cis-Acting Elements within an RNA Coliphage Genome: Fold as You Please, but Fold You Must!!

Arora, Ruchi; Priano, Christine; Jacobson, Ann B.; Mills, Donald R.

doi:10.1006/jmbi.1996.0260

Cited by 29 publications

(22 citation statements)

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“…Induction of E. coli BL21(DE3) host transformants with IPTG results in transcription of the entire 4217 nucleotide Qb RNA plus-strand sequence. When wild-type Qb sequences are produced, an infectious cycle ensues during which mature Qb phage particles are generated and released upon lysis of the host (Mills et al, 1989(Mills et al, , 1990Priano et al, 1995;Arora et al, 1996).…”

Section: Resultsmentioning

confidence: 98%

Translational activation in coliphage qβ: on a polycistronic messenger RNA, repression of one gene can activate translation of another 1 1Edited by M. Gottesman

Priano

Arora

Jayant

et al. 1997

Journal of Molecular Biology

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Section: Resultsmentioning

confidence: 98%

Translational activation in coliphage qβ: on a polycistronic messenger RNA, repression of one gene can activate translation of another 1 1Edited by M. Gottesman

Priano

Arora

Jayant

et al. 1997

Journal of Molecular Biology

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“…Several elements have been described at the 3Ј end of RNA viral genomes that regulate viral gene expression (1,12). Poly(A) tails, for example, are known to be intimately involved in the control of mRNA turnover by degradation (2,11). In addition, AU-rich elements present at the 3Ј end of the RNAs are bound by a number of cellular and viral proteins that alter the stability and translation rate of the RNAs (8).…”

Section: Discussionmentioning

confidence: 99%

The 3′ End of Norwalk Virus mRNA Contains Determinants That Regulate the Expression and Stability of the Viral Capsid Protein VP1: a Novel Function for the VP2 Protein

Bertolotti-Ciarlet

Crawford

Hutson

et al. 2003

J Virol

186

133

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Norwalk virus (NV) is the prototype strain of a group of noncultivable human caliciviruses responsible for epidemic outbreaks of acute gastroenteritis. The capsid protein VP1 is synthesized from a subgenomic RNA that contains two open reading frames (ORFs), ORF2 and ORF3, and the 3 untranslated region (UTR). ORF2 and ORF3 code for the capsid protein (VP1) and a small structural basic protein (VP2), respectively. We discovered that the yields of virus-like particles (VLPs) composed of VP1 are significantly reduced when this protein is expressed from ORF2 alone. To determine how the 3 terminus of the NV subgenomic RNA regulates VP1 expression, we compared VP1 expression levels by using recombinant baculovirus constructs containing different 3 elements. High VP1 levels were detected by using a recombinant baculovirus that contained ORF2, ORF3, and the 3UTR (ORF2؉3؉3UTR). In contrast, expression of VP1 from constructs that lacked the 3UTR (ORF2؉3), ORF3 (ORF2؉3UTR), or both (ORF2 alone) was highly reduced. Elimination of VP2 synthesis from the subgenomic RNA by mutation resulted in VP1 levels similar to those obtained with the ORF2 construct alone, suggesting a cis role for VP2 in upregulation of VP1 expression levels. Comparisons of the kinetics of RNA and capