tRNA-Cys Genes Research Articles

TRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana

Although most of the genes encoding tRNAs in plants are dispersed throughout the genome, a fraction of them form tRNA gene clusters. In Arabidopsis thaliana, the smallest of tRNA clusters on chromosome 5 consists of four tRNA-Cys-GCA genes placed within repeating units of 0.4 kbp. A systematic analysis of the genomic sequences of syntenic regions from various ecotypes of A. thaliana showed that the general structure of the cluster, consisting of a tRNA-Cys pseudogene followed by repeating units containing tRNA-Cys genes, is well conserved. However, there is significant heterogeneity in the number of repeating units between different ecotypes. A unique feature of this cluster is the presence of putative transposable elements (Helitron). In addition, two further tRNA-Cys gene mini-clusters (gene pairs) in A. thaliana were identified. RNA-seq-based evaluation of expression of tRNA-Cys-GCA genes showed a positive signal for 11 out of 13 unique transcripts. An analysis of the conservation of the tRNA-Cys clusters from A. thaliana with the corresponding regions from four other Arabidopsis species suggests a sequence of events that led to the divergence of these regions.

Phylogenetic Analysis of Bacillus cereus sensu lato Isolates from Commercial Bee Pollen Using tRNACys-PCR.

Endospore-forming bacteria related to the Bacillus cereus group produce toxins that cause illnesses in organisms from invertebrates to mammals, including foodborne illnesses in humans. As commercial bee pollen can be contaminated with these bacteria, a comprehensive microbiological risk assessment of commercial bee pollen must be incorporated into the relevant regulatory requirements, including those that apply in Mexico. To facilitate detection of members of this group of bacteria, we have developed a PCR strategy that is based on the amplification of the single-copy tRNACys gene and specific genes associated with tRNACys to detect Bacillus cereus sensu lato (B. cereus s.l.). This tRNACys-PCR-based approach was used to examine commercial bee pollen for endospore-forming bacteria. Our analysis revealed that 3% of the endospore-forming colonies isolated from a commercial source of bee pollen were related to B. cereus s.l., and this result was corroborated by phylogenetic analysis, bacterial identification via MALDI-TOF MS, and detection of enterotoxin genes encoding the HBL and NHE complexes. The results show that the isolated colonies are closely related phylogenetically to B. cereus, B. thuringiensis, and B. bombysepticus. Our results indicate that the tRNACys-PCR, combined with other molecular tools, will be a useful approach for identifying B. cereus s.l. and will assist in controlling the spread of potential pathogens.

Complete mitochondrial genome of the Yellow-spotted skate Okamejei hollandi (Rajiformes: Rajidae)

The complete mitochondrial genome of the Yellow-spotted skate Okamejei hollandi was determined in this study. It is 16,974 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one putative control region. The overall base composition is 30.5% A, 27.8% C, 14.0% G, and 27.8% T. There are 28 bp short intergenic spaces located in 12 gene junctions and 31 bp overlaps located in nine gene junctions in the whole mitogenome. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The lengths of 22 tRNA genes range from 68 (tRNA-Ser2) to 75 (tRNA-Leu1) bp. The origin of L-strand replication (OL) sequence (37 bp) was identified between the tRNA-Asn and tRNA-Cys genes. The control region is 1311 bp in length with high A + T and poor G content.

Complete mitochondrial genome of Gnathopogon taeniellus (Cypriniformes: Cyprinidae)

The complete mitochondrial genome of Gnathopogon taeniellus was first determined in this study. It is 16,596 bp in length, contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and one control region in the typical vertebrate gene order and transcriptional direction. There are total of 29 bp short overlaps and 34 bp non-coding intergenic spacers were found in the mitogenome. Overall nucleotide base composition of light strand is 29.3% A, 25.8% C, 17.9% G and 27.0% T. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The origin of light strand replication (OL) was identified between tRNAAsn and tRNACys genes and could fold a hairpin structure. The nucleotide composition of control region is 31.8% A, 20.9% C, 14.0% G and 33.3% T.

