ATP6 Gene Research Articles

Research Progress in the Molecular Functions of Plant mTERF Proteins.

Present-day chloroplast and mitochondrial genomes contain only a few dozen genes involved in ATP synthesis, photosynthesis, and gene expression. The proteins encoded by these genes are only a small fraction of the many hundreds of proteins that act in chloroplasts and mitochondria. Hence, the vast majority, including components of organellar gene expression (OGE) machineries, are encoded by nuclear genes, translated into the cytosol and imported to these organelles. Consequently, the expression of nuclear and organellar genomes has to be very precisely coordinated. Furthermore, OGE regulation is crucial to chloroplast and mitochondria biogenesis, and hence, to plant growth and development. Notwithstanding, the molecular mechanisms governing OGE are still poorly understood. Recent results have revealed the increasing importance of nuclear-encoded modular proteins capable of binding nucleic acids and regulating OGE. Mitochondrial transcription termination factor (mTERF) proteins are a good example of this category of OGE regulators. Plant mTERFs are located in chloroplasts and/or mitochondria, and have been characterized mainly from the isolation and analyses of Arabidopsis and maize mutants. These studies have revealed their fundamental roles in different plant development aspects and responses to abiotic stress. Fourteen mTERFs have been hitherto characterized in land plants, albeit to a different extent. These numbers are limited if we consider that 31 and 35 mTERFs have been, respectively, identified in maize and Arabidopsis. Notwithstanding, remarkable progress has been made in recent years to elucidate the molecular mechanisms by which mTERFs regulate OGE. Consequently, it has been experimentally demonstrated that plant mTERFs are required for the transcription termination of chloroplast genes (mTERF6 and mTERF8), transcriptional pausing and the stabilization of chloroplast transcripts (MDA1/mTERF5), intron splicing in chloroplasts (BSM/RUG2/mTERF4 and Zm-mTERF4) and mitochondria (mTERF15 and ZmSMK3) and very recently, also in the assembly of chloroplast ribosomes and translation (mTERF9). This review aims to provide a detailed update of current knowledge about the molecular functions of plant mTERF proteins. It principally focuses on new research that has made an outstanding contribution to unravel the molecular mechanisms by which plant mTERFs regulate the expression of chloroplast and mitochondrial genomes.

Epilepsy in MT-ATP6 - related mils/NARP: correlation of elettroclinical features with heteroplasmy.

The study aims to characterize the epilepsy phenotype of maternally inherited Leigh's syndrome (MILS) and neuropathy, ataxia, retinitis pigmentosa (NARP) due to mutations in the mitochondrial ATP6 gene and to correlate electroclinical features with mutant heteroplasmy load (HL). We investigated 17 individuals with different phenotype, from asymptomatic carriers to MILS: 11 carried the m.8993T> G mutation, 5 the m.8993T> C and one the novel, de novo m.8858G> A mutation. Seizures occurred in 37.5% of patients, EEG abnormalities in 73%. We ranked clinical and EEG abnormalities severity and performed quantitative EEG to estimate Abnormality Ratio (AR) and Spectral Relative Power (SRP). Spearman’s rho and Kruskal–Wallis test were used for correlation with heteroplasmy load (HL). HL correlated with disease severity (Rho = 0.63, P = 0.012) and was significantly higher in patients with seizures or EEG abnormalities (P = 0.014). HL correlated with EEG severity score only for the m.8993T> G (Rho = 0.73, P = 0.040), showing a trend toward a positive correlation with AR and delta SPR, irrespective of the mutation.

Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications

BackgroundThe Eucotylidae Cohn, 1904 (Superfamily: Microphalloidea), is a family of digeneans parasitic in kidneys of birds as adults. The group is characterized by the high level of morphological similarities among genera and unclear systematic value of morphological characters traditionally used for their differentiation. In the present study, we sequenced the complete or nearly complete mitogenomes (mt genome) of two eucotylids representing the genera Tamerlania (T. zarudnyi) and Tanaisia (Tanaisia sp.). They represent the first sequenced mt genomes of any member of the superfamily Microphalloidea.MethodsA comparative mitogenomic analysis of the two newly sequenced eucotylids was conducted for the investigation of mitochondrial gene arrangement, contents and genetic distance. Phylogenetic position of the family Eucotylidae within the order Plagiorchiida was examined using nucleotide sequences of mitochondrial protein-coding genes (PCGs) plus RNAs using maximum likelihood (ML) and Bayesian inference (BI) methods. BI phylogeny based on concatenated amino acids sequences of PCGs was also conducted to determine possible effects of silent mutations.ResultsThe complete mt genome of T. zarudnyi was 16,188 bp and the nearly complete mt genome of Tanaisia sp. was 13,953 bp in length. A long string of additional amino acids (about 123 aa) at the 5′ end of the cox1 gene in both studied eucotylid mt genomes has resulted in the cox1 gene of eucotylids being longer than in all previously sequenced digeneans. The rrnL gene was also longer than previously reported in any digenean mitogenome sequenced so far. The TΨC and DHU loops of the tRNAs varied greatly between the two eucotylids while the anticodon loop was highly conserved. Phylogenetic analyses based on mtDNA nucleotide and amino acids sequences (as a separate set) positioned eucotylids as a sister group to all remaining members of the order Plagiorchiida. Both ML and BI phylogenies revealed the paraphyletic nature of the superfamily Gorgoderoidea and the suborder Xiphidiata.ConclusionsThe average sequence identity, combined nucleotide diversity and Kimura-2 parameter distances between the two eucotylid mitogenomes demonstrated that atp6, nad5, nad4L and nad6 genes are better markers than the traditionally used cox1 or nad1 for the species differentiation and population-level studies of eucotylids because of their higher variability. The position of the Dicrocoeliidae and Eucotylidae outside the clade uniting other xiphidiatan trematodes strengthened the argument for the need for re-evaluation of the taxonomic content of the Xiphidiata.Graphical

Enrichment effects of fermented by-product of Shochu distillery on Brachionus plicatilis sp. rotifer and larviculture performance in Japanese flounder (Paralichthys olivaceus)

The effective use of distillery by-products of the shochu sweet potato has long been considered as a rich source of protein, fiber, amino acids, fatty acids, probiotics with a great potential as a functional feed for animals. This study applied fermented by-product of Shochu distillery (FBPSD) and salmon roe emulsion oil for rotifer enrichment to evaluate its effects on the: (i) nutritional composition of rotifers and (ii) feeding responses of Paralichthys olivaceus larvae when fed with enriched rotifers. The salmon roe oil enrichment was set as a control diet and FBPSD was supplemented at different doses (1, 5 and 10 % based on the salmon roe oil amount). The results showed that the rotifers supplemented with FBPSD at 5 and 10 % significantly enhanced protein, carbohydrate, and HUFA content. Similarly, the activity and expression profiles of targeted enzymes including trypsin, chymotrypsin, lipase and amylase effectively responded at early and middle-metamorphosis of the larvae to 5 and 10 % enrichment regiment. These two treatments were also found to be better supported in energy metabolism evidenced by Cytochrome-C-Oxidase (cox) and ATPase-pk (atp) gene expression in the larvae. Moreover, the expression levels of immune-related genes (IL-10, IL-1β, TNF-α, P2Y6) and antioxidant-related genes (SOD, CAT) were significantly improved at 5 and 10 % of FBPSD. Cessation of feeding and delay in growth during the metamorphic process was also molecularly demonstrated. Larvae suffered low survival (24.5–25.3 %) in control and 1 % supplementation of FBPSD, but significantly improved at 5 and 10 % (36.4–38.7%). However, the growth performance of larval fish was not remarkable after 40 days of culture. The results of this study revealed that FBPSD could be considered as a potential supplementary enrichment for live feed in fish larviculture, especially at 5 and 10 % rotifer enrichment dosage.

