Structure Of tRNA Research Articles

Identification and Quantification of (t)RNA Modifications in Pseudomonas aeruginosa by Liquid Chromatography-Tandem Mass Spectrometry.

Transfer RNA (tRNA) modifications impact the structure and function of tRNAs, thus affecting the efficiency and fidelity of translation. In the opportunistic pathogen Pseudomonas aeruginosa translational regulation plays an important but less defined role in adaptation to changing environments. In this study, we have explored tRNA modifications in P. aeruginosa through LC-MS/MS approaches. Neutral loss scanning (NLS) demonstrated the potential to identify previously unknown modifications, whereas multiple reaction monitoring (MRM) was able to detect modifications with high specificity and sensitivity. In this study, the MRM-based external calibration method allowed for quantification of the four canonical and 32 modified ribonucleosides, out of which 21 tRNA modifications were quantified in the total tRNA pool of P. aeruginosa PA14. We also purified the single tRNA isoacceptors tRNA-ArgUCU, tRNA-LeuCAA, and tRNA-TrpCCA and determined their specific modification patterns, both qualitatively and quantitatively. Deeper insights into the nature and dynamics of tRNA modifications in P. aeruginosa should pave the way for further studies on post-transcriptional gene regulation as a relatively unexplored molecular mechanism of controlling bacterial pathogenicity and mode of growth.

Novel Alterations of Some Mitochondrial tRNA Genes in Vienamese Colorectal Cancer Patients

Some mutations of mt-DNA which encode tRNA (mt-tRNA) were previously reported to be associated with clinical manifestations of neuromuscular disorders syndrome. In addition, alterations of the mitochondrial genome have been suggested to contribute to mitochondrial dysfunction and tumorigenesis. Alterations in some mt-tRNA genes have also been identified in breast cancer, lung cancer and colorectal cancer. However, so far, we have not found any report on mt-tRNA gene alteration in the Vietnamese colorectal cancer patients. So that, in this study, we analyzed the alterations of some mt-tRNA genes in a group of Vietnamese colorectal cancer patients and predicted influence of the alterations to secondary structure of tRNA based on bioinformatic tools. PCR-RFLP and DNA sequencing methods were used to screening alterations, secondary structure of tRNA was predicted in silico by using a tool of the Vienna RNA Websuite. Results: both A12309G and A12310G of tRNALeu were identified together in two out of 98 patients, and both T12150G and C12154G of tRNAHis were indentified in one out of 19 patients. All of these alterations were heteroplasmic and have not been reported in cancer patients. In particular, the C12154G alteration in the DHR loop led to change of secondary structure of tRNAHis and may affect to function of this tRNA molecule.
 Keywords
 mt-tRNA, Vietnamese colorectal cancer, PCR-RFLP, DNA sequencing
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Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus.

Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50–83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.

Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2.

Double stranded RNA-binding domain (dsRBD) is a ubiquitous domain specialized in the recognition of double-stranded RNAs (dsRNAs). Present in many proteins and enzymes involved in various functional roles of RNA metabolism, including RNA splicing, editing, and transport, dsRBD generally binds to RNAs that lack complex structures. However, this belief has recently been challenged by the discovery of a dsRBD serving as a major tRNA binding module for human dihydrouridine synthase 2 (hDus2), a flavoenzyme that catalyzes synthesis of dihydrouridine within the complex elbow structure of tRNA. We here unveil the molecular mechanism by which hDus2 dsRBD recognizes a tRNA ligand. By solving the crystal structure of this dsRBD in complex with a dsRNA together with extensive characterizations of its interaction with tRNA using mutagenesis, NMR and SAXS, we establish that while hDus2 dsRBD retains a conventional dsRNA recognition capability, the presence of an N-terminal extension appended to the canonical domain provides additional residues for binding tRNA in a structure-specific mode of action. Our results support that this extension represents a feature by which the dsRBD specializes in tRNA biology and more broadly highlight the importance of structural appendages to canonical domains in promoting the emergence of functional diversity.

