Programmed −1 ribosomal frameshifting in the SARS coronavirus

2004 ◽  
Vol 32 (6) ◽  
pp. 1081-1083 ◽  
Author(s):  
F. Dos Ramos ◽  
M. Carrasco ◽  
T. Doyle ◽  
I. Brierley
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Causative Agent ◽  
Open Reading Frames ◽  
Replication Proteins ◽  
Ribosomal Frameshifting ◽  
Cis Acting ◽  
Alternate Mechanism ◽  
Novel Coronavirus ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Programmed −1 ribosomal frameshifting is an alternate mechanism of translation used by coronavirus to synthesize replication proteins encoded by two overlapping open reading frames. For some coronaviruses, the mRNA cis-acting stimulatory structures involved in this process have been characterized, but their precise contribution to ribosomal frameshifting is not completely understood. Recently, a novel coronavirus was identified as the causative agent of the severe acute respiratory syndrome. This review describes the mRNA motifs involved in programmed −1 ribosomal frameshifting in this virus.

scholarly journals Bias between the Left and Right Inverted Repeats during IS911 Targeted Insertion

2008 ◽  
Vol 190 (18) ◽  
pp. 6111-6118 ◽  
Author(s):  
P. Rousseau ◽  
C. Loot ◽  
C. Turlan ◽  
S. Nolivos ◽  
M. Chandler
Keyword(s):  
Insertion Sequence ◽  
Regulatory Protein ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Functional Differences ◽  
Left And Right ◽  
Ordered Assembly ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

ABSTRACT IS911 is a bacterial insertion sequence composed of two consecutive overlapping open reading frames (ORFs [orfA and orfB]) encoding the transposase (OrfAB) as well as a regulatory protein (OrfA). These ORFs are bordered by terminal left and right inverted repeats (IRL and IRR, respectively) with several differences in nucleotide sequence. IS911 transposition is asymmetric: each end is cleaved on one strand to generate a free 3′-OH, which is then used as the nucleophile in attacking the opposite insertion sequence (IS) end to generate a free IS circle. This will be inserted into a new target site. We show here that the ends exhibit functional differences which, in vivo, may favor the use of one compared to the other during transposition. Electromobility shift assays showed that a truncated form of the transposase [OrfAB(1-149)] exhibits higher affinity for IRR than for IRL. While there was no detectable difference in IR activities during the early steps of transposition, IRR was more efficient during the final insertion steps. We show here that the differential activities between the two IRs correlate with the different affinities of OrfAB(1-149) for the IRs during assembly of the nucleoprotein complexes leading to transposition. We conclude that the two inverted repeats are not equivalent during IS911 transposition and that this asymmetry may intervene to determine the ordered assembly of the different protein-DNA complexes involved in the reaction.

Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

2021 ◽  
Author(s):  
Yang Sun ◽  
Yan qiong Li ◽  
Wen han Dong ◽  
Ai li Sun ◽  
Ning wei Chen ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Rna Virus ◽  
Dsrna Virus ◽  
Open Reading Frames ◽  
The Family ◽  
Significant Amino Acid Sequence ◽  
Overlapping Open Reading Frames ◽  
Significant Amino Acid ◽  
Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

scholarly journals Genome Sequences of Two Dual-Serotype-Specific Echovirus 20 Strains from Nigeria

2019 ◽  
Vol 8 (43) ◽  
Author(s):  
T. O. C. Faleye ◽  
O. M. Adewumi ◽  
D. Klapsa ◽  
M. Majumdar ◽  
J. Martin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Complete Genome ◽  
Neutralization Assay ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Here, we describe nearly complete genome sequences (7,361 nucleotides [nt] and 6,893 nt) of two echovirus 20 (E20) isolates from Nigeria that were simultaneously typed as CVB and E20 (dual serotype) by neutralization assay. Both include two overlapping open reading frames (ORFs) of 67 and 2,183 amino acids that encoded a recently described gut infection-facilitating protein and the classic enterovirus proteins, respectively.

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals Overexpression of 7a, a Protein Specifically Encoded by the Severe Acute Respiratory Syndrome Coronavirus, Induces Apoptosis via a Caspase-Dependent Pathway

2004 ◽  
Vol 78 (24) ◽  
pp. 14043-14047 ◽  
Author(s):  
Yee-Joo Tan ◽  
Burtram C. Fielding ◽  
Phuay-Yee Goh ◽  
Shuo Shen ◽  
Timothy H. P. Tan ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Cell Lines ◽  
Cellular Localization ◽  
Viral Proteins ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Dependent Pathway ◽  
Reading Frames ◽  
Viral Structural Proteins

ABSTRACT Besides genes that are homologous to proteins found in other coronaviruses, the severe acute respiratory syndrome coronavirus genome also contains nine other potential open reading frames. Previously, we have characterized the expression and cellular localization of two of these “accessory” viral proteins, 3a (previously termed U274) and 7a (previously termed U122). In this study, we further examined whether they can induce apoptosis, which has been observed clinically. We showed that the overexpression of 7a, but not of 3a or the viral structural proteins, nucleocapsid, membrane, and envelope, induces apoptosis. 7a induces apoptosis via a caspase-dependent pathway and in cell lines derived from different organs, including lung, kidney, and liver.

