tRNA Thr Gene Research Articles

Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae.

In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.

The complete mitochondrial genome of Hapalogenys analis (Perciformes, Haemulidea) except for control region, obtained by whole genome sequencing

In this study, we obtained the complete mitochondrial genome of Hapalogenys analis using whole genome sequencing. With the exception for control region, this mitochondrial genome, consisting of 16,355 base pairs (bp), contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 21 transfer RNAs (tRNAs). This mitochondrial genome also lacks a tRNA-Pro gene after tRNA-Thr gene. The overall base composition shows 25.45% of T, 29.73% of C, 28.68% of A and 16.14% of G, with a slight A + T rich feature (54.13%). Sanger sequencing is needed to confirm the accuracy of control region, as well as the lack of tRNA-Pro gene. The mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

Maternally Inherited Diabetes Mellitus Associated with a Novel m.15897G>A Mutation in Mitochondrial tRNAThr Gene.

We report here the clinical, genetic, and molecular characteristics of type 2 diabetes in a Chinese family. There are differences in the severity and age of onset in diabetes among these families. By molecular analysis of the complete mitochondrial genome in this family, we identified the homoplasmic m.15897G>A mutation underwent sequence analysis of whole mitochondrial DNA genome, which localized at conventional position ten of tRNAThr, and distinct sets of mtDNA polymorphisms belonging to haplogroup D4b1. This mutation has been implicated to be important for tRNA identity and stability. Using cybrid cell models, the decreased efficiency of mitochondrial tRNAThr levels caused by the m.15897G>A mutation results in respiratory deficiency, protein synthesis and assembly, mitochondrial ATP synthesis, and mitochondrial membrane potential. These mitochondrial dysfunctions caused an increase in the production of reactive oxygen species in the mutant cell lines. These data provide a direct evidence that a novel tRNA mutation was associated with T2DM. Thus, our findings provide a new insight into the understanding of pathophysiology of maternally inherited diabetes.

Next-generation sequencing yields a nearly complete mitochondrial genome of The Yarkand toad-headed agama (Phrynocephalus axillaris) from the Turpan Depression

The Yarkand toad-headed agama, Phrynocephalus axillaris, is endemic to an arid region in Northwest China from the Taklamakan Desert eastward to Dunhuang and Turpan depressions. A nearly complete mitochondrial genome of one individual from the Turpan Depression was determined using next-generation sequencing. The mitogenome is 15,883 bp in length, comprising two ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and a control region (CR). The gene arrangement and composition is similar to those of other Agaminae lizards, albeit with one part of CR (651 bp) existing between the tRNA-Thr gene and tRNA-Pro gene and another part of CR (with 107 bp already sequenced) inserting between the tRNA-Phe and 12S rRNA. Bayesian phylogenetic analyses confirmed the monophyly of both genus Phrynocephalus and its viviparous species. The mitogenome sequence may provide fundamental data to investigate altitude-related evolution of mitochondrial genes in Phrynocephalus.

Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive

BackgroundMutations in mitochondrial tRNA genes have been widely reported association with human reproductions. It is also important to explore the effect on the number of piglets born alive (NBA). Here, 1017 sows were used to investigate the association between polymorphisms in mitochondrial tRNA genes and NBA.ResultsIn total, 16 mutations were found in mitochondrial tRNA genes, of which 13 mutations were significantly associated with NBA (P < 0.05). The reproductions of mutant carriers were significantly greater than that of wild carriers by 0.989 piglets born alive/sow farrowing. To test whether the mutations altered the structure of mitochondrial tRNAs, the secondary and tertiary structures were predicted. In result, C2255T changed the secondary structure of tRNA-Val by elongating the T stem and shrinking the T loop, and C2255T and G2259A in the tRNA-Val gene, C6217T and T6219C in the tRNA-Ala gene, and T15283C in the tRNA-Glu gene altered the tertiary structure of their tRNAs, respectively by changing the folding form of the T arm, and C16487T in the tRNA-Thr gene changed the tertiary structure of mitochondrial tRNA-Thr by influencing the folding form of the acceptor arm.ConclusionsResults highlight the effect of mitochondrial tRNA genes on the number of piglets born alive, and suggest that polymorphic sites of the tRNA genes be genetic markers for selection of pig reproduction.