Complete mitochondrial genome of the Indonesian whaler shark Carcharhinus tjutjot

In this study, we first present the complete mitochondrial genome of the Indonesian whaler shark Carcharhinus tjutjot. It is 16,705 bp in length and encodes 37 mitochondrial genes with the typical gene order and transcriptional direction in vertebrates. The overall nucleotide base content is 31.6% A, 26.4% C, 13.0% G and 29.0% T. A total of 33 bp short overlaps and 22 bp short intergenic spaces were found at 9 and 11 gene junctions, respectively. Two initiated codon types (ATG and GTG) and three terminal codon types (TAA, TAG and AGG) were used in the protein-coding genes. The tRNA-Ser2 replaced the DHU arm by a simple loop and could not be folded into the typical secondary structure. The origin of L-strand replication (OL) was identified between the tRNA-Asn and tRNA-Cys genes. The termination-associated sequence (TAS) was found near the tRNA-Pro in the control region.

Complete mitochondrial genome of the Sharpnose stingray Himantura gerrardi (Myliobatiformes: Dasyatidae)

In this study, we presented the complete mitochondrial genome of the Sharpnose stingray Himantura gerrardi for the first time, which was 17,685 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a putative control region. The overall nucleotide composition was 30.1% A, 27.5% C, 14.5% G and 28.0% T. A total of 22 bp overlaps and 83 bp short intergenic spaces were found in the mitogenome. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The origin of L-strand replication (OL) sequence formed a hairpin structure between the tRNA-Asn and tRNA-Cys genes. The termination associated sequence (TAS) formed a hairpin structure near the tRNA-Pro in the control region.

The complete mitochondrial genome of the mudsnail Cipangopaludina cathayensis (Gastropoda: Viviparidae)

We present the complete mitochondrial genome of Cipangopaludina cathayensis in this study. The mitochondrial genome is 17,157 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. All of them are encoded on the heavy strand except 7 tRNA genes on the light strand. Overall nucleotide compositions of the light strand are 44.51% of A, 26.74% of T, 20.48% of C and 8.28% of G. All the protein-coding genes start with ATG initiation codon except ATP6 with ATA and ND4 with TTG, and 2 types of termination codons are TAA (ATP6, ND2, COX1, COX2, ATP8, ND1, ND6, Cytb, COX3, ND4) and TAG (ND4L, ND5, ND3). There are 29 intergenic spacers and 5 gene overlaps. The tandem repeat sequences are observed in COX2, tRNAAsp, ATP6, tRNACys, S-rRNA, ND1, Cytb, ND4 and COX3 genes. Gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but at least one lengthy non-coding region is essential regulatory element for the initiation of transcription and replication.

Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of Occidozyga martensii.

In this study, the complete nucleotide sequence (18,321 bp) of the mitochondrial (mt) genome of the round-tongued floating frog, Occidozyga martensii was determined. Although, the base composition and codon usage of O. martensii conformed to the typical vertebrate patterns, this mt genome contained 23 tRNAs (a tandem duplication of tRNA-Met gene). The LTPF tRNA-gene cluster, and the derived position of the ND5 gene downstream of the control region, were present in this mitogenome. Moreover, we found that in the WANCY tRNA-gene cluster, the tRNA-Asn gene was located between the tRNATyr and COI genes instead of between the tRNA-Ala and tRNA-Cys genes, which is a novel mtDNA gene rearrangement in vertebrates. Based on the concatenated nucleotide sequences of the 13 protein-coding genes, phylogenetic analysis (BI, ML, MP) was performed to further clarify the phylogenetic relations of this species within anurans.

Complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis

The complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis is presented in this study. It is 17,693 bp in length and contains 37 genes in typical gene order and transcriptional orientation observed in vertebrates. There were a total of 86 bp short intergenic spacers and 22 bp overlaps in the genome. The overall base composition was 31.4% A, 25.5% C, 13.2% G and 29.9% T. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were found in 13 protein-coding genes. The length of 22 tRNA genes ranged from 68 (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1). The origin of L-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes. The base composition of the control region (1940 bp) was similar to the whole mitogenome.

Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus (Carcharhiniformes: Carcharhinidae)

The complete mitochondrial genome of the whitetip reef shark Triaenodon obesus is determined in this study. It is 16,700 bp in length, with the typical gene composition, arrangement and transcriptional orientation in vertebrates. The overall base composition is 31.4% A, 25.8% C, 13.2% G and 29.7% T. Two start codons and two stop codons are found in the protein-coding genes. The 22 tRNA genes ranged from 67 to 75 nucleotides. The tRNA-Ser2 lost the DHU arm and could not be folded to the typical cloverleaf secondary structure. The origin of L-strand replication (OL) sequence was identified between tRNA-Asn and tRNA-Cys genes. The high A+T content of control region is due to a lot of poly A and poly T.