scholarly journals Mapping the Non-Structural Transmembrane Proteins of SARS-CoV-2

2020 ◽  
Author(s):  
Sunil Thomas
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Drug Targets ◽  
Transmembrane Proteins ◽  
Host Immunity ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Wild Animals ◽  
Cell Organelles ◽  
Enveloped Virus ◽  
Reading Frames

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the disease COVID-19 has wreaked havoc on the health and economy of humanity. In addition, the disease is observed in domestic and wild animals. The disease has impacted directly and indirectly every corner of the planet. Currently, there are no vaccines and effective therapies for COVID-19. SARS-CoV-2 is an enveloped virus with a single-stranded RNA genome of 29.8 kb. More than two-thirds of the genome comprises Orf1ab encoding 16 non-structural proteins (nsps) followed by mRNAs encoding structural proteins, spike (S), envelop (E), membrane (M), and nucleocapsid (N). These genes are interspaced with several accessory genes (open reading frames [Orf] 3a, 3b, 6, 7a, 7b, 8, 9b, 9c and 10). The functions of these proteins are of particular interest for understanding the pathogenesis of SARS-CoV-2. Several of the nsps (nsp3, nsp4, nsp6) and Orf3a are transmembrane proteins involved in regulating the host immunity, modifying host cell organelles for viral replication and escape and hence considered drug targets. In this paper we report mapping the transmembrane structure of the non-structural proteins of SARS-CoV-2.

scholarly journals ICTV Virus Taxonomy Profile: Redondoviridae

2020 ◽  
Author(s):  
Arwa Abbas ◽  
Louis J. Taylor ◽  
Ronald G. Collman ◽  
Frederic D. Bushman ◽  
Keyword(s):  
Critical Illness ◽  
Causative Agent ◽  
Human Subjects ◽  
International Committee ◽  
Open Reading Frames ◽  
Metagenomic Sequencing ◽  
Virus Taxonomy ◽  
Single Stranded Dna ◽  
The Family ◽  
Reading Frames

Viruses in the family Redondoviridae have a circular genome of 3.0 kb with three open reading frames. The packaged genome is inferred to be single-stranded DNA by analogy to related viruses. Redondoviruses were discovered through metagenomic sequencing methods in samples from human subjects and are inferred to replicate in humans. Evidence of redondovirus infection is associated with periodontitis and critical illness, but redondoviruses have not been shown to be the causative agent of any diseases. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Redondoviridae, which is available at ictv.global/report/redondoviridae.

scholarly journals Cloning, Sequencing, and Characterization of thecgmB Gene of Sinorhizobium meliloti Involved in Cyclic β-Glucan Biosynthesis

1999 ◽  
Vol 181 (15) ◽  
pp. 4576-4583 ◽  
Author(s):  
Ping Wang ◽  
Cheryl Ingram-Smith ◽  
Jill A. Hadley ◽  
Karen J. Miller
Keyword(s):  
Sinorhizobium Meliloti ◽  
Rhizobium Leguminosarum ◽  
Genomic Library ◽  
Rhizobium Meliloti ◽  
Functional Expression ◽  
Open Reading Frames ◽  
Inverse Pcr ◽  
Insertion Mutant ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

ABSTRACT Periplasmic cyclic β-glucans of Rhizobium species provide important functions during plant infection and hypo-osmotic adaptation. In Sinorhizobium meliloti (also known asRhizobium meliloti), these molecules are highly modified with phosphoglycerol and succinyl substituents. We have previously identified an S. meliloti Tn5 insertion mutant, S9, which is specifically impaired in its ability to transfer phosphoglycerol substituents to the cyclic β-glucan backbone (M. W. Breedveld, J. A. Hadley, and K. J. Miller, J. Bacteriol. 177:6346–6351, 1995). In the present study, we have cloned, sequenced, and characterized this mutation at the molecular level. By using the Tn5 flanking sequences (amplified by inverse PCR) as a probe, an S. meliloti genomic library was screened, and two overlapping cosmid clones which functionally complement S9 were isolated. A 3.1-kb HindIII-EcoRI fragment found in both cosmids was shown to fully complement mutant S9. Furthermore, when a plasmid containing this 3.1-kb fragment was used to transformRhizobium leguminosarum bv. trifolii TA-1JH, a strain which normally synthesizes only neutral cyclic β-glucans, anionic glucans containing phosphoglycerol substituents were produced, consistent with the functional expression of an S. meliloti phosphoglycerol transferase gene. Sequence analysis revealed the presence of two major, overlapping open reading frames within the 3.1-kb fragment. Primer extension analysis revealed that one of these open reading frames, ORF1, was transcribed and its transcription was osmotically regulated. This novel locus of S. meliloti is designated thecgm (cyclic glucan modification) locus, and the product encoded by ORF1 is referred to as CgmB.

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