mestizo men with overweight or obesity

Mitochondrial defects have been related to obesity and prostate cancer. We investigated if Mexican–Mestizo men presenting this type of cancer, exhibited somatic mutations of ATP6 and/or ND3.Body mass index (BMI) was determined; the degree of prostate cancer aggressiveness was demarcated by the Gleason score. DNA from tumor tissue and from blood leukocytes was amplified by the polymerase chain reaction and ATP6 and ND3 were sequenced. We included 77 men: 20 had normal BMI, 38 were overweight and 19 had obesity; ages ranged from 52 to 83. After sequencing ATP6 and ND3, from DNA obtained from leukocytes and tumor tissue, we did not find any somatic mutations. All changes observed, in both genes, were polymorphisms. In ATP6 we identified, in six patients, two non-synonymous nucleotide changes and in ND3 we observed that twelve patients presented non-synonymous polymorphisms. To our knowledge, this constitutes the first report where the complete sequences of the ATP6 and ND3 have been analyzed in Mexican–Mestizo men with prostate cancer and diverse BMI. Our results differ with those reported in Caucasian populations, possibly due to ethnic differences.

Culture-Independent Identification of Nontuberculous Mycobacteria in Cystic Fibrosis Respiratory Samples.

Respiratory tract infections with nontuberculous mycobacteria (NTM) are increasing in prevalence and are a significant cause of lung function decline in individuals with cystic fibrosis (CF). NTM have been detected in culture-independent analyses of CF airway microbiota at lower rates than would be expected based on published prevalence data, likely due to poor lysing of the NTM cell wall during DNA extraction. We compared a standard bacterial lysis protocol with a modified method by measuring NTM DNA extraction by qPCR and NTM detection with bacterial 16S rRNA gene sequencing. The modified method improved NTM DNA recovery from spiked CF sputum samples by a mean of 0.53 log10 copies/mL for M. abscessus complex and by a mean of 0.43 log10 copies/mL for M. avium complex as measured by qPCR targeting the atpE gene. The modified method also improved DNA sequence based NTM detection in NTM culture-positive CF sputum and bronchoalveolar lavage samples; however, both qPCR and 16S rRNA gene sequencing remained less sensitive than culture for NTM detection. We highlight the limitations of culture-independent identification of NTM from CF respiratory samples, and illustrate how alterations in the bacterial lysis and DNA extraction process can be employed to improve NTM detection with both qPCR and 16S rRNA gene sequencing.

Yeast models of mutations in the mitochondrial ATP6 gene found in human cancer cells

Since the discovery of somatic mtDNA mutations in tumor cells, multiple studies have focused on establishing a causal relationship between those changes and alterations in energy metabolism, a hallmark of cancer cells. Yet the consequences of these mutations on mitochondrial function remain largely unknown. In this study, Saccharomyces cerevisiae has been used as a model to investigate the functional consequences of four cancer-associated missense mutations (8914C>A, 8932C>T, 8953A>G, 9131T>C) found in the mitochondrial MT-ATP6 gene. This gene encodes the a-subunit of F1FO-ATP synthase, which catalyzes the last steps of ATP production in mitochondria. Although the four studied mutations affected well-conserved residues of the a-subunit, only one of them (8932C>T) had a significant impact on mitochondrial function, due to a less efficient incorporation of the a-subunit into ATP synthase. Our findings indicate that these ATP6 genetic variants found in human tumors are neutral mitochondrial genome substitutions with a limited, if any, impact on the energetic function of mitochondria.

Helicobacter apri sp. nov., isolated from wild boars.

Three isolates (A19T, C21 and F12) with spiral-shaped cells and one bipolar sheathed flagellum were obtained from gastric mucosa and caecal contents of three different wild boars (Sus scrofa) and subjected to a polyphasic taxonomic study. A genus-specific PCR showed that these isolates belonged to the genus Helicobacter. Phylogenetic analysis based on 16S rRNA, 60-kDa heat-shock protein (HSP60) and atpA genes demonstrated they formed a novel lineage within this genus. Pairwise 16S rRNA, HSP60 and atpA gene sequence comparisons of the three isolates revealed 99.7, 99.4 and 99.9 % similarity, respectively, among the three isolates; the 16S rRNA gene of isolate A19T shared 98.5 % sequence similarity with its nearest validly named neighbouring species, Helicobacter mastomyrinus (to the type strain MIT 97-5577T). The taxonomic uniqueness of the wild boar isolates was confirmed by protein analysis performed by matrix-assisted laser desorption/ionization time-of-flight MS and by a distinctive biochemical profile. These data indicated that isolates A19T, C21 and F12 represent a novel taxon, for which the name Helicobacter apri sp. nov. is proposed, with isolate A19T (=DSM 28990T=LMG 28471T) as the type strain.

