RESUMO
Nucleotide and codon usage are typically examined to investigate viral evolution. In this study, we analyzed the genetic information of 46 strains of classical swine fever virus (CSFV) RNA, nucleotide usage in the internal ribosome entry site (IRES), the nucleotide context surrounding the initiation codon, and synonymous codon usage in the translation initiation region. Phylogenetic analysis of the IRES element indicated that the genetic diversity of this element is generally similar to the phylogenetic clusters of CSFV genotypes. Nucleotides surrounding the initiation codon of CSFV RNA were generally more stable (ACAUGGCACAUGGAGUUG) compared to the internal AUG in the CSFV coding sequence. The second codon position after the initiation codon was generally selected to be GAG, which has lower tRNA abundance in pigs than its synonymous member (GAA). Regarding the synonymous codon usage bias in the CSFV translation initiation region, some codons showing low tRNA abundance in pigs are more frequently located in the translation initiation region than in the open reading frame of CSFV. Although CSFV, similarly to other RNA viruses, has a high mutation rate in nature, the regulatory features of nucleotide and synonymous codon usage of the IRES element, the nucleotide context surrounding the initiation codon and the translation initiation region in CSFV RNA have been 'branded' in the system of translation initiation to accommodate gene expression mediated by the cap-independent translation mechanism.
Assuntos
Vírus da Febre Suína Clássica/classificação , Vírus da Febre Suína Clássica/genética , RNA Viral/genética , Sequências Reguladoras de Ácido Ribonucleico , Animais , Vírus da Febre Suína Clássica/fisiologia , Códon de Iniciação , Evolução Molecular , Variação Genética , Filogenia , Biossíntese de Proteínas , RNA de Transferência/genética , Análise de Sequência de RNARESUMO
Adaptation in the overall codon usage pattern of West Nile virus (WNV) to that of two hosts was estimated based on the synonymous codon usage value (RSCU). Synonymous codon usage biases for the beginning coding sequence of this virus were also analyzed by calculating the usage fluctuation for each synonymous codon along the target region (the first 270 codon sites of the whole coding sequence of WNV). Adaptation of WNV to Anopheles gambiae regarding the overall codon usage revealed a mixture of synonymous codon usage patterns between this virus and its vector. Regarding the adaptation of WNV to its dead-end host and codon usage, although a mixture of overall codon usage patterns exists, the number of codons with reversed tendency codon usage is lower than that between the virus and its vector. In addition, some codons with low RSCU values for this virus are highly selected in the beginning translation region of WNV, while codons with low RSCU values in this region tend to pair with tRNAs present in low abundance in the host, suggesting that highly selected codons in a specific region in the beginning region of WNV are, to some degree, influenced by the corresponding low tRNA abundance of hosts to regulate the translation speed of the WNV polyprotein.
Assuntos
Códon , Fases de Leitura Aberta , RNA Viral , Vírus do Nilo Ocidental/genética , Interações Hospedeiro-Patógeno , RNA de TransferênciaRESUMO
MicroRNAs (miRNAs) are small non-coding RNA molecules that play key roles in the regulation of development processes of many tissues and organs at the post-transcriptional level. However, little is known about how they affect chicken gonadal development. We examined the expression of four miRNAs (miR-218, -200b, -196, and -206) in chicken embryonic gonads at embryonic days 3.5-6.5. Their target genes were predicted by miRDB, TargetScan and PicTar algorithms. The expression levels of these four miRNAs differed with sex to varying degrees; miR-200b was expressed at a significantly higher level in female gonads during the entire interval. The whole mount in situ hybridization result showed considerably higher expression of miR-200b in females than in males in E5.5 embryos. The miRNA target scanning results indicated several genes with functions in gonad development and gonad function. We conclude that miR-200b is involved in the regulation of gonad development and sexual differentiation of chicken embryos.
Assuntos
Regulação da Expressão Gênica no Desenvolvimento , MicroRNAs/biossíntese , Diferenciação Sexual/genética , Animais , Embrião de Galinha , Galinhas/genética , Feminino , Perfilação da Expressão Gênica , Gônadas/crescimento & desenvolvimento , Gônadas/metabolismo , Hibridização In Situ , Masculino , MicroRNAs/genética , Ovário/crescimento & desenvolvimento , Ovário/metabolismoRESUMO
The titin immunoglobulin domain (TTID) protein localizes to the Z line in muscle and binds to alpha-actinin and gamma-filamin. It plays an indispensable role in stabilizing and anchoring of thin filaments. In this study, the 5'-regulatory region of the porcine TTID gene was analyzed with bioinformatic methods. Another objective of this study was to further investigate the polymorphism in the intron 6 of the porcine TTID gene. We determined allele frequency among six Chinese porcine purebreds. The polymorphisms were genotyped in a population of 280 F2 pigs representing two Large White x Meishan reference families. Different TTID genotypes were significantly associated with carcass traits, including skin percentage (P < 0.05), loin eye area (P < 0.05), and average skin thickness (P < 0.01). Our study will continue to lay the groundwork for further investigations into the detailed function of the porcine TTID gene.
Assuntos
Composição Corporal , Conectina/genética , Estudos de Associação Genética/métodos , Região 5'-Flanqueadora , Criação de Animais Domésticos , Animais , Sequência de Bases , Frequência do Gene , Genótipo , Análise dos Mínimos Quadrados , Dados de Sequência Molecular , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , SuínosRESUMO
To analyze the synonymous codon usage patterns of sequence regions flanking cleavage sites in the hepatitis A virus (HAV) polyprotein, the codon usage bias at codon positions and the synonymous codon usage in the target contexts of 30 virus strains were estimated by two simple methods that were based on the values for relative synonymous codon usage. In addition, the pattern of synonymous codon usage was compared between the genomic sequences in HAV and those of its human host. Our results indicated that HAV adopts a combination of coincidence and antagonism with the synonymous codon usage in humans. This characteristic may help HAV to efficiently use the translational machinery in its human host. We also observed that codon usage exhibited a strong bias in some specific positions in these contexts, and that the underrepresented synonymous codons, CUA for Leu, ACG for Thr, GUA for Val, and UCG for Ser, are preferentially used in these positions. These underrepresented synonymous codons likely play roles in regulating the rate of protein translation and influencing the secondary structure of the sequence regions flanking the cleavage sites.