High frequency of bedaquiline resistance in programmatically treated drug-resistant TB patients with sustained culture-positivity in Cape Town, South Africa

Aims & objectives: Potentially transformative new tuberculosis (TB) drugs like bedaquiline are undergoing roll-out, however, this is largely in the absence of programmatic drug susceptibility testing (DST). We lack information on how susceptibility changes during treatment in patients on bedaquiline-containing regimens, especially in at risk patients who have complex treatment histories, are in programmatic rather than trial environments, and have a delayed treatment response (defined here as sustained culture-positivity). Methods: Serial isolates from 51 patients with drug resistant (DR-)TB who were culture-positive after ≥4 months of a programmatically administered bedaquiline-containing regimen, were collected. Bedaquiline phenotypic DST in MGIT 960 (1μg/ml), targeted deep sequencing (Rv0678, atpE, pepQ) and whole genome sequencing was done on paired isolates (pre-bedaquiline initiation, post-four-month). Results: 24/51 (47%) patients were phenotypically and genotypically resistant (39% acquired resistance). Excluding one patient with an unknown history, prior clofazimine exposure was associated with bedaquiline-resistance [21/24 (88%) bedaquiline resistant cases had prior clofazimine vs. 12/26 (46%) susceptibles; p=0.002]. Diverse combinations of single nucleotide polymorphisms (SNPs) and indels were in the Rv0678 promoter region and the Rv0678 and atpE genes. Examples of newly described resistance associated variants (RAVs) include Rv0678 -8 T/G and atpE 223 C/T. RAVs were not in defined hotspots and sometimes occurred concurrently with atpE RAVs. Discussion: The rate of bedaquiline resistance acquisition in this population is alarmingly high and associated with prior clofazimine exposure. The diverse RAVs pose challenges to molecular test development. This study highlights the existence of a potentially infectious pool of bedaquiline-resistant patients present under programmatic conditions in a resource-constrained setting and illustrates the danger of starting patients with complex histories on a novel drug without routinely available DST.

Hysterangiales revisited: expanded phylogeny reveals new genera and two new suborders.

Hysterangiales (Phallomycetidae, Agaricomycetes, Basidiomycota) is a diverse, nearly cosmopolitan order of predominantly hypogeous, sequestrate, ectomycorrhizal fungi. Expanding on previously published phylogenies, we significantly increased sampling of Hysterangiales specimens, emphasizing representatives from Australia. Using protein-coding genes atp6 (adenosine triphosphate synthase subunit 6) and tef1 (translation elongation factor 1-á), we recovered 26 provisional novel genera, and corroborated existing genera and families. Further, two new suborders (Phallogastrineae subord. nov. and Hysterangineae subord. nov.) and a new family (Phallogastraceae fam. nov.) are described, and three new combinations made to Phallogaster. Aspects of classification and biogeography are presented.

Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficient afo1- Yeast Suppressed by a Dominant Mutation in ATP3.

A yeast deletion mutation in the nuclear-encoded gene, AFO1, which codes for a mitochondrial ribosomal protein, led to slow growth on glucose, the inability to grow on glycerol or ethanol, and loss of mitochondrial DNA and respiration. We noticed that afo1- yeast readily obtains secondary mutations that suppress aspects of this phenotype, including its growth defect. We characterized and identified a dominant missense suppressor mutation in the ATP3 gene. Comparing isogenic slowly growing rho-zero and rapidly growing suppressed afo1- strains under carefully controlled fermentation conditions showed that energy charge was not significantly different between strains and was not causal for the observed growth properties. Surprisingly, in a wild-type background, the dominant suppressor allele of ATP3 still allowed respiratory growth but increased the petite frequency. Similarly, a slow-growing respiratory deficient afo1- strain displayed an about twofold increase in spontaneous frequency of point mutations (comparable to the rho-zero strain) while the suppressed strain showed mutation frequency comparable to the respiratory-competent WT strain. We conclude, that phenotypes that result from afo1- are mostly explained by rapidly emerging mutations that compensate for the slow growth that typically follows respiratory deficiency.

Comparative Mitochondrial Analysis of Cnaphalocrocis exigua (Lepidoptera: Crambidae) and Its Close Relative C. medinalis.

