ATG Initiation Codon Research Articles

The Autoimmune Regulator (Aire) transactivates HLA-G gene expression in thymic epithelial cells.

The Autoimmune Regulator (Aire) protein coordinates the negative selection of developing thymocytes by inducing the expression of hundreds of tissue-specific antigens within the thymic medulla, which is also a primary site of the expression of the immune checkpoint HLA-G molecule. Considering the immunomodulatory properties of Aire and HLA-G, and considering that the role of the constitutive thymus expression of HLA-G has not been elucidated, we studied the effect of AIRE cDNA transfection on HLA-G expression in 4D6 thymic cells and in the HLA-G-positive JEG-3 choriocarcinoma cells. Aire promoted the transactivation of HLA-G gene by increasing the overall transcription, inducing the transcription of at least G1 and G2/G4 isoforms, and incrementing the occurrence and distribution of intracellular HLA-G protein solely in 4D6 thymic cells. Luciferase-based assays and chromatin immunoprecipitation experiments performed in 4D6 cells revealed that Aire targeted at least two regions within the 5'-untranslated regulatory region (5'-URR) extending 1·4kb from the first ATG initiation codon. The interaction occurs independently of three putative Aire-binding sites. These results indicate that the Aire-induced upregulation of HLA-G in thymic cells is likely to act through the interaction of Aire with specific HLA-G 5'-URR DNA-binding factors. Such a multimeric transcriptional complex might operate in the thymus during the process of promiscuous gene expression.

The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes.

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To further analyze the phylogeny of Platycephalidae, we sequenced the complete mitogenome of Cociella crocodilus of the Platycephalidae family within Scorpaeniformes for the first time. The mitogenome was 17,314 bp in length, contained two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two typical noncoding control regions (the control region (CR) and origin of the light strand (OL)). All PCGs used standard initiation codons ATG, apart from cox1. The majority of the tRNA genes could be folded into cloverleaf secondary structures, whereas the secondary structure of tRNASer (AGN) lacked a dihydrouridine (DHU) stem. The CR contained several conserved sequence blocks (CSBs) and eight tandem repeats. In addition, the phylogenetic relationship based on the concatenated nucleotides sequences of 13 PCGs indicated that the Platycephalidae species are relatively basal in the phylogenetic relationships of Scorpaeniformes. Our results may not only advance the origin and the evolution of Scorpaeniformes, but also provide information for the genetic evolution and taxonomy of the teleostean species.

The complete mitochondrial genome of Archamia macropterus (Perciformes; Apogonidae) and phylogenetic studies of Perciformes

The complete mitochondrial genome sequence of Archamia macropterus was determined. The complete mitochondrial genome was 16,513 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 non-coding region (the control region and the origin of light strand replication). The overall base composition was A 26.37%, T 25.61%, C 30.80%, and G 17.22%. All protein-coding genes started with an ATG initiation codon, except COI used GTG. With the exception of ND6, all other genes were encoded on the heavy strand, the NJ tree demonstrated that A. macropterus has a closest relationship with Cheilodipterus quinquelineatus and Apogon semilineatus.

The complete mitochondrial genome of ostorhinchus fleurieu (kurtiformes: Apogonidae) and phylogenetic studies of apogoninae

The complete mitochondrial genome of Ostorhinchus fleurieu was first determined, which was 16,521 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region and one origin of replication on the light-strand. The overall base composition included C(29.2%), A(26.7%), T(26.7%) and G(17.4%). Moreover, the 13 PCGs encoded 3800 amino acids in total, twelve of which used the initiation codon ATG except for COI started with GTG. Most of them ended with complete stop codon, whereas three protein-coding genes (COII, ND4 and Cytb) used incomplete stop codon and represented as T. The phylogenetic tree based on the Neighbour Joining method was constructed to provide relationship within Apogoninae, which could be a useful basis for management of this species.