Mitochondrial genome of the longtail butterfly ray Gymnura poecilura (Myliobatiformes: Gymnuridae)

The complete mitogenome the longtail butterfly ray (Gymnura poecilura) was first presented in this study. It is 17,874 bp in length, contains 37 genes with the typical gene order and transcriptional direction in vertebrates. The overall base composition is: 28.5% A, 26.5% T, 15.0% G and 30.1% C. There are 26 bp overlaps and 41 bp short intergenic spaces located in 7 and 16 gene junctions, respectively. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in protein-coding genes. The origin of L-strand replication (OL) was found between tRNA-Asn and tRNA-Cys genes. The control region has the same A and C contents (28.8%).

Complete mitochondrial genome of milk sole fish Aseraggodes kobensis (Pleuronectiformes: Soleidae)

The complete mitochondrial genome of the milk sole fish Aseraggodes kobensis was determined in this study. It is 16,944 bp in length, contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one putative control region with the typical gene order and transcriptional orientation in vertebrates. The nucleotide base content of A. kobensis mitochondrial genome is: 31.7% A, 27.3% C, 15.3% G and 25.8% T. There are 24 bp overlaps and 48 bp short intergenic spaces located in 6 and 12 gene junctions, respectively. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were found in protein-coding genes. The origin of L-strand replication sequence was found between the tRNAAsn and tRNACys genes, and could be folded into a hairpin structure. The control region is 1239 bp in length with the rich A+T (66.4%) and poor G (13.1%) content.

Is mitochondrial tRNACys G5821A a deleterious mutation?

Although there are increasing reports showed a positive link between mitochondrial tRNACys G5821A mutation and mitochondrial diseases. However, its role remained controversial. In this paper, we took a comprehensive data analysis concerning this mutation and clinical diseases. Our data indicated that this mutation lacked an evolutionary conservation and did not get involved in the thermodynamic change of tRNACys gene. Therefore, based on these observations, we proposed that G5821A mutation is not deleterious mutation.

Complete mitogenome of the brown guitarfish Rhinobatos schlegelii (Rajiformes, Rhinobatidae)

The complete mitochondrial genome of the brown guitarfish Rhinobatos schlegelii is presented for the first time in this study. It is 16,780 bp in length, consisting 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 putative control region with the typical gene order and direction of transcription in vertebrates. The overall base composition is 32.1% A, 26.3% C, 13.2% G and 28.3% T. Two start codon (GTG and ATG) and two stop codon patterns (TAG and TAA/T) were found in protein-coding genes. The 22 tRNA genes ranged from 67 (tRNA-Ser2) to 75 (tRNA-Leu1) bp in length. The origin of L-strand replication (OL) was between tRNA-Asn and tRNA-Cys genes within the WANCY region. The tRNA-Ser2 could not be fold into the typical cloverleaf secondary structure because of the replacement of its dihydrouridine arm by a simple loop. The control region was 1089 bp in length with high A + T content (64.0%).

Complete mitogenome of Hemiculter leucisculus (Cyprinidae: Cultrinae)

The complete mitogenome was first determined for a minnow Hemiculter leucisculus in this study. It is 16,622 bp in length and has 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. Overall nucleotide base composition is 30.4% A, 27.10% C, 17.10% G and 25.40% T. All the tRNA genes can fold into the typical clover-leaf secondary structures, except the tRNA-Ser2 which loses the dihydrouridine arm and is replaced with one 11 bp loop. The origin of light-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes while the termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) were found in the control region.

Mitochondrial genome of the spotless smooth-hound Mustelus griseus (Carcharhiniformes: Triakidae)

The complete mitochondrial genome of Mustelus griseus was first determined in this study. It is 16,754 bp in length, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region with the typical gene order in vertebrates. Overall nucleotide base composition of the mitogenome is 30.7% A, 24.9% C, 14.0% G and 30.3% T. After aligning, it comes to us that the mitogenomic portions of M. griseus are very similar to those of Mustelus manazo, ranging from 86.92% (control region) to 100% (tRNA-His and tRNA-Leu2). The origin of L-strand replication (OL) is identified between tRNA-Asn and tRNA-Cys genes. The control region is located between the tRNA-Pro and tRNA-Phe genes, containing one termination-associated sequence (TAS) and three short conserved sequences (CSB 1-3).