Rice leaffolders are important pests on rice in Asia, Oceania, and Africa, causing serious loss to rice production. There are two main rice leaffolders in China, namely Cnaphalocrocis medinalis (Guenée) and C. exigua (Butler) with the former having the ability of long-distance migration. To reveal the differences in the mitochondrial genomes (mitogenome) between them, we compared the completed mitogenome of C. exigua with three C. medinalis individuals. Although phylogenetic analysis based on the mitogenomic data strongly supported the close relationship between these two species, many differences were still being revealed. The results showed that the mitogenome of C. exigua was shorter in length (15,262 bp) and slight lower in AT content than that of C. medinalis. Except for the different start codons of nad3 and nad6 gene, we also found the cox1 gene had a typical start codon ‘ATG’ which suggested that the starting position of this gene must be reconsidered in the entire superfamily Pyraloidea. All tRNAs have a typical clover-leaf structure, except for the dihydrouridine (DHU) stem losing of trnS1, which has the atypical anticondon ‘TCT’ instead of ‘GCT’ in C. medinalis and most Pyraloidea species. Two intergenic regions (between trnY and cox1, nad3 and trnA) featured by AT repeats were only found in C. medinalis and even rarely appeared in reported Pyraloidea species. Furthermore, regardless of interspecific comparison or intraspecific comparison of these two species, protein coding genes, especially the atp8 genes, had quite different evolutionary rates.

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils.

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

Helicobacter delphinicola sp. nov., isolated from common bottlenose dolphins Tursiops truncatus with gastric diseases.

Gastritis and gastric ulcers are well-recognized symptoms in cetaceans, and the genus Helicobacter is considered as the main cause. In this study, we examined the gastric fluid of captive common bottlenose dolphins Tursiops truncatus with gastric diseases in order to isolate the organisms responsible for diagnosis and treatment. Four Gram-negative, rod-shaped isolates (TSBT, TSH1, TSZ, and TSH3) with tightly coiled spirals with 2-4 turns and 2-6 bipolar, sheathed flagella, were obtained from gastric fluids of common bottlenose dolphins with gastric diseases. Phylogenetic analysis, based on 16S rRNA, atpA, and 60 kDa heat-shock protein (hsp60) genes, demonstrated that these isolates form a novel lineage within the genus Helicobacter. Analyses of 16S rRNA, atpA, and hsp60 gene sequences showed that isolate TSBT was most closely related to H. cetorum MIT99-5656T (98.5% similarity), H. pylori ATCC 43504T (76.7% similarity), and H. pylori ATCC 43504T (78.0% similarity), respectively. Type strains of Helicobacter showing resistance to 2% NaCl have not been reported previously; however, these novel isolates were resistant to 2% NaCl. Culture supernatant of some isolates induced intracellular vacuolization in mammalian cultured cells. These data, together with the different morphological and biochemical characteristics of the isolates, reveal that these isolates represent a novel species for which we propose the name Helicobacter delphinicola sp. nov. with type strain TSBT (= JCM 32789T = TSD-183T). Future studies will confirm whether H. delphinicola plays a role in lesion etiopathogenesis in cetaceans.

Molecular Detection ofArcobacterin Human Stool Samples Using Housekeeping Genes

Background: Arcobacter is one of the most common bacteria in humans and livestock, leading to gastroenteritis in humans as well as genital and enteric diseases in animals. This bacterium is known to be the main cause of diarrhea. In molecular studies, the 16SrRNA gene was primarily used as the standard gene for the determination of the Arcobacter. The purpose of this study was to investigate the molecular detection of Arcobacter using glyA, atpA, and gyrA genes compared to16SrRNA. Methods: In this study, 61 samples of Arcobacter DNA isolated from fecal specimens of patients and healthy individuals in the sample bank were used. In order to detect Arcobacter, the intended primers for 16SrRNA as well as glyA, atpA, and gyrA genes were used for polymerase chain reaction (PCR). The products obtained from the PCR were sequenced. Results: The results of the proliferation reactions indicated the accuracy of the intended primers and the associated molecular experiments. Our results showed that 65.57% of the cases were detected to be positive for Arcobacter among 61 samples using the glyA gene. This percentage was higher compared to 16SrRNA (42.62%), gyrA (42.62%), and atpA (24.59%). The analysis was statistically significant. Conclusions: Given the presence of repetitive sequences in the 16SrRNA in most bacteria, the interpretation of the results is likely to be difficult for researchers. The results of this study showed more sensitivity and accurate diagnosis of Arcobacter using the glyA gene than other studied genes. In diagnostic studies of Arcobacter, the glyA gene is proposed as an alternative to the 16SrRNA.