Complete mitochondrial genome of smoothshell shrimp Parapenaeopsis tenella (Bate, 1888) (Crustacea: Decapoda: Penaeidae)

In this study, the complete mitochondrial genome of smoothshell shrimp Parapenaeopsis tenella was determined for the first time. The mitogenome of P. tenella is 15,893 bp in length and encodes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region (CR). The overall base composition is 34.0%, 35.3%, 11.9%, and 18.9% for A, T, C, and G, respectively. All PCGs are initiated by ATN codons. Four of the 13 PCGs harbor the incomplete termination codon by T. Twenty-one tRNA genes have a typical clover-leaf structure of mitochondrial tRNA, except for tRNA-Ser (AGC), in which the dihydrouridine (DHU) arm stem is absent. Phylogenetic analysis among the available malacostracans species supports the current morphology-based hypothesis that P. tenella is grouped to the genus Parapenaeopsis.

Accurate prediction of secondary structure of tRNAs

RNA structure plays a key role in understanding its biological function. Currently, the most successful de novo methods for RNA secondary structure prediction are based on free energy minimization. Existing free energy minimization methods focus more on building energy calculation models and optimizing energy parameters while paying less effort on developing structure space search algorithm. This study proposes a de novo method, namely DPARSS, for RNA secondary structure prediction. DPARSS proposes a novel dynamic programming algorithm for structure space search and intends to generate predictions with minimal free energy. An evaluation on a benchmark dataset consisting of tRNAs indicates that the DPARSS method achieves better predictive performance than existing free energy minimization methods. Additionally, case studies suggest that the improvement achieved by the DPARSS algorithm is likely due to the fact that the predictions generated by DPARSS algorithm form more base pairs, contain less mismatches and form longer base pair segments.

7-Methylguanosine Modifications in Transfer RNA (tRNA).

More than 90 different modified nucleosides have been identified in tRNA. Among the tRNA modifications, the 7-methylguanosine (m7G) modification is found widely in eubacteria, eukaryotes, and a few archaea. In most cases, the m7G modification occurs at position 46 in the variable region and is a product of tRNA (m7G46) methyltransferase. The m7G46 modification forms a tertiary base pair with C13-G22, and stabilizes the tRNA structure. A reaction mechanism for eubacterial tRNA m7G methyltransferase has been proposed based on the results of biochemical, bioinformatic, and structural studies. However, an experimentally determined mechanism of methyl-transfer remains to be ascertained. The physiological functions of m7G46 in tRNA have started to be determined over the past decade. For example, tRNA m7G46 or tRNA (m7G46) methyltransferase controls the amount of other tRNA modifications in thermophilic bacteria, contributes to the pathogenic infectivity, and is also associated with several diseases. In this review, information of tRNA m7G modifications and tRNA m7G methyltransferases is summarized and the differences in reaction mechanism between tRNA m7G methyltransferase and rRNA or mRNA m7G methylation enzyme are discussed.

The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference

The Pamphilioidea represents a small superfamily of the phytophagous suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genomes (mitogenomes) of three pamphilioid species: Chinolyda flagellicornis (Pamphiliidae), Megalodontes spiraeae and M. cephalotes (Megalodontesidae) were newly sequenced using next generation sequencing and comparatively analysed with the previously reported symphytan mitogenomes. A positive AT skew (0.013) and a negative GC skew (−0.194) were found in pamphilioid mitogenome, and a deviation from strand asymmetry was also observed in the PCGs encoded on both strands. Several gene rearrangement events were observed in four tRNA gene clusters (WCY, IQM, ARNS1EF and TP clusters), which have not been reported from symphytan mitogenomes to date. As the most parsimonious explanation, compared with the inferred insect ancestral mitogenome architecture, the occurrence of gene rearrangements in pamphilioid mitogenomes requires totally five evolutionary steps, including four transpositions and one inversion. The predicted secondary structures of tRNAs, rrnS and rrnL genes are mostly consistent with reported hymenopteran species. Phylogenetic analyses recovered the monophyly of superfamily Pamphilioidea and indicated the relationship Tenthredinoidea + (Pamphilioidea + (Cephoidea + (Orussoidea + Apocrita))) with strong nodal supports.