Overexpressing F0/F1 operon of ATPase in Rhodobacter sphaeroides enhanced its photo-fermentative hydrogen production

The effect of atp genes overexpression in Rhodobacter sphaeroides HY01 on the amount of ATP, nitrogenase activity and hydrogen production were studied. The ATP content of ZTHF0 (F0 operon+), ZTHF1 (F1 operon+) and ZTHFF (F0 operon+, F1 operon+) was 6.5 ± 0.2 nmol/mL, 7.6 ± 0.2 nmol/mL and 8.3 ± 0.3 nmol/mL, respectively, which enhanced by 20.3%, 40.7%, and 53.7% compared with that of the control strain ZTH (pRK415+), respectively. However, the nitrogenase activities of ZTHF0, ZTHF1 and ZTHFF were 35.8 ± 0.5 nmol acetylene/(min·mg-dcw), 40.1 ± 0.7 nmol acetylene/(min·mg-dcw) and 29.3 ± 0.7 nmol acetylene/(min·mg-dcw), respectively, which increased by 18.2%, 32.3% and 0% compared with that of ZTH, respectively. The expression level of atp genes by real-time PCR showed that ZTHF0 or ZTHF1 only enhanced the expression of F0 operon or F1 operon, respectively, and ZTHFF enhanced the expression of both F0 and F1 operons. At the 5000 ± 200 lux with 10 mL culture, the hydrogen yields of ZTHF0 and ZTHF1 were 7636 ± 59 mL/L-culture and 8458 ± 76 mL/L, which increased by 10.5% and 27.8% compared with that of the control strain, respectively. Moreover, the maximum hydrogen evolution rate of ZTHF0 and ZTHF1 were 94.5 ± 4.1 mL/(Lh) and 103.1 ± 5.0 mL/(Lh), which enhanced by 15.4% and 20.6% compared with that of the control strain, respectively. The results suggested that overexpressing F0 operon or F1 operon could improve ATP content and hydrogen production performance in R. sphaeroides.

STX, a Novel Membrane Estrogen Receptor Ligand, Protects Against Amyloid-β Toxicity.

Because STX is a selective ligand for membrane estrogen receptors, it may be able to confer the beneficial effects of estrogen without eliciting the deleterious side effects associated with activation of the nuclear estrogen receptors. This study evaluates the neuroprotective properties of STX in the context of amyloid-β (Aβ) exposure. MC65 and SH-SY5Y neuroblastoma cell lines, as well as primary hippocampal neurons from wild type (WT) and Tg2576 mice, were used to investigate the ability of STX to attenuate cell death, mitochondrial dysfunction, dendritic simplification, and synaptic loss induced by Aβ. STX prevented Aβ-induced cell death in both neuroblastoma cell lines; it also normalized the decrease in ATP and mitochondrial gene expression caused by Aβ in these cells. Notably, STX also increased ATP content and mitochondrial gene expression in control neuroblastoma cells (in the absence of Aβ). Likewise in primary neurons, STX increased ATP levels and mitochondrial gene expression in both genotypes. In addition, STX treatment enhanced dendritic arborization and spine densities in WT neurons and prevented the diminished outgrowth of dendrites caused by Aβ exposure in Tg2576 neurons. These data suggest that STX can act as an effective neuroprotective agent in the context of Aβ toxicity, improving mitochondrial function as well as dendritic growth and synaptic differentiation. In addition, since STX also improved these endpoints in the absence of Aβ, this compound may have broader therapeutic value beyond Alzheimer's disease.

Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species.

Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co‐occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next‐generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein‐encoding genes, with the Complex IV genes (coxI‐III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.

Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity.