Diagnosis, genetic variations, virulence, and toxicity of AHPND-positive Vibrio parahaemolyticus in Penaeus monodon

Acute hepatopancreatic necrosis disease (AHPND) is an emerging shrimp (Penaeus monodon) disease caused by Vibrio parahaemolyticus (VP) since 2013 in Bangladesh. The aim of this work was to evaluate a PCR and RT-PCR techniques as rapid methods for detecting V. parahaemolyticus AHPND-positive P. monodon using genetic markers. Healthy and diseased shrimp (P. monodon) samples were collected from three monitoring stations. The samples were enriched in TCBS plates and DNA extraction from the cultured bacteria. DNA quantifications, PCR amplification, RT-PCR, and gene sequencing were done for the detection of V. parahaemolyticus AHPND-positive P. monodon. The sequence of PCR amplicons showed 100% identity and significant alignment with V. parahaemolyticus. The primers used provided high specificity for V. parahaemolyticus in PCR detection compared with another Vibrio species. In the PCR, amplification resulted positive amplicons, whereas, non-AHPND isolates showed no amplicons. Neighbor-joining methods indicated that all genes evolved from a common ancestor and clades have different traits with very low genetic distance and low variability. The pairwise alignment scores of atpA, tox, blaCARB, 16S rRNA, and pirA genes were 100.0, 98.90, 98.89, 95.53, and 41.42, respectively. The RT-qPCR exposed variable expression levels for all genes in the AHPND-positive strain. Homology analysis and distance matrix exhibited all genes to have the lowest similarity and most divergence, offering the highest specificity. In this study, the expression and variability of target genes confirmed the presence of V. parahaemolyticus in all sampling sites. The results suggested that PCR amplification, RT-qPCR, and gene sequencing can be used for the rapid detection of V. parahaemolyticus in AHPND-positive P. monodon that may lead to subsequent prevention and treatment research in the future for managing this disease.

Case Report: Identification of a Novel Variant (m.8909T>C) of Human Mitochondrial ATP6 Gene and Its Functional Consequences on Yeast ATP Synthase.

With the advent of next generation sequencing, the list of mitochondrial DNA (mtDNA) mutations identified in patients rapidly and continuously expands. They are frequently found in a limited number of cases, sometimes a single individual (as with the case herein reported) and in heterogeneous genetic backgrounds (heteroplasmy), which makes it difficult to conclude about their pathogenicity and functional consequences. As an organism amenable to mitochondrial DNA manipulation, able to survive by fermentation to loss-of-function mtDNA mutations, and where heteroplasmy is unstable, Saccharomyces cerevisiae is an excellent model for investigating novel human mtDNA variants, in isolation and in a controlled genetic context. We herein report the identification of a novel variant in mitochondrial ATP6 gene, m.8909T>C. It was found in combination with the well-known pathogenic m.3243A>G mutation in mt-tRNALeu. We show that an equivalent of the m.8909T>C mutation compromises yeast adenosine tri-phosphate (ATP) synthase assembly/stability and reduces the rate of mitochondrial ATP synthesis by 20–30% compared to wild type yeast. Other previously reported ATP6 mutations with a well-established pathogenicity (like m.8993T>C and m.9176T>C) were shown to have similar effects on yeast ATP synthase. It can be inferred that alone the m.8909T>C variant has the potential to compromise human health.

In vitro Study of Bedaquiline Resistance in Mycobacterium tuberculosis Multi-Drug Resistant Clinical Isolates.

