Structure Of Open Reading Frame Research Articles

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae.

The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.

Chromatin reassembly following RNA polymerase II transcription

During the process of transcription elongation, the chromatin structure of transcribed sequences can be perturbed, exposing cryptic promoter-like sequences within the body of transcribed genes to function as initiation sites. Re-establishing a stable repressive structure of open reading frames requires histone chaperones, methyltransferases, deacetylases and chromatin remodeling complexes. The Set2/Rpd3S pathway is used by elongating RNA polymerase II to signal for histone deacetylation in its wake. Set2 associates with the elongating form of RNA polymerase II and co-transcriptionally methylates histone H3K36. H3K36 is recognized by the Rpd3S deacetylase complex to deacetylate histones in transcribed sequences. In recent work, we have found that a major source of cotranscriptional histone acetylation is the incorporation of soluble, Rtt109 H3K56-acetylated histones by the Asf1 histone chaperone. Set2 methylation of H3K36 promotes retention of the original histones and suppresses the incorporation of soluble histones by Asf1. By identifying factors that interact with H3K36 methylated nucleosomes, we have found that chromatin remodeling is also required to stabilize the chromatin structures of open reading frames following transcription elongation. Our studies identified the ATP-dependent chromatin remodelers Isw1 and Chd1 as two factors involved in this pathway as deletion of ISW1 and CHD1 enhanced the cryptic transcript phenotype caused by set2. Moreover, loss of ISW1 and CHD1 also enhanced the incorporation of new histones from the soluble pool into chromatin. Thus, retention of original histones, deacetylation of any new ones and their organization by chromatin remodeling are all required to re-establish stable chromatin resistant to cryptic transcription initiation.

Complete Genome Sequences of Two Chinese Virulent Avian Coronavirus Infectious Bronchitis Virus Variants

Avian coronavirus infectious bronchitis virus (IBV) is variable, which causes many serotypes. Here we reported the complete genome sequences of two virulent IBV variants from China, GX-YL5 and GX-YL9, belonging to different serotypes. Differences between GX-YL5 and GX-YL9 were found mainly in stem-loop structure I in the predicted RNA secondary structure of open reading frame (ORF) 1b and the S protein gene fusion region, which will help us understand the molecular evolutionary mechanism of IBV and the disconcordance between the genotypes and serotypes of coronavirus.

Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations

BackgroundCodon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution.Methodologies/Principal FindingsHere we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases.ConclusionsSince in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli and for decoding efficiency in mammalian cells, our data support the hypothesis that, like codon usage, codon context modulates the evolution of gene primary structure and fine tunes the structure of open reading frames for high genome translational fidelity and efficiency in the 3 domains of life.

Open reading frame structure analysis as a novel genotyping tool for hepatitis E virus and the subsequent discovery of an inter-genotype recombinant

Accurate viral genotyping is important. Here I investigate genotypes in hepatitis E virus (HEV) and find that the open reading frame (ORF) structure (the lengths of three ORFs and the overlapping relationships among the ORFs) can be a good criterion for genotyping HEV. An inter-genotype recombinant (GenBank accession no. DQ450072) was revealed by analysing the ORF structure and confirmed by phylogenetic analyses. This discovery of the inter-genotype recombinant indicates that genotyping in HEV should be based on full-length sequences. The Mexican strain which is currently classified as a genotype 2 strain also exhibited the mosaic sequence pattern, although without statistical support.

Full-genome analysis of a highly divergent simian T-cell lymphotropic virus type 1 strain in Macaca arctoides

Full-genome sequencing and analysis of the highly divergent simian T-cell lymphotropic virus type 1 (STLV-1) strain MarB43 in Macaca arctoides indicated that its open reading frame structure is compatible with proper functioning of its Gag, Pol, Env, Tax and Rex proteins. Detailed analysis of the coding potential, however, revealed that MarB43 is probably forced to use the human T-cell lymphotropic virus type 2/STLV-2 env-tax-rex splice-acceptor homologue and that the proximal pX auxiliary proteins p12(I), p13(II), p30(II) and p27(I) seem to have lost their function. Full-genome (gag-pol-env-tax), long terminal repeat and env phylogenetic analyses conclusively identified STLV-1 in M. arctoides as the currently most divergent STLV-1 strain. The long branching pattern of the monophyletic STLV-1 Macaca subspecies clades suggests that macaques might be the ancestral reservoir for primate T-cell lymphotropic virus type 1 in Asia. Full-genome molecular-clock analysis supports an archaic introduction of STLV-1 on the Asian continent, at least 269 000-156 000 years ago.

Primary structure of open reading frame 2 and 3 of the hepatitis E virus isolated from Morocco

The nucleotide sequence from position 5,014 to 7,186 of the hepatitis E virus (HEV) genome was determined using a set of 10 polymerase chain reaction (PCR) fragments amplified directly from a pool of fecal specimens obtained from patients with well-documented epidemic HEV infection in Morocco. This sequence contains the 3′-terminal region of open reading frame 1 (ORF1), full length ORF2 and ORF3, and a portion of the 3′-noncoding region. The HEV Morocco nucleotide sequence was compared with the corresponding sequences of 13 HEV strains. A region of ORF2 that overlaps with ORF3 was found to be the most conserved region of ORF2, whereas a protein segment encoded by this region was found to be the most variable. Theoretical RNA secondary structure analysis predicted that this region may be folded into a strong secondary structure that may constrain nucleotide sequence variability. In addition, the nucleotide sequence comparison revealed that the HEV Morocco sequence is most homologous to the sequences of the HEV Asian strains compared with the HEV Mexico, swine, and US strains. Phylogenetic analysis performed on the entire ORF2 and ORF3 sequences and on a small fragment of ORF2 allowed classification of the HEV Morocco strain together with a few other known African strains as a separate subtype within the Asian–African genotype. J. Med. Virol. 57:126–133, 1999. Published 1999 Wiley-Liss, Inc.

Primary structure of open reading frame 2 and 3 of the hepatitis E virus isolated from Morocco

The nucleotide sequence from position 5,014 to 7,186 of the hepatitis E virus (HEV) genome was determined using a set of 10 polymerase chain reaction (PCR) fragments amplified directly from a pool of fecal specimens obtained from patients with well-documented epidemic HEV infection in Morocco. This sequence contains the 3'-terminal region of open reading frame 1 (ORF1), full length ORF2 and ORF3, and a portion of the 3'-noncoding region. The HEV Morocco nucleotide sequence was compared with the corresponding sequences of 13 HEV strains. A region of ORF2 that overlaps with ORF3 was found to be the most conserved region of ORF2, whereas a protein segment encoded by this region was found to be the most variable. Theoretical RNA secondary structure analysis predicted that this region may be folded into a strong secondary structure that may constrain nucleotide sequence variability. In addition, the nucleotide sequence comparison revealed that the HEV Morocco sequence is most homologous to the sequences of the HEV Asian strains compared with the HEV Mexico, swine, and US strains. Phylogenetic analysis performed on the entire ORF2 and ORF3 sequences and on a small fragment of ORF2 allowed classification of the HEV Morocco strain together with a few other known African strains as a separate subtype within the Asian-African genotype.