Mitochondrial DNA (mtDNA) haplotypes were determined using restriction fragment length polymorphism (RFLP) for P. infestans sampled from 513 foliar lesions of late blight found on potato and tomato in different regions of Ethiopia. Among the four reported mitochondrial haplotypes of Phytophthora infestans, Ia, Ib and IIb were detected in 93% of the samples analyzed but the vast majority of these were Ia. The remaining 7% represented a previously unreported haplotype. DNA sequencing of this new haplotype also confirmed a single base nucleotide substitution that resulted in loss of EcoRI restriction site and gain of two additional MspI sites in cox1 and atp1 genes, respectively. There were 28 polymorphic sites among all nucleotide sequences including five reference isolates. Sites with alignment gaps were observed in P4 with one nucleotide deletion in 11 Ethiopian isolates. None of the reference sequence produced frame-shifts, with the exception of the 3-nucleotide deletion in the P4 region by Phytophthora andina, a feature that can be used to distinguish the new Ethiopian isolates from P. andina. While a distinguishing molecular data presented here clearly separated them from P. infestans, 7% of the isolates that share this feature formed an important component of the late blight pathogen causing disease on Solanum tuberosum in Ethiopia. Thus, these Ethiopian isolates could represent a novel Phytophthora species reported for the first time here.

Fifteen new earthworm mitogenomes shed new light on phylogeny within the Pheretima complex.

The Pheretima complex within the Megascolecidae family is a major earthworm group. Recently, the systematic status of the Pheretima complex based on morphology was challenged by molecular studies. In this study, we carry out the first comparative mitogenomic study in oligochaetes. The mitogenomes of 15 earthworm species were sequenced and compared with other 9 available earthworm mitogenomes, with the main aim to explore their phylogenetic relationships and test different analytical approaches on phylogeny reconstruction. The general earthworm mitogenomic features revealed to be conservative: all genes encoded on the same strand, all the protein coding loci shared the same initiation codon (ATG), and tRNA genes showed conserved structures. The Drawida japonica mitogenome displayed the highest A + T content, reversed AT/GC-skews and the highest genetic diversity. Genetic distances among protein coding genes displayed their maximum and minimum interspecific values in the ATP8 and CO1 genes, respectively. The 22 tRNAs showed variable substitution patterns between the considered earthworm mitogenomes. The inclusion of rRNAs positively increased phylogenetic support. Furthermore, we tested different trimming tools for alignment improvement. Our analyses rejected reciprocal monophyly among Amynthas and Metaphire and indicated that the two genera should be systematically classified into one.

Regulation of mitochondrial translation of the ATP8/ATP6 mRNA by Smt1p.

Expression of the mitochondrially encoded ATP6 and ATP8 genes is translationally regulated by F1 ATPase. We report a translational repressor (Smt1p) of the ATP6/8 mRNA that, when mutated, restores translation of the encoded Atp6p and Atp8p subunits of the ATP synthase. Heterozygous smt1 mutants fail to rescue the translation defect, indicating that the mutations are recessive. Smt1p is an intrinsic inner membrane protein, which, based on its sedimentation, has a native size twice that of the monomer. Affinity purification of tagged Smt1p followed by reverse transcription of the associated RNA and PCR amplification of the resultant cDNA with gene-specific primers demonstrated the presence in mitochondria of Smt1p-ATP8/ATP6 and Smt1p-COB mRNA complexes. These results indicate that Smt1p is likely to be involved in translational regulation of both mRNAs. Applying Occam's principle, we favor a mechanistic model in which translation of the ATP8/ATP6 bicistronic mRNA is coupled to the availability of F1 for subsequent assembly of the Atp6p and Atp8p products into the ATP synthase. The mechanism of this regulatory pathway is proposed to entail a displacement of the repressor from the translationally mute Smt1-ATP8/ATP6 complex by F1, thereby permitting the Atp22p activator to interact with and promote translation of the mRNA.

A Novel PCR-Based Approach for Accurate Identification of Vibrio parahaemolyticus.

A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the blaCARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Homologous analysis showed that blaCARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this blaCARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of blaCARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by blaCARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification.