The first two mitochondrial genomes of wood wasps (Hymenoptera: Symphyta): Novel gene rearrangements and higher-level phylogeny of the basal hymenopterans

The Symphyta has long been recognized as a paraphyletic grade forming the base of the remaining Hymenopteran, and the superfamily relationships within Symphyta remain controversial. Here, the first two representative mitochondrial genomes from the superfamily Siricoidea and Xiphydrioidea (Hymenoptera: Symphyta) are obtained using next-generation sequencing. The complete mitochondrial genome of Xiphydria sp. is 16,482 bp long with an A + T content of 84.18% while the incomplete one of Tremex columba is 16,847 bp long and A + T content is 81.69%. All 37 typical mitochondrial genes are possessed in both species. The secondary structure of tRNAs and rRNAs for both species are successfully predicted. Compared with the ancestral organization, seven and five tRNA genes are rearranged in mitochondrial genomes of Tremex and Xiphydria, respectively, which are the most rearrangement events within Symphyta. The rearrangement patterns in Tremex and Xiphydria present in this study are all novel to the Symphyta. Phylogenetic relationships among the major lineages of Symphyta are reconstructed using mitochondrial genomes. Both maximum likelihood and Bayesian inference analyses highly support Symphyta is a paraphyletic grade, Xyeloidea + (Tenthredinoidea + (Pamphilioidea + (Xiphydrioidea + (Cephoidea + (Orussoidea + Apocrita))))).

Recent Advances in Our Understanding of the Biosynthesis of Sulfur Modifications in tRNAs.

Sulfur is an essential element in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, introduced post-transcriptionally, that function to ensure proper codon recognition or stabilization of tRNA structure, thereby enabling accurate and efficient translation. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems that are closely related to cellular sulfur metabolism, and “modification enzymes” that incorporate sulfur atoms into tRNA. Herein, recent biochemical and structural characterization of the biosynthesis of sulfur modifications in tRNA is reviewed, with special emphasis on the reaction mechanisms of modification enzymes. It was recently revealed that TtuA/Ncs6-type 2-thiouridylases from thermophilic bacteria/archaea/eukaryotes are oxygen-sensitive iron-sulfur proteins that utilize a quite different mechanism from other 2-thiouridylase subtypes lacking iron-sulfur clusters such as bacterial MnmA. The various reaction mechanisms of RNA sulfurtransferases are also discussed, including tRNA methylthiotransferase MiaB (a radical S-adenosylmethionine-type iron-sulfur enzyme) and other sulfurtransferases involved in both primary and secondary sulfur-containing metabolites.

Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA.

To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.

Structure and Dynamics of tRNAMet Containing Core Substitutions.

The fidelity of protein synthesis is largely dominated by the accurate recognition of transfer RNAs (tRNAs) by their cognate aminoacyl-tRNA synthetases. Aminoacylation of each tRNA with its cognate amino acid is necessary to maintain the accuracy of genetic code input. Aminoacylated tRNAMet functions in both initiation and elongation steps during protein synthesis. As a precursor to the investigation of a methionyl-tRNA synthetase–tRNAMet complex, presented here are the results of molecular dynamics (MD) for single nucleotide substitutions in the D-loop of tRNAMet (G15A, G18A, and G19A) probing structure/function relationships. The core of tRNAMet likely mediates an effective communication between the tRNA anticodon and acceptor ends, contributing an acceptor stem rearrangement to fit into the enzyme-active site. Simulations of Escherichia coli tRNAMet were performed for 1 μs four times each. The MD simulations showed changes in tRNA flexibility and long-range communication most prominently in the G18A variant. The results indicate that the overall tertiary structure of tRNAMet remains unchanged with these substitutions; yet, there are perturbations to the secondary structure. Network-based analysis of the hydrogen bond structure and correlated motion indicates that the secondary structure elements of the tRNA are highly intraconnected, but loosely interconnected. Specific nucleotides, including U8 and G22, stabilize the mutated structures and are candidates for substitution in future studies.

Characterization of the complete mitochondrial genome of Parabreviscolexniepini Xi et al., 2018 (Cestoda, Caryophyllidea).