A comparison of complete mitochondrial DNA sequences of Mnais costalis Selys, 1869 (Odonata: Calopterygidae) from three different populations (one allopatric and two sympatric)

In Japan, two closely-related damselflies, Mnais costalis Selys, 1869 (Odonata: Calopterygidae) and M. pruinosa Selys-Longchamps (Odonata: Calopterygidae), 1853, coexist, and they exhibit geographic variations in wing color, body size, and habitat preference. In this study, we analyzed the complete mitochondrial genome of M. costalis from Saga Prefecture, Japan (sympatric populations that exhibit wing color polymorphism), and compared the genome with M. costalis that exhibit monomorphic orange wing color. The mitochondrial genome of M. costalis from Saga Prefecture was identified as a circular molecule of 15,488 bp, similar to that found in other M. costalis populations. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, along with one A + T-rich control region. Among the PCGs, ATP8 and ATP6, ATP6 and COIII, ND4 and ND4L, and ND6 and Cytb shared seven, one, seven, and one nucleotides, respectively. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one, while the termination codons TAA, TAG, TA, and T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.06%. From a phylogenetic analysis, the loss of wing color polymorphism in monomorphic sympatric populations is likely to occur with the coexistence of two Mnais species.

Phylogenetic analysis of the complete mitochondrial genome of Orestias ascotanensis (Cyprinodontiformes, Cyprinodontidae)

The complete mitochondrial genome of this species was first determined in this study, which is 16,617 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region, and 1 origin of replication on the light-strand. The overall base composition includes C(27.11%), A(26.68%), T(29.15%), G(17.04%) and three degenerate bases are R, R and S. Moreover, the 13 PCGs encode 3800 amino acids in total, 12 of which use the initiation codon ATG except COI that uses GTG. Most of them have TAA as the stop codon, whereas ND5 ends with AGA, four protein-coding genes (ND1, ND2, ND3 and Cytb) ended with TAG, and two protein-coding genes (COII and ND4) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Cyprinodontidae, which could be a useful basis for management of this species.

Complete mitochondrial genome sequence of the broad-winged damselfly, Mnais pruinosa Selys, 1853 (Odonata: Calopterygidae)

In this study, we analyzed the complete mitochondrial genome of the Mnais pruinosa Selys, 1853 from Saga Prefecture, Japan. The mitochondrial genome of M. pruinosa was identified as a circular molecule of 15,494 bp, and was found to be similar to that of other damselfly species. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, as well as one A + T-rich control region. The genes ATP8 and ATP6 shared seven nucleotides, ATP6 and COIII shared one nucleotide, ND4 and ND4L shared seven nucleotides, and ND6 and Cytb shared one nucleotide. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one; the termination codons TAA, TAG, incomplete TA, and single T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.18%.

Phylogenetic relationship and characterization of the complete mitochondrial genome of the black citrus aphid, Aphis aurantii (Hemiptera: Aphididae)

The black citrus aphid Aphis aurantii is a major pest of citrus and tea plants. In this study, we determined the complete mitochondrial genome (mitogenome) of A. aurantii. The mitogenome was 15,469 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. Gene order of A. aurantii was highly conserved and identical to most other previously sequenced Aphididae. Initiation codons ATT, ATA, and ATG were identified in eight, three, and two PCGs, respectively, while stop codon TAA was found in 11 genes except for 2 genes (cox1 and nad4) which use incomplete stop codon T–. Phylogenetic analysis showed the topology (Pemphigidae + (Hormaphididae + (Greenideidae + Aphididae))) within Aphidoidea, and A. aurantii was more closely related to Aphis craccivora than to Aphis gossypii.