A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia

D-aminoacyl-tRNA deacylase (DTD), a bacterial/eukaryotic trans-editing factor, removes d-amino acids mischarged on tRNAs and achiral glycine mischarged on tRNAAla. An invariant cross-subunit Gly-cisPro motif forms the mechanistic basis of l-amino acid rejection from the catalytic site. Here, we present the identification of a DTD variant, named ATD (Animalia-specific tRNA deacylase), that harbors a Gly-transPro motif. The cis-to-trans switch causes a “gain of function” through L-chiral selectivity in ATD resulting in the clearing of l-alanine mischarged on tRNAThr(G4•U69) by eukaryotic AlaRS. The proofreading activity of ATD is conserved across diverse classes of phylum Chordata. Animalia genomes enriched in tRNAThr(G4•U69) genes are in strict association with the presence of ATD, underlining the mandatory requirement of a dedicated factor to proofread tRNA misaminoacylation. The study highlights the emergence of ATD during genome expansion as a key event associated with the evolution of Animalia.

The complete mitochondrial genome of Myanmar warty newt Tylototriton shanorum (Salamandridae: Tylototriton)

Tylototriton shanorum, an endemic species of Myanmar, is threatened by illegal capture and environmental destruction. Here, the complete mitochondrial genome (mitogenome) of T. shanorum is described. The entire mitogenome sequence of T. shanorum is 17,096 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region. In addition, two additional 3′ Cytb like sequences and two complete tRNAThr genes, one pseudo tRNAThr, and three noncoding sequences (NC1, NC1′ and NC2) were situated between Cytb and tRNAPro genes. The new complete mitogenome sequence of T. shanorum will be useful for conservation genetics, evolutionary biology, phylogeography, as well as phylogenetic relationships studies of this threatened species.

A Site-Specific Integrative Plasmid Found in Pseudomonas aeruginosa Clinical Isolate HS87 along with A Plasmid Carrying an Aminoglycoside-Resistant Gene.

Plasmids play critical roles in bacterial fitness and evolution of Pseudomonas aeruginosa. Here two plasmids found in a drug-resistant P. aeruginosa clinical isolate HS87 were completely sequenced. The pHS87b plasmid (11.2 kb) carries phage-related genes and function-unknown genes. Notably, pHS87b encodes an integrase and has an adjacent tRNAThr-associated attachment site. A corresponding integrated form of pHS87b at the tRNAThr locus was identified on the chromosome of P. aeruginosa, showing that pHS87b is able to site-specifically integrate into the 3’-end of the tRNAThr gene. The pHS87a plasmid (26.8 kb) displays a plastic structure containing a putative replication module, stability factors and a variable region. The RepA of pHS87a shows significant similarity to the replication proteins of pPT23A-family plasmids. pHS87a carries a transposon Tn6049, a truncated insertion sequence ΔIS1071 and a Tn402-like class 1 integron which contains an aacA4 cassette that may confer aminoglycoside resistance. Thus, pHS87b is a site-specific integrative plasmid whereas pHS87a is a plastic antibiotic resistance plasmid. The two native plasmids may promote the fitness and evolution of P. aeruginosa.

The complete mitochondrial genome of the fulvous parrotbill Paradoxornis fulvifrons (Passeriformes: Muscicapidae)

The complete mitochondrial genome of the fulvous parrotbill (Paradoxornis fulvifrons) has been determined from Illumina sequencing data. The circular genome is 17 059 bp long, comprising 37 genes (13 protein-coding genes/PCGs, 22 tRNA genes and two rRNA genes) and a putative control region. Except for COX1 with GTG as its start codon, all PCGs are initiated with the ATR (ATA/ATG) codons. One PCG (COX1) is terminated with AGG, three PCGs (COX3, ND2 and ND4) with the incomplete stop codon T––/TA–, while all the others with TAA. The 22 tRNAs range in size from 64 bp (tRNA-Ser) to 75 bp (tRNA-Leu). The two rRNAs are 982 bp (12S rRNA) and 1600 bp (16S rRNA) long, respectively. The putative control region is located between tRNA-Thr and tRNA-Pro genes with a length of 1235 bp. The base composition is biased (29.06% A, 31.10% C, 14.97% G and 24.87% T) with an overall A + T content of 53.93% (“light strand”). Phylogenetic analysis indicated that P. fulvifrons is closely related to the congeneric vinous-throated parrotbill (P. webbianus).

