共查询到20条相似文献,搜索用时 31 毫秒
1.
2.
3.
4.
Alterations of the three short open reading frames in the Rous sarcoma virus leader RNA modulate viral replication and gene expression. 总被引:5,自引:4,他引:1
下载免费PDF全文
![点击此处可从《Journal of virology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
The Rous sarcoma virus (RSV) leader RNA has three short open reading frames (ORF1 to ORF3) which are conserved in all avian sarcoma-leukosis retroviruses. Effects on virus propagation were determined following three types of alterations in the ORFs: (i) replacement of AUG initiation codons in order to prohibit ORF translation, (ii) alterations of the codon context around the AUG initiation codon to enhance translation of the normally silent ORF3, and (iii) elongation of the ORF coding sequences. Mutagenesis of the AUG codons for ORF1 and ORF2 (AUG1 and AUG2) singly or together delayed the onset of viral replication and cell transformation. In contrast, mutagenesis of AUG3 almost completely suppressed these viral activities. Mutagenesis of ORF3 to enhance its translation inhibited viral propagation. When the mutant ORF3 included an additional frameshift mutation which extended the ORF beyond the initiation site for the gag, gag-pol, and env proteins, host cells were initially transformed but died soon thereafter. Elongation of ORF1 from 7 to 62 codons led to the accumulation of transformation-defective virus with a delayed onset of replication. In contrast, viruses with elongation of ORF1 from 7 to 30 codons, ORF2 from 16 to 48 codons, or ORF3 from 9 to 64 codons, without any alterations in the AUG context, exhibited wild-type phenotypes. These results are consistent with a model that translation of the ORFs is necessary to facilitate virus production. 相似文献
5.
6.
Gerhard Miksch W. Arnold P. Lentzsch U. B. Priefer A. Pühler 《Molecular & general genetics : MGG》1994,242(5):539-550
7.
Alain J. Kemp Russell Betney Luca Ciandrini Alexandra C. M. Schwenger M. Carmen Romano Ian Stansfield 《Molecular microbiology》2013,87(2):284-300
In Saccharomyces cerevisiae, the SUP70 gene encodes the CAG‐decoding tRNAGlnCUG. A mutant allele, sup70‐65, induces pseudohyphal growth on rich medium, an inappropriate nitrogen starvation response. This mutant tRNA is also a UAG nonsense suppressor via first base wobble. To investigate the basis of the pseudohyphal phenotype, 10 novel sup70 UAG suppressor alleles were identified, defining positions in the tRNAGlnCUG anticodon stem that restrict first base wobble. However, none conferred pseudohyphal growth, showing altered CUG anticodon presentation cannot itself induce pseudohyphal growth. Northern blot analysis revealed the sup70‐65 tRNAGlnCUG is unstable, inefficiently charged, and 80% reduced in its effective concentration. A stochastic model simulation of translation predicted compromised expression of CAG‐rich ORFs in the tRNAGlnCUG‐depleted sup70‐65 mutant. This prediction was validated by demonstrating that luciferase expression in the mutant was 60% reduced by introducing multiple tandem CAG (but not CAA) codons into this ORF. In addition, the sup70‐65 pseudohyphal phenotype was partly complemented by overexpressing CAA‐decoding tRNAGlnUUG, an inefficient wobble‐decoder of CAG. We thus show that introducing codons decoded by a rare tRNA near the 5′ end of an ORF can reduce eukaryote translational expression, and that the mutant tRNACUGGln constitutive pseudohyphal differentiation phenotype correlates strongly with reduced CAG decoding efficiency. 相似文献
8.
Nucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants
Wei Dan Yan Jin Zizhong Tang Yongmin Li 《Journal of biomolecular structure & dynamics》2020,38(16):4764-4773
AbstractNorovirus GII.4 variants, a genotype in genogroup II belonging to the genus Norovirus, is a single-strand positive sense RNA containing three open reading frames (ORF1, ORF2 and ORF3) and is the most important pathogen causing nonbacterial gastroenteritis outbreaks. By using bioinformatic softwares such as Codon W, SPSS and so on, a total of 292 strains of the viruses isolated from 1974 to 2016 were analyzed for nucleotide composition and synonymous codon usage in each ORF. The result shows that it is enriched for A over the other bases in nucleotide composition, G behind the other bases in the 3rd site of all synonymous codons in the three ORFs. The patterns of nucleotide composition and codon bias of ORF2 are similar to those of ORF3 and different from those of ORF1. There are generally UpA motif and CpG motif in the codons with the lowest proportion. Correspondence analysis indicates that the codon usage may be changing over a certain time period for ORF1 in 2006 and 2012, ORF2 in 2012, and ORF3 in 2013. ENC (effective number of codons) plot and other analyses indicate that both natural selection and mutational pressure play partly roles in the ORFs, but natural selection is more important for ORF2 and ORF3. Besides, we also found all optimal codons in the ORFs. The study provides a basic understanding of the mechanism for norovirus GII.4 codon usage bias. Abbreviations ORF Open Reading Frame ENC Effective Number of Codons COA correspondence analysis RSCU Relative Synonymous Codon Usage CAI Codon Adaptation Index CBI Codon Bias Index Fop frequency of optimal codons L_sym number of synonymous codons L_aa length amino acids GRAVY grand average of hydropathicity Aroma aromaticity Communicated by Ramaswamy H. Sarma 相似文献
9.