Tandem repeats of the 5′ flanking region of human MUC5AC have a role as a novel enhancer in MUC5AC gene expression

MUC5AC is a well-known gastric differentiation marker, which has been frequently used for the classification of stomach cancer. However, the molecular mechanism of regulation of MUC5AC expression remains to be elucidated. In previous studies, we have shown that Gli regulated MUC5AC transcription through the Gli-binding motif in the 5′ region of MUC5AC. Gli played important roles, but independently was not sufficient for MUC5AC expression. In this study, we analyzed a 4010 bp fragment of the 5′-flanking promoter region of the human MUC5AC gene by luciferase assay, and found a novel distal enhancer region located between −1434 bp to −3000 bp upstream from the first ATG initiation codon. This region is composed of repetitive DNA sequences 5′-TCACTCAC-3′. The strength of enhancer activities depended on the length of the repetitive region. The tandem repeats are conserved among primates, but not in other mammals. The tandem repeat regions enhanced promoter activities not only of MUC5AC but also of other genes. The enhancer effect of the tandem repeat regions was maintained even when inverted. ChIP analysis revealed that H3K9me3 binds to the tandem repeat regions. Together, our results suggest that the tandem repeat region in the MUC5AC promoter has the potential to act as a strong enhancer, and H3K9me3 may contribute to histone modifications of this region.

The Complete Mitochondrial Genome of Terapon jarbua (Centrarchiformes: Terapontidae) and Comparative Analysis of the Control Region among Eight Centrarchiformes Species

In this article, we determined and described the complete mitochondrial genome of Terapon jarbua, which is 16 664 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, one origin of replication on the light-strand (OL), and a putative control region (CR). The gene order and the base composition of T. jarbua mitogenome are similar to that of most other vertebrates. The overall base composition is 27.5% A, 26.0% T, 29.9% C, 16.6% G, respectively, with a slight AT bias (53.5%). All the protein-coding genes use the initiation codon ATG except COI use GTG. Most of them have TAA or TAG as the stop codon, except COII and ND4 use AGA, COIII and Cyt b use an incomplete stop codon TA and T, respectively. In order to further explore the structure of CR in Centrarchiformes, eight CR sequences from representative species were compared. Like that of other teleosts, the CR of the Centrarchiformes is also partitioned into three domains, including the termination associated sequence (TAS), the central conserved sequence blocks (CSB-E, D, B and A), and the conserved sequence blocks (CSB-2 and 3). We hope these results will provide consensus sequences of the conserved units of the CR in Centrarchiformes genomes, as well as useful molecular information for phylogenetic studies of Centrarchiformes.

The complete mitochondrial genome of Stolephorus insularis (Clupeiformes: Engraulidae) and phylogenetic studies of Engraulidae

The complete mitochondrial genome of this species was first determined in this study. We describe the complete mitogenome of Stolephorus insularis in this study. The mitogenome is 16711 nucleotides long and contains 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two main non-coding regions. The overall base composition includes A (28.0%), C (26.8%), T (27.8%), and G (17.4%). Furthermore, the 13 PCGs encode 3624 amino acids in total. All the PCGs use the initiation codon ATG except COI uses GTG, most of them have TAA or TAG as the stop codon, except three PCGs (COII, ND4, and Cytb) use an incomplete stop codon T. The phylogenetic tree based on the neighbour-joining method was constructed to provide relationship within Engraulidae, which could be a useful basis for management of this species.

Complete mitochondrial genome of Buffon’s river garfish Zenarchopterus buffonis (Valenciennes, 1847)

The complete mitochondrial genome of Buffon’s river garfish Zenarchopterus buffonis from South China Sea has been obtained for the first time. It is 16,462 bp long, and contains 21 tRNA genes, 2 rRNA genes, 13 protein-coding genes (PCGs), and 1 control region. The overall base composition is significantly biased (A, G, T, and C was 33%, 12.94%, 29.78%, and 24.27%, respectively) with A + T contents of 62.79%. In total, most PCGs use the initiation codon ATG except COX1 uses GTG. Seven PCGs have a complete codon TAA or TAG, whereas the other six genes end with the incomplete stop codon T–– or TA–. Phylogenetic analysis showed that Z. buffonis forms a monophyletic cluster with the species of Belonidae, Zenarchopteridae, and Sconberesocidae.