Variability of cytochrome b gene and adjacent part of tRNA-Thr gene of mitochondrial DNA in the northern mole vole Ellobius talpinus (Mammalia, Rodentia)

The Northern mole vole E. talpinus, despite its wide distribution, is characterized by a stable karyotype (2n = NF = 54) and slight morphological polymorphism. We made a preliminary analysis of a mitochondrial DNA fragment to clarify the level of genetic variation and differentiation of E. talpinus The complete cytochrome b gene (cyt b, 1143 bp) and a short part of its flanking gene tRNA-Thr (27 bp) were sequenced. We studied 16 specimens of E. talpinus from eight localities, including Crimea, the Volga region, the Trans-Volga region, the Southern Urals, Western Siberia, and Eastern Turkmenistan. Mitotypes of E. talpinus were distributed on a ML dendrogram as four distinct clusters: the first (I) contains specimens from the Crimea, the second (II) combines individuals from the Volgograd region, the left bank of the Don River; the third (III) includes those from the Trans-Volga region, Southern Urals, the left bank of the Irtysh River, and Eastern Turkmenistan; the fourth (IV) are those from the right bank of the Irtysh River. These clusters were relatively distant from each other: the mean genetic distances (D) between them are 0.021–0.051. The Eastern mole vole E. tancrei differed from E. talpinus population groups 1.5–2 times more (D = 0.077–0.084) than the latters did among themselves. Such variations indirectly proved the unity of E. talpinus, despite its high intraspecific differentiation for the studied fragment of mitochondrial DNA. This differentiation apparently occurred because of the long isolation of E. talpinus population groups by geographic barriers, in particular, the large rivers that completely separate the species range meridionally (the Volga River, the Irtysh River). Sociality and underground lifestyle could accelerate the fixation of mutations in disjunct populations. The composition and distribution of intraspecific groups of E. talpinus, which were identified in analysis of the mitochondrial DNA fragment, do not coincide with the subspecies taxonomy. The subspecies E. t. talpinus is actually a complex taxon, including two or three genetically discrete forms (III, IV, and probably II). Moreover, one of the forms (III) occupies the territory where three subspecies, E. t. talpinus, E. t. rufescens, and E. t. transcaspiae, were described.

The complete mitochondrial genome sequence of the Xizang Plateau frog, Nanorana parkeri (Anura: Dicroglossidae)

The Xizang Plateau frog (Nanorana parkeri) belongs to the family Dicroglossidae, which distributes in southern and eastern Xizang, southern-most Qinghai in China, high elevations of north-central Nepal, Himalayan Bhutan, northeastern Kashmir and India. In this study, the complete mitochondrial genome of N. parkeri was sequenced. The mitogenome was 17,837 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a non-coding control region (CR). As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. The overall base composition of the N. parkeri is A: 27.7 % A, T: 30.1 % T, C: 26.6% and G: 15.6%. The alignment of the Nanorana species CRs exhibited high genetic variability and rich A + T content. In comparison with the mtDNA sequences typical of vertebrates, a tandem duplication of the tRNAMet gene and a rearrangement of the tRNAThr, tRNAPro and tRNALeu (CUN) genes were found. The complete mitogenome of N. parkeri can provided an important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.