Complete mitochondrial genome of Copadichromis virginalis (Cichlidae)

In this study, we report the complete mitochondrial genome of Copadichromis virginalis (Cichlidae fish). The mitochondrial genome is 16 704 bp in length and has a base composition of A (27.6%), T (30.1%), C (15.7%) and G (26.6%), demonstrating a slight bias of high AT content (57.6%). It contains 35 genes (13 protein-coding genes, 22 tRNAs and two rRNAs) and a non-coding A + T rich region (D-loop region). The mitochondial genome of Copadichromis virginalis presents a clear bias in nucleotied composition with a positive AT-skew and a negative GC-skew. Except for ND6 gene, all other protein-coding genes were located on the H-strand. ND4 gene and ND4L gene were overlapped by 5 bp, ATP8 gene and ATP6 gene were overlapped by 9 bp. The nucleotide sequence of 13 protein-coding genes of Copadichromis virginalis and other 19 Cichlidae species were used for phylogenetic analysis. The result indicated Copadichromis virginalis a close relationship with species Astatotilapia calliptera.

Mitochondrial genome sequence of black paradise flycatcher (Aves: Monarchidae) and its phylogenetic position

We generated the complete mitochondrial genome of the black paradise flycatcher (Terpsiphone atrocaudata; Family: Monarchidae), an ecologically important insectivorous bird in Asian forest ecosystems. The mitogenome was 16,984 bp in length and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. Gene composition and arrangement in the mitogenome were similar to those of related families Corvidae and Laniidae available in GenBank. However, tRNAAla was located between COXII and ATP8 genes in the mitogenome of T. atrocaudata while tRNALys, was in the same location in the mitogenomes of Corvidae and Laniidae. The phylogenetic tree based on the mitogenomes of T. atrocaudata and the related families supported that Monarchidae was the sister taxa to the clade of Laniidae and Corvidae. The mitogenome of T. atrocaudata will be a valuable genetic resource for phylogenetic analyses and implication of conservation and management of the species.

The complete mitochondrial genome of a parasitic flatworm Senga ophiocephalina (Cestoda: Bothriocephalidae)

Mitochondrial DNA of nematodes undergoes frequent rearrangements, so it is a very good model for studying the mitochondrial genome evolution. The complete mitochondrial genome of a parasitic nematode Senga ophiocephalina was sequenced and annotated. The 13,816 bp-long genome contained 12 protein-coding genes (atp8 gene was missing), two ribosomal RNAs, 22 transfer RNAs, and a 391 bp non-coding region. Phylogenetic analysis showed that S. ophiocephalina forms a monophyletic cluster with the remaining two Bothriocephalidae species.

Complete mitochondrial genome of Ulva prolifera, the dominant species of green macroalgal blooms in Yellow Sea, China

Ulva prolifera (U. prolifera), a green macroalgae, is widely known as the dominant species of the world’s largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U. prolifera (GenBank accession number: KU161104). The genome consists of circular chromosomes of 61 962 bp and encodes a total of 26 protein-coding genes include nine ribosomal protein genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. prolifera clustered into Ulvo phyceae clade and had close genetic relationship with algae Ulva fasciata.

Complete mitochondrial genome of Ulva linza, one of the causal species of green macroalgal blooms in Yellow Sea, China

Ulva linza, a green macroalgae, is one of the causal species of the world’s largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U.linza (GenBank accession no. KU189740). The genome consists of circular chromosomes of 70 858 bp and encodes a total of 28 protein-coding genes including eight rps genes, three rpl genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. linza clustered into Ulvophyceae clade and had close genetic relationship with algae Ulva prolifera.

The first representative of Coelomactra antiquata mitochondrial genome from Liaoning (China) and phylogenetic consideration