Parabreviscolexniepini is a recently described caryophyllidean monozoic tapeworm from schizothoracine fish on the Tibetan Plateau. In the present study, the complete mitochondrial genome of P.niepini is determined for the first time. The mitogenome is 15,034 bp in length with an A+T content of 59.6%, and consists of 12 protein-encoding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. The secondary structure of tRNAs exhibit the conventional cloverleaf structure, except for trnS1(AGN) and trnR, which lack DHU arms. The anti-codon of trnS1(AGN) in the mitogenome of P.niepini is TCT. The two major non-coding regions, 567 bp and 1428 bp in size, are located between trnL2 and cox2, trnG and cox3, respectively. The gene order of P.niepini shows a consistent pattern with other caryophyllideans. Phylogenetic analysis based on mitogenomic data indicates that P.niepini has a close evolutionary relationship with tapeworms Breviscolexorientalis and Atractolytocestushuronensis.

TRNA diversification among uncultured archeon clones.

Whole genome sequences (DNA sequences) of four uncultured archeon clones (1B6:CR626858.1, 4B7:CR626856.1, 22i07:JQ768096.1 and 19c08:JQ768095.1) were collected from NCBI BioSample database for the construction of digital data on tRNA. tRNAscan-SE 2.0 and ENDMEMO tools were used to identify and sketch tRNA structure as well as calculate Guanine-Cytosine (GC) percentage respectively. Eight true/functional tRNAs were identified from above 4 sequences which showed cove score greater than 20% with no variable loop. The tRNAs from the uncultured archeon clones were classified as Ala, Arg, Ile, Thr, Pro and Val type tRNA with cove score ranging from 34.22%-79.03%. The range of GC content was found 42.89%-56.91%; while tRNA contributed GC content ranging from 52%-64.86% to the total GC content in these sequences. The data fabricated in this study could be very useful for studying the diversity of tRNA among prokaryotes.

Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax.

As adapter molecules to convert the nucleic acid information into the amino acid sequence, tRNAs play a central role in protein synthesis. To fulfill this function in a reliable way, tRNAs exhibit highly conserved structural features common in all organisms and in all cellular compartments active in translation. However, in mitochondria of metazoans, certain dramatic deviations from the consensus tRNA structure are described, where some tRNAs lack the D- or T-arm without losing their function. In Enoplea, this miniaturization comes to an extreme, and functional mitochondrial tRNAs can lack both arms, leading to a considerable size reduction. Here, we investigate the secondary and tertiary structure of two such armless tRNAs from Romanomermis culicivorax. Despite their high AU content, the transcripts fold into a single and surprisingly stable hairpin structure, deviating from standard tRNAs. The three-dimensional form is boomerang-like and diverges from the standard L-shape. These results indicate that such unconventional miniaturized tRNAs can still fold into a tRNA-like shape, although their length and secondary structure are very unusual. They highlight the remarkable flexibility of the protein synthesis apparatus and suggest that the translational machinery of Enoplea mitochondria may show compensatory adaptations to accommodate these armless tRNAs for efficient translation.

Comparison of two complete mitochondrial genomes from Perlodidae (Plecoptera: Perloidea) and the family-level phylogenetic implications of Perloidea

To obtain a better understanding of the mitochondrial genome in Perlodidae and the phylogeny of Perloidea, we sequenced two perlodid mitochondrial genomes and present comparative analyses in the family Perlodidae. Our results show that genome organization, base composition, codon usage and non-coding and overlapping regions, the sequences of mitochondrial transcription termination factor (DmTTF) and structural elements in control region were conserved in Perlodidae. The unique non-coding regions in COI-trnL2 and trnL2-COII were present in Perlodidae but were incomplete or absent from other stoneflies, and we also discuss the conservative property of the sequences between trnE and trnF, trnS1 and ND1. The secondary structure of tRNAs showed that the trnK, trnP, trnS1 and trnW were identical and the trnS1 could not be folded into typical secondary structure due to its absence of DHU arm. Phylogenetic implications supported that Chloroperlidae is a sister group to Perlodidae and the Perlidae is a sister group to the clade Chloroperlidae + Perlodidae. This study contributes to understanding the comparative mitogenomic analysis of Perlodidae and phylogenetic relationships within the Perloidea.