10.
Patricia B. Lodato Ping‐Kun Hsieh Joel G. Belasco James B. Kaper 《Molecular microbiology》2012,86(5):1167-1182
Enterohaemorrhagic Escherichia coli harbours a pathogenicity island encoding a type 3 secretion system used to translocate effector proteins into the cytosol of intestinal epithelial cells and subvert their function. The structural proteins of the translocon are encoded in a major espADB mRNA processed from a precursor. The translocon mRNA should be highly susceptible to RNase E cleavage because of its AU‐rich leader region and monophosphorylated 5′‐terminus, yet it manages to avoid rapid degradation. Here, we report that the espADB leader region contains a strong Shine–Dalgarno element (SD2) and a translatable mini‐ORF of six codons. Disruption of SD2 so as to weaken ribosome binding significantly reduces the concentration and stability of esp mRNA, whereas codon substitutions that impair translation of the mini‐ORF have no such effect. These findings suggest that occupancy of SD2 by ribosomes, but not mini‐ORF translation, helps to protect espADB mRNA from degradation, likely by hindering RNase E access to the AU‐rich leader region. 相似文献
11.
Jing Wang Le Yang Dan Wang Lichun Dong Rachel Chen 《Journal of industrial microbiology & biotechnology》2016,43(4):505-516
In this study, a novel engineering Escherichia coli strain (CBMG111) with the expression of mgtCB gene was constructed for the enhanced fermentative production of succinic acid by utilizing the synergetic effect of mgtC gene to improve the growth of strains at the environment of low Mg2+ concentration and mgtB to enhance the transport of Mg2+ into cells. After the effect of the expression of the individual genes (mgtA, mgtB, mgtC) on the growth of E. coli was clarified, the fermentative production of succinic acid by CBMG111 was studied with the low-price mixture of Mg(OH)2 and NH3·H2O as the alkaline neutralizer and the biomass hydrolysates as the carbon sources, which demonstrated that the expression of mgtCB gene can significantly increase the productivity of succinic acid (2.97 g L?1 h?1) compared with that by using the engineering strain with the overexpression of mgtA gene. 相似文献
12.
Gerhard Miksch W. Arnold P. Lentzsch U. B. Priefer A. Pühler 《Molecular genetics and genomics : MGG》1994,242(5):539-550
13.
Banana streak virus (BSV), a member of genus Badnavirus, is a causal agent of banana streak disease throughout the world. The genetic diversity of BSVs from different regions of
banana plantations has previously been investigated, but there are relatively few reports of the genetic characteristic of
episomal (non-integrated) BSV genomes isolated from China. Here, the complete genome, a total of 7722bp (GenBank accession
number DQ092436), of an isolate of Banana streak virus (BSV) on cultivar Cavendish (BSAcYNV) in Yunnan, China was determined. The genome organises in the typical manner of badnaviruses.
The intergenic region of genomic DNA contains a large stem-loop, which may contribute to the ribosome shift into the following
open reading frames (ORFs). The coding region of BSAcYNV consists of three overlapping ORFs, ORF1 with a non-AUG start codon
and ORF2 encoding two small proteins are individually involved in viral movement and ORF3 encodes a polyprotein. Besides the
complete genome, a defective genome lacking the whole RNA leader region and a majority of ORF1 and which encompasses 6525bp
was also isolated and sequenced from this BSV DNA reservoir in infected banana plants. Sequence analyses showed that BSAcYNV
has closest similarity in terms of genome organization and the coding assignments with an BSV isolate from Vietnam (BSAcVNV).
The corresponding coding regions shared identities of 88% and ∼95% at nucleotide and amino acid levels, respectively. Phylogenetic
analysis also indicated BSAcYNV shared the closest geographical evolutionary relationship to BSAcVNV among sequenced banana
streak badnaviruses. 相似文献
14.
15.
16.
17.
The mitochondrial genome (mtDNA) of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae, with a total size of 24,673 bp, was one of the smallest known mtDNAs of Pezizomycotina. It contained the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, a single intron that harbored an intronic ORF coding for a putative ribosomal protein (rps) within the large rRNA gene (rnl), and a set of 24 tRNA genes which recognized codons for all amino acids, except proline and valine. Gene order comparison with all known mtDNAs of Sordariomycetes illustrated a highly conserved genome organization for all the protein- and rRNA-coding genes, as well as three clusters of tRNA genes. By considering all mitochondrial essential protein-coding genes as one unit a phylogenetic study of these small genomes strongly supported the common evolutionary course of Sordariomycetes (100% bootstrap support) and highlighted the advantages of analyzing small genomes (mtDNA) over single genes. In addition, comparative analysis of three intergenic regions demonstrated sequence variability that can be exploited for intra- and inter-specific identification of Metarhizium.
Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. 相似文献
18.
19.
20.