Tuberculosis (TB) is one of the major causes of death related to antimicrobial resistance worldwide because of the spread of Mycobacterium tuberculosis multi- and extensively drug resistant (multi-drug resistant (MDR) and extensively drug-resistant (XDR), respectively) clinical isolates. To fight MDR and XDR tuberculosis, three new antitubercular drugs, bedaquiline (BDQ), delamanid, and pretomanid were approved for use in clinical setting. Unfortunately, BDQ quickly acquired two main mechanisms of resistance, consisting in mutations in either atpE gene, encoding the target, or in Rv0678, coding for the repressor of the MmpS5-MmpL5 efflux pump. To better understand the spreading of BDQ resistance in MDR- and XDR-TB, in vitro studies could be a valuable tool. To this aim, in this work an in vitro generation of M. tuberculosis mutants resistant to BDQ was performed starting from two MDR clinical isolates as parental cultures. The two M. tuberculosis MDR clinical isolates were firstly characterized by whole genome sequencing, finding the main mutations responsible for their MDR phenotype. Furthermore, several M. tuberculosis BDQ resistant mutants were isolated by both MDR strains, harboring mutations in both atpE and Rv0678 genes. These BDQ resistant mutants were further characterized by studying their growth rate that could be related to their spreading in clinical settings. Finally, we also constructed a data sheet including the mutations associated with BDQ resistance that could be useful for the early detection of BDQ-resistance in MDR/XDR patients with the purpose of a better management of antibiotic resistance in clinical settings.

Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris).

A fructose-6-phosphate phosphoketolase-positive strain (GSD1FST) was isolated from a faecal sample of a 3 weeks old German Shepherd dog. The closest related taxa to isolate GSD1FST based on results from the EZBioCloud database were Bifidobacterium animalis subsp. animalis ATCC 25527T, Bifidobacterium animalis subsp. lactis DSM 10140T and Bifidobacterium anseris LMG 30189T, belonging to the Bifidobacterium pseudolongum phylogenetic group. The resulting 16S rRNA gene identities (compared length of 1454 nucleotides) towards these taxa were 97.30, 97.23 and 97.09 %, respectively. The pairwise similarities of strain GSD1FST using argS, atpA, fusA, hsp60, pyrG, rpsC, thrS and xfp gene fragments to all valid representatives of the B. pseudolongum phylogenetic group were in the concatenated range of 83.08-88.34 %. Phylogenomic analysis based on whole-genome methods such as average nucleotide identity revealed that bifidobacterial strain GSD1FST exhibits close phylogenetic relatedness (88.17 %) to Bifidobacetrium cuniculi LMG 10738T. Genotypic characteristics and phylogenetic analyses based on nine molecular markers, as well as genomic and comparative phenotypic analyses, clearly proved that the evaluated strain should be considered as representing a novel species within the B. pseudolongum phylogenetic group named as Bifidobacterium canis sp. nov. (GSD1FST=DSM 105923T=LMG 30345T=CCM 8806T).

Comparative mitogenomic analysis of the superfamily Tellinoidea (Mollusca: Bivalvia): Insights into the evolution of the gene rearrangements

The superfamily Tellinoidea is widespread and contains approximately 180 living species, which is one of the most diverse and representative groups among the bivalves. In order to extend our knowledge on evolution of tellinoidean species, we newly determined five tellinoidean mitochondrial genomes (mitogenomes). The newly determined mitogenome vary in size from 16,333 to 16,986 bp. The results show that the genome size and genome organization are conserved in tellinoideans. However, gene arrangement and the location of the major non-coding region (NCR) show diversity. The atp8 gene presents in all the five new mitogenomes. Two trnK and trnP genes were detected in Gari togata mitogenome. Phylogenetic analysis supports the monophyly of Tellinoidea, however, it's family Psammobiidae is polyphyletic. CREx analysis suggests that the gene order of Nuttallia olivacea is assumed as the most primitive condition of Tellinoidea. We map the gene order onto the phylogeny and infers the possible gene rearrangement scenarios among tellinoidean mitogenomes. The mitochondrial gene rearrangement is a useful information that help reassessing the phylogeny of Tellinoidea. Phylogenetic relationship and gene arrangement analyses suggest that a careful review for the current taxonomy of the family Psammobiidae is required.

Sequencing and Analysis of the Complete Organellar Genomes of Prototheca wickerhamii.