The complete mitogenome sequence of Pseudohynobius jinfo (Urodela: Hynobiidae)

The complete mitogenome sequence of Pseudohynobius jinfo, which is endemic to China, is sequenced in the present study. The genome was 16,393 bp in length, including 13 typical vertebrate protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 non-coding control region. Except for ND6 and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The gene order and composition of P. jinfo was similar to that of the most Hynobiidae. Seven genes (ND1, ND2, COII, COIII, ND3, ND4 and Cytb) had an incomplete stop codon. Base composition of the genome was A (33.6%), T (31.8%), C (20.6%) and G (14.1%) with an A + T-rich feature (65.4%) as that of other vertebrate mitochondrial genomes. There was a long non-coding region (126 bp) between tRNA-Thr and tRNA-Pro genes.

GW25-e2275 Mitochondrial tRNA-Thr Gene Mutation in Maternally Inherited Hypertension and the Regulatory Mechanism in Adiponectin Pathway

The offspring hypertension and mother hypertension has a significant correlation, and also, mtDNA mutations are related with elevated blood pressure, but the underlying mechanism is unclear. Based on a study with small sample size and two pedigrees maternal family mumbers, we tried to reveal the

The complete mitochondrial genome of Feirana taihangnica (Anura: Dicroglossidae)

The complete mitochondrial genome sequence of the Feirana taihangnica (Anura: Dicroglossidae) was determined. It is a circular molecule of 17,412 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The tRNAThr gene located in the LTPF tRNA gene cluster typically found in other anurans is absent from the F. taihangnica mtDNA and a tandem duplication of tRNAMet gene is observed. The A+T content of the overall base compositon of H-strand is 57.2% and the length of control region is 1972 bp with 61.8% A+T content.

Variations in mitochondrial tRNAThr gene may not be associated with coronary heart disease

Mutations in mitochondrial tRNAThr gene were recently reported to be associated with coronary heart disease. These mutations, such as T15889C, G15927A, G15930A and A15951G, were claimed to be pathogenic. To examine whether these mutations contributed to the genetic susceptibility to coronary heart disease, we analyzed the conservation index of these mutations between different species. In particular, reports concerning the role of the G15927A mutation was the most controversial. Therefore, based on the previous and this study, we conducted that mutations in mitochondrial tRNAThr gene may not be associated with coronary heart disease.

The complete mitochondrial genome of secret toad-headed agama, Phrynocephalus mystaceus (Reptilia, Squamata, Agamidae)

The complete mitogenome sequence of a mystical lizard species Phrynocephalus mystaceus was determined using polymerase chain reaction and directly sequenced with a primer walking method. The complete mitogenome was 16,660 bp in length, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region (D-loop). The gene arrangement and composition of P. mystaceus was similar to most other vertebrates, but the Proline tRNA gene was translocated to be adjacent to tRNA-Phe gene. The D-loop consisted of two parts, with part I existing between the tRNA-Thr gene and tRNA-Pro gene and another part inserting between the tRNA-Phe and 12S rRNA. In part I, one conserved sequence (CSB I) could be identified. In part II, two pair of motifs, “TACAT” and its reverted and complemented sequence “ATGTA”, could be found in the domain of an extended termination-associated sequence. The mitogenome sequence of P. mystaceus could contribute to a better solution of its phylogenetic position within toad-headed agamids based on the whole mitogenomic data.

The complete mitochondrial genome of the Yarkand toad-headed agama, Phrynocephalus axillaris (Reptilia, Squamata, Agamidae)

The complete mitochondrial genome of the Yarkand toad-headed agama Phrynocephalus axillaris, the first complete mitogenome from the genus Phrynocephalus, was determined. The total length of this complete mitogenome is 17,937 bp, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions (CRs). The overall base composition of the H-strand is 36.4% A, 26.0% T, 25.4% C, and 12.3% G. The gene arrangement and composition of the mitogenome are similar to those of other Agaminae lizards, albeit with one CR existing between the tRNAThr gene and tRNAPro gene and another CR containing 17 copies of 77-bp tandem repeats inserting between the tRNAPhe and 12S rRNA. The complete mitogenome sequence of P. axillaris provided fundamental data for resolving phylogenetic and genetic problems related to this species and genus Phrynocephalus.