Complete mitochondrial genome of Myersina filifer (Gobiiformes, Gobiidae) and phylogenetic analysis of Gobiidae

The complete mitogenome of Myersina filifer was sequenced, which is a closed double-stranded circular molecule of 16,505 bp, we analyzed the main features in terms of the genome organization, gene arrangement, and codon usage. The overall base composition includes A(27.4%), C(28.0%), T(27.1%) and G(17.5%). Moreover, the 13 protein-coding genes (PCGs) encode 3801 amino acids in total, 12 of which use the initiation codon ATG except COI uses GTG, most of them have a complete stop codon, whereas four PCGs end with the incomplete stop codon TA– or a single T. The phylogenetic tree based on the Neighbor-Joining method was conducted to provide relationship within Gobiidae, the NJ tree demonstrated that M. filifer has the closest relationship with M. macrostoma, which contributed to phylogenetic studies of Gobiidae and additional information of management for this species.

The complete mitochondrial genome of Sardinella fijiensis (Clupeiformes: clupeidae) and phylogenetic studies of clupeidae

The complete mitochondrial genome of Sardinella fijiensis was determined in this study, which was 16,651bp long, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region and one origin of replication on the light-strand. The overall base composition includes C (29.4%), A (26.4%), T (24.7%), and G (19.5%). Moreover, the 13 PCGs encode 3799 amino acids in total, 12 of which use the initiation codon ATG except COI uses GTG, most of them have complete stop codon, whereas three protein-coding genes (COII, ND4, and Cytb) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Clupeidae, which could be a useful basis for the further understanding of this species.

The complete mitochondrial genome of the Adonis ladybird, Hippodamia variegata (Coleoptera: Coccinellidae)

Hippodamia variegata is an important predator of aphid pests. In this study, we determined the complete mitochondrial genome (mitogenome) of H. variegata. The mitogenome is 17,823 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one non-coding control region. Initiation codons ATA, ATG, ATT, and AAT were identified in two, five, five, and one PCGs, respectively, whereas stop codons TAA or TAG were found in eight genes except for five genes which use incomplete stop codon T–. The phylogenetic analysis indicated that three species in Hippodamia (H. variegata, H. convergens, and H. undecimnotata) were closely related and had a close relationship with the genus Harmonia.

Complete mitochondrial genome sequence for the seahorse adulteration Hippocampus camelopardalis Bianconi 1854

In the study, we report the complete mitochondrial genome of giraffe seahorse, Hippocampus camelopardalis Bianconi, 1854. The genome of H. camelopardalis is found to be 16,523 bp in length, containing 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a control region (D-loop). The overall base composition of H. camelopardalis is 32.46% for A, 23.54% for C, 14.54% for G, and 29.46% for T, respectively. All PCGs use the typical initiation codon ATG, except for COX1 that uses GTG. The lengths of 12S rRNA and 16S rRNA were 939 and 1685 bp, respectively. Phylogenetic analysis results showed that H. camelopardalis is closely related to the Jayakar’s seahorse H. jayakari. The complete mitochondrial genome of Hippocampus camelopardalis provided essential and important molecular data for evolutionary analysis of genus Hippocampus.

Characterization of the complete mitochondrial genome of Eriocheir leptognathus with phylogenetic analysis

Eriocheir leptognathus is a dominant species in the Yangtze River estuary. In this study, we first determined the complete mitochondrial genome (mitogenome) of E. leptognathus. The mitogenome is 16,143 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one non-coding control region. Initiation codons ATG and ATT were identified in eight and four PCGs, respectively, while stop codons TAA or TAG were found in eleven genes except for two genes which use incomplete stop codon T–. The phylogenetic analysis indicated that three species (E. hepuensis, E.japonica, E. sinensis) and E. leptognathus are very closely related. The complete mitogenome of E. leptognathus can provide population genetics information to further explore the taxonomic status of this species.