Of the Prototheca genus, Prototheca wickerhamii has the highest clinical significance in humans. However, neither nuclear nor organellar genomes of this species were sequenced until now. The hitherto determined and analyzed mitochondrial and plastid genomes of the alleged P. wickerhamii species belong in fact to another species, recently named Prototheca xanthoriae. This study provides a first insight into the organellar genomes of a true P. wickerhamii (type strain ATCC 16529). The P. wickerhamii mitochondrion had a 53.8-kb genome, which was considerably larger than that of Prototheca ciferrii (formerly Prototheca zopfii gen. 1) and Prototheca bovis (formerly Prototheca zopfii gen. 2), yet similarly functional, with the differences in size attributable to a higher number of introns and the presence of extra unique putative genes. The 48-kb plastid genome of P. wickerhamii, compared to autotrophic Trebouxiophyceae, was highly reduced due to the elimination of the photosynthesis-related genes. The gene content of the plastid genome of P. wickerhamii was, however, very similar to other colorless Prototheca species. Plastid genome-based phylogeny reinforced the polyphyly of the genus Prototheca, with Helicosporidium and Auxenochlorella branching within clades of Prototheca species. Phylogenetic reconstruction also confirmed the close relationship of P. wickerhamii and P. xanthoriae, which is reflected in the synteny of their organellar genomes. Interestingly, the entire set of atp genes was lost in P. wickerhamii plastid genome while being preserved in P. xanthoriae.

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

The whole mitochondrial genome ofLateolabrax maculatus(Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity ofL. maculatuswere 0.998 and 0.00169, respectively. Pairwise FSTvalues between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history ofL. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation ofL. maculatus.

Male sterility induction and evolution of cytoplasmic male sterility related atp9 gene from Boehmeria nivea (L.) Gaudich

Cytoplasmic male sterility (CMS) is an important tool for hybrid seed production in the fibrous crop Boehmeria nivea (L.) Gaudich. Dysfunction of mitochondrial ATP synthase normally leads to male sterility. However, the expression regulation and evolution of the ATP synthase subunit genes controlling male development is still unclear. While few available mitochondrial transformation strategies limited studying mitochondrial copy of atp9, the function of nuclear atp9 copy with exactly the same coding sequence are not clearly elucidated. In this article, we show that transformation of B. nivea atp9 RNAi vectors into tobacco plants resulted in nearly half of the pollens sterile, which provide direct experimental evidence that the atp9 gene could be used in developing male sterile lines in plants. Bioinformatics analysis revealed that H+-binding site Glu57 of the c subunit of ATP synthase is highly conservative in B. nivea, showing essential function of atp9 during evolution. Molecular evolution analysis revealed that the synonymous substitution rate (dS) of mitochondrial atp9 in B. nivea is faster than in other plants, which could be a reason for its cytoplasmic male sterility and strong environmental adaptations.

Identification of Genes Associated with Sensitivity to Ultraviolet A (UVA) Irradiation by Transposon Mutagenesis of Vibrio parahaemolyticus

Ultraviolet (UV) irradiation is used to disinfect water and food and can be classified as UVA (detected at wavelengths 320–400 nm), UVB (280–320 nm), and UVC (<280 nm). We developed a method for UVA sterilization of equipment with a UVA-light-emitting diode (LED); however, a high rate of fluence was needed to promote pathogen inactivation. The aim of this study was to identify genes associated with UVA sensitivity with the goal of improving UVA-LED-mediated bactericidal activity. We constructed a transposon-mutant library of Vibrio parahaemolyticus and selected six mutants with high sensitivity to UVA irradiation. Genes associated with this phenotype include F-type H+-transporting ATPases (atp), as well as those involved in general secretion (gsp), and ubiquinone and terpenoid-quinone biosynthesis (ubi). Gene complementation resulted in decreased sensitivity to UVA-LED. The atp mutants had lower intracellular adenosine triphosphate (ATP) concentrations than the wild-type treatment, with 20 mM L-serine resulting in elevated ATP concentrations and decreased sensitivity to UVA-LED. The gsp mutants exhibited high levels of extracellular protein transport and the ubi mutants exhibited significantly different intracellular concentrations of ubiquinone-8. Taken together, our results suggest that the protein products of the atp, gsp, and ubi genes may regulate sensitivity to UVA irradiation.