The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?

BackgroundMitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in Aleuroglyphus ovatus, Caloglyphus berlesei, Dermatophagoides farinae, D. pteronyssinus, Histiostoma blomquisti and Psoroptes cuniculi. Loss of 16 mt tRNA genes, however, was reported in Steganacarus magnus; loss of 2–3 tRNA genes was reported in Tyrophagus longior, T. putrescentiae and Sarcoptes scabiei. Nevertheless, convincing evidence for mt gene loss is lacking in these mites.ResultsWe sequenced the mitochondrial genomes of two sarcoptiform mites, Histiostoma feroniarum (13,896 bp) and Rhizoglyphus robini (14,244 bp). Using tRNAScan and ARWEN programs, we identified 16 and 17 tRNA genes in the mt genomes of H. feroniarum and R. robini, respectively. The other six mt tRNA genes in H. feroniarum and five mt tRNA genes in R. robini can only be identified manually by sequence comparison when alternative anticodons are considered. We applied this manual approach to other mites that were reported previously to have lost mt tRNA genes. We were able to identify all of the 16 mt tRNA genes that were reported as lost in St. magnus, two of the three mt tRNA genes that were reported as lost in T. longior and T. putrescentiae, and the two mt tRNA genes that were reported as lost in Sa. scabiei. All of the tRNA genes inferred from these manually identified genes have truncation in the arms and mismatches in the stems.ConclusionsOur results reveal very unconventional tRNA structures in sarcoptiform mites and do not support the loss of mt tRNA genes in these mites. The functional implication of the drastic structural changes in these tRNA genes remains to be investigated.

Crystal Structure of the Archaeosine Synthase QueF‐Like – Insights into Amidino Transfer and tRNA Recognition by the Tunnel Fold

Crystal Structure of the Archaeosine Synthase QueF‐Like – Insights into Amidino Transfer and tRNA Recognition by the Tunnel Fold

Overexpression of human mitochondrial alanyl-tRNA synthetase suppresses biochemical defects of the mt-tRNAAla mutation in cybrids.

Mutations of mitochondrial transfer RNAs (mt-tRNAs) play a major role in a wide range of mitochondrial diseases because of the vital role of these molecules in mitochondrial translation. It has previously been reported that the overexpression of mitochondrial aminoacyl tRNA synthetases is effective at partially suppressing the defects resulting from mutations in their cognate mt-tRNAs in cells. Here we report a detailed analysis of the suppressive activities of mitochondrial alanyl-tRNA synthetase (AARS2) on mt-tRNAAla 5655 A>G mutant. Mitochondrial defects in respiration, activity of oxidative phosphorylation complexes, ATP production, mitochondrial superoxide, and membrane potential were consistently rescued in m.5655A>G cybrids upon AARS2 expression. However, AARS2 overexpression did not result in a detectable increase in mutated mt-tRNAAla but caused an increase incharged mt-tRNAAla in mutant cybrids, leading to enhanced mitochondrial translation. This indicated that AARS2 improved the aminoacylation activity in the case of m.5655A>G, rather than having a stabilizing effect on the tRNA structure. The data presented in this paper deepen our understanding of the pathogenesis of mt-tRNA diseases.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Bodianus oxycephalus (Perciformes, Labridae)

Bodianus oxycephalus is a fish species at a high risk of extinction and is included in the International Union for Conservation of Nature Red List of Threatened Species. This study determined for the first time the complete mitochondrial genome (mitogenome) of B. oxycephalus. The mitogenome is 16514 nucleotides long, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and 2 main non-coding regions. The overall base composition of B. oxycephalus mitogenome includes C (30.3%), A (26%), T (25.3%), and G (18.4%). Moreover, the gene arrangement, base composition, and tRNA structures of the mitogenome are similar to those of other teleosts. The conserved motif 5′-GCCGG-3′ was identified in the origin of light strand replication. In addition, terminal-associated sequences and conserved sequence blocks were detected in the control region. Phylogenetic analysis showed that B. oxycephalus and Choerodon schoenleinii clustered in a clade and formed a sister relationship.