Complete sequence of the mitochondrial genome of Odontamblyopus rubicundus (Perciformes: Gobiidae): genome characterization and phylogenetic analysis

Odontamblyopus rubicundus is a species of gobiid fishes, inhabits muddy-bottomed coastal waters. In this paper, the first complete mitochondrial genome sequence of O. rubicundus is reported. The complete mitochondrial genome sequence is 17119 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a control region and an L-strand origin as in other teleosts. Most mitochondrial genes are encoded on H-strand except for ND6 and seven tRNA genes. Some overlaps occur in protein-coding genes and tRNAs ranging from 1 to 7 bp. The possibly nonfunctional L-strand origin folded into a typical stem-loop secondary structure and a conserved motif (5'-GCCGG-3') was found at the base of the stem within the tRNACys gene. The TAS, CSB-2 and CSB-3 could be detected in the control region. However, in contrast to most of other fishes, the central conserved sequence block domain and the CSB-1 could not be recognized in O. rubicundus, which is consistent with Acanthogobius hasta (Gobiidae). In addition, phylogenetic analyses based on different sequences of species of Gobiidae and different methods showed that the classification of O. rubicundus into Odontamblyopus due to morphology is debatable.

Unusual features of control region and a novel NADH 6 genes in mitochondrial genome of the finespot goby, Chaeturichthys stigmatias (Perciformes, Gobiidae)

In this article, we determined the complete mitogenome of finespot goby Chaeturichthys stigmatias with emphasis on the arranged gene order and gene feature with published Gobiidae species. The C. stigmatias mtDNA was 18,562 bp in length (56.94% AT), and comprised 37 genes (13 protein genes, 2 rRNAs and 22 tRNAs) that was typical for mitochondrial genome of Gobiidae species. Unusually, the NADH 6 gene was very large in length compared with other Gobiidae species. Mitogenome of C. stigmatias had a long putative control region with high AT content (71.28%). Within this sequence, we determined repeat regions, the termination-associated sequence and the conserved sequence block for this region. The origin of L-strand replication in C. stigmatias was located in a cluster of five tRNA genes (WANCY). The conserved motif (5′-GCCGG-3′) was also determined at the base of the stem in the tRNA-Cys gene. This study will provide a better understanding of Gobiidae mitogenomes and offer useful information for future studies concerning Gobiidae mitogenome evolution.

Mitochondrial genome of the ringstraked guitarfish Rhinobatos hynnicephalus (Elasmobranchii: Rajiformes)

The complete mitochondrial genome of the ringstraked guitarfish Rhinobatos hynnicephalus is firstly presented in this study, which is also the first representative in the family Rhinobatidae. It is 16,776 bp in length and contains 37 genes and one control region as the typical gene arrangement and transcriptional direction in vertebrates. The overall base composition is 31.7% A, 26.8% C, 13.5% G and 28.1% T. The 22 tRNA genes ranged from 67 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The origin of L-strand replication (OL) sequence was identified between tRNA-Asn and tRNA-Cys genes. The termination associated sequence (TAS) and the conserved sequence blocks (CSB 1--3) were recognized in the control region.

Complete mitochondrial genome of Chinese lake gudgeon Sarcocheilichthys sinensis (Cypriniformes, Cyprinidae)

The complete mitochondrial genome of the Chinese lake gudgeon Sarcocheilichthys sinensis was first determined in this study. It is a circular DNA double strand of 16,684 bp in length, encodes genes for 13 proteins, 2 ribosomal RNA subunits, 22 transfer RNAs and an A + T-rich control region with the typical gene order in vertebrate mitogenomes. Overall nucleotide composition is 30.5% A, 26.6% C, 16.7% G and 26.3% T. Three start codons (ATG, GTG and ATA) and three stop codons (TAG, TAA and T) were found in all protein-coding genes. The tRNA-SerAGY lacked the dihydrouridine arm and could not fold into typical cloverleaf secondary structure. The origin of L-strand replication was identified between the tRNA-Asn and tRNA-Cys genes.