Coelomactra antiquata is a famous delicacy and a promising new candidate for aquaculture, which belongs to the family Mactridae (Mollusca: Veneroida). The complete mitochondrial genome of C. antiquata (Liao Ning province, in China, LN) was finished, which is the first representative from this province. The results showed that the total length of LN-mtDNA sequence is 16,797 bp and the content of A + T is 65.01%. It encodes 35 genes, including 12 protein-coding genes, 21 transfer RNA genes and two ribosomal RNA genes. All coding genes are encoded on the heavy strand. Compared with the typical gene content of animal mitochondrial genomes, atp8 and trnSer(UCN) genes are missing in the mitochondrial genome. The complete mitochondrial genome contains 26 non-coding regions (1598 bp), one major non-coding region consists of 1046 bp in which 4.9 tandem repeat sequences (99bp per sequence) was observed. The phylogenetic tree showed that Liaoning population was clustered into one clade with Shandong (Rizhao, Jiaonan and Jimo) and Guangxi (Beihai) populations, meanwhile all of them are far from the Fujian populations (Pingtan, Zhangzhou and Changle). So, Liaoning, Shandong and Guangxi populations have a close relationship. Actually, Fujian is located between Liaoning, Shandong and Guangxi. So, the result challenges the previously assumed relevance between geographic distance and genetic distance. The genetic distance of Liaoning C. antiquata and Fujian (Changle, Zhangzhou and Pingtan) C. antiquata (0.176–0.177) is greater than the genetic distance between Mytilus galloprovincialis and Mytilus trossulus (0.160). The genetic difference of Liaoning population and Fujian populations has reached species level.

Genotoxic risk of quinocetone and its possible mechanism in in vitro studies.

Quinoxalines possessing the quinoxaline-1,4-dioxide (QdNOs) basic structure are used for their antibacterial action, although their mechanism of genotoxicity is not clear. After comparing the sensitivity of V79 cells and HepG2 cells to quinocetone (QCT) and other QdNOs, it was found that HepG2 cells are more sensitive. The results show that QCT induces the generation of O2˙- and OH˙ during metabolism. Free radicals could then attack guanine and induce 8-hydroxy-deoxyguanine (8-OHdG) generation, causing DNA strand breakage, the inhibition of topoisomerase II (topo II) activity, and alter PCNA, Gadd45 and topo II gene expression. QCT also caused mutations in the mtDNA genes COX1, COX3 and ATP6, which might affect the function of the mitochondrial respiratory chain and increase the production of reactive oxygen species (ROS). Nuclear extracts from HepG2 cells treated with QCT had markedly reduced topo II activity, as judged by the inability to convert pBR322 DNA from the catenated to the decatenated form by producing stable DNA-topo II complexes. This study suggests that QCT electrostatically bound to DNA in a groove, affecting the dissociation of topo II from DNA and impacting DNA replication. Taken together, these data reveal that DNA damage induced by QCT resulted from O2˙- and OH˙ generated in the metabolism process. This data throws new light onto the genotoxicity of quinoxalines.

The complete mitochondrial genome of Diadema setosum (Aulodonta: diadematidae)

The complete mitochondrial genome of Diadema setosum was sequenced by using long-PCR and primer walking methods. The complete mitochondrial genome is a 15,708 bp circular molecule, which contains 22 tRNAs, 2 rRNAs, and 13 protein-coding genes as well as a non-coding control region as in other urchin. The genome was composed of 27.5% A, 30.7% T, 24.3% C, and 17.5% G. The control region is 133 bp. Twelve of the 13 mitochondrial protein-coding genes use ATG as their start codon while the ATP8 gene starts with GTG. Six of the 13 mitochondrial protein-coding genes use TAA as their complete stop codon while seven of them use TAG as their complete stop codon.

Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda)

The mitochondrial genomes of three North American stygobiont amphipods Stygobromus tenuis potomacus, S. foliatus and S. indentatus collected from Caroline County, VA, were sequenced using a shotgun sequencing approach on an Illumina NextSeq500 (Illumina Inc., San Diego, CA). All three mitogenomes displayed 13 protein-coding genes, 22 tRNAs and two rRNAs typical of metazoans. While S. tenuis and S. indentatus displayed identical gene orders similar to the pancrustacean ground pattern, S. foliatus displayed a transposition of the trnL2-cox2 genes to after atp8-atp6. In addition, a short atp8 gene, longer rrnL gene and large inverted repeat within the Control Region distinguished S. foliatus from S. tenuis potomacus and S. indentatus. Overall, it appears that gene order varies considerably among amphipods, and the addition of these Stygobromus mitogenomes to the existing sequenced amphipod mitogenomes will prove useful for characterizing evolutionary relationships among various amphipod taxa, as well as investigations of the evolutionary dynamics of the mitogenome in general.