Characterization of a strong and constitutive promoter from the Arabidopsis serine carboxypeptidase-like gene AtSCPL30 as a potential tool for crop transgenic breeding

BackgroundTransgenic technology has become an important technique for crop genetic improvement. The application of well-characterized promoters is essential for developing a vector system for efficient genetic transformation. Therefore, isolation and functional validation of more alternative constitutive promoters to the CaMV35S promoter is highly desirable.ResultsIn this study, a 2093-bp sequence upstream of the translation initiation codon ATG of AtSCPL30 was isolated as the full-length promoter (PD1). To characterize the AtSCPL30 promoter (PD1) and eight 5′ deleted fragments (PD2-PD9) of different lengths were fused with GUS to produce the promoter::GUS plasmids and were translocated into Nicotiana benthamiana. PD1-PD9 could confer strong and constitutive expression of transgenes in almost all tissues and development stages in Nicotiana benthamiana transgenic plants. Additionally, PD2-PD7 drove transgene expression consistently over twofold higher than the well-used CaMV35S promoter under normal and stress conditions. Among them, PD7 was only 456 bp in length, and its transcriptional activity was comparable to that of PD2-PD6. Moreover, GUS transient assay in the leaves of Nicotiana benthamiana revealed that the 162-bp (− 456~ − 295 bp) and 111-bp (− 294~ − 184 bp) fragments from the AtSCPL30 promoter could increase the transcriptional activity of mini35S up to 16- and 18-fold, respectively.ConclusionsAs a small constitutive strong promoter of plant origin, PD7 has the advantage of biosafety and reduces the probability of transgene silencing compared to the virus-derived CaMV35S promoter. PD7 would also be an alternative constitutive promoter to the CaMV35S promoter when multigene transformation was performed in the same vector, thereby avoiding the overuse of the CaMV35S promoter and allowing for the successful application of transgenic technology. And, the 162- and 111-bp fragments will also be very useful for synthetic promoter design based on their high enhancer activities.

The complete genome of Cyprinid herpesvirus 2, a new strain isolated from Allogynogenetic crucian carp

The haemorrhagic disease of the gill is caused by Cyprinid herpesvirus 2 (CyHV2) infection, which often results in the severe economic losses in the farm of Allogynogenetic crucian carp (ACC). In this study, the genome of CyHV2 strain CyHV2-SY (SY) collected from Sheyang County, Jiangsu Province, China was sequenced. The complete genome of SY is at length of 290,455 bp with 154 potential open reading frames (ORFs) and a terminal direct repeat (TR) of 15,353 bp. Many variations were found by comparison the sequenced CyHV2 genomes. The ORF10, ORF107, ORF156 of SY genome have insertions or deletions of repeat sequences compared with ST-J1 and SY-C1, which may be used as the marks of SY strains. Besides, the promoter sequence analysis showed that 13 of the 150 ORFs have TATA-box elements and 119 of the 150 ORFs have SP1 cis-acting elements in the promoter region (350 bp upstream sequence of the initiation codon ATG). Twenty-eight viral miRNAs candidates were predicted in the CyHV2 genome and expression of 24 virogenes may be regulated by viral miRNAs. Horizontal transfer analysis indicated that 16 and 2 genes in the CyHV2 genome may transfer from the host and bacteria, respectively. By the genome sequencing and sequence mining, our results provided more new clues to further understand CyHV2 genome.

The complete mitochondrial genome of Lagocephalus sceleratus (Tetraodontiformes; Tetraodontidae) and phylogenetic studies of Tetraodontidae

The complete mitochondrial genome sequence of Lagocephalus sceleratus was determined. The complete mitochondrial genome was 16,444 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding region (the control region and the origin of light strand replication). The overall base composition was A 27.59%, C 31.43%, G 17.12%, T 23.85%. All protein-coding genes started with an ATG initiation codon, except COI used GTG. With the exception of ND6 and eight tRNA genes, all other genes were encoded on the heavy strand. Additionally, the phylogenetic relationship of 37 Tetraodontidae species based on the complete genome was analyzed, and the result showed that L. sceleratus was clustered with other Lagocephalus species. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Tetraodontidae.