Accurate Localization of the Mobile Genomic Islands in &lt;i&gt;Pseudomonas putida&lt;/i&gt;

Pseudomonas putida is a safety gammaproteobacterium that plays an important role in bioremediation. Twenty nine mobile genomic islands were accurately localized in four strains of P. putida, six in P. putida F1, six in P. putida GB-1, nine in P. putida KT2440, and eight in P. putida W619, respectively. The integration sites include the tRNA gene, such as tRNAMet gene, tRNASer gene, tRNALeu gene, tRNAGly gene, tRNAThr gene, tRNACys gene, tRNAPro gene, and some structural genes, such as arsenate reductase gene, DNA mismatch repair protein MutS gene, thymidylate synthase gene, and 6-pyruvoyl tetrahydropterin synthase gene. 6-pyruvoyl tetrahydropterin synthase gene was firstly determined as the integration site of the genomic islands. The action sites of the lambda integrases are the stem-loop sequence, and the action sites of the P4 integrase are the asymmetric sequence. KT2440GI-5 can produce R2-type pyocin particle that is a bacteriocin and can kill sensitive bacterium. KT2440GI-9 can code ectoine-induced proteins that cause the cells to survive in high salt concentration.

Genomic Heterogeneity in a Natural Archaeal Population Suggests a Model of tRNA Gene Disruption

Understanding the mechanistic basis of the disruption of tRNA genes, as manifested in the intron-containing and split tRNAs found in Archaea, will provide considerable insight into the evolution of the tRNA molecule. However, the evolutionary processes underlying these disruptions have not yet been identified. Previously, a composite genome of the deep-branching archaeon Caldiarchaeum subterraneum was reconstructed from a community genomic library prepared from a C. subterraneum–dominated microbial mat. Here, exploration of tRNA genes from the library reveals that there are at least three types of heterogeneity at the tRNAThr(GGU) gene locus in the Caldiarchaeum population. All three involve intronic gain and splitting of the tRNA gene. Of two fosmid clones found that encode tRNAThr(GGU), one (tRNAThr-I) contains a single intron, whereas another (tRNAThr-II) contains two introns. Notably, in the clone possessing tRNAThr-II, a 5′ fragment of the tRNAThr-I (tRNAThr-F) gene was observed 1.8-kb upstream of tRNAThr-II. The composite genome contains both tRNAThr-II and tRNAThr-F, although the loci are >500 kb apart. Given that the 1.8-kb sequence flanked by tRNAThr-F and tRNAThr-II is predicted to encode a DNA recombinase and occurs in six regions of the composite genome, it may be a transposable element. Furthermore, its dinucleotide composition is most similar to that of the pNOB8-type plasmid, which is known to integrate into archaeal tRNA genes. Based on these results, we propose that the gain of the tRNA intron and the scattering of the tRNA fragment occurred within a short time frame via the integration and recombination of a mobile genetic element.

Genetically structured population and demographic history of the goldlined spinefoot Siganus guttatus in the northwestern Pacific

Sequence variation of the mitochondrial DNA was analyzed to examine the genetic structure and demographic history of the goldlined spinefoot Siganus guttatus in the northwestern Pacific. In total, 451 nucleotide sequences spanning from the tRNAThr gene to the middle of the control region were determined from 254 specimens collected from five localities; three in the Ryukyu Islands (Okinawa, Miyako, and Ishigaki Islands), Taiwan, and Cebu Island of the Philippines; 73 variable sites and 75 haplotypes were detected. Our results showed restricted gene flow and genetic differentiation among all populations, with the exception of genetic homogeneity between the Miyako and Ishigaki populations; that is, this species will be able to cross between Miyako and Ishigaki (ca. 120 km) by the transport of pelagic larvae, and gene flow between Okinawa and Miyako/Ishigaki Islands (ca. 330–450 km) is restricted. A non-dispersal strategy will lead to restricted gene flow and genetic structuring in S. guttatus. Both the neutrality tests and the mismatch distribution indicated that S. guttatus might have been in populations at demographic equilibrium. This suggests that population range expansion may have been restricted owing to a non-dispersal strategy that may have restrained S. guttatus from demographic expansion after glaciation. The result will be of fundamental importance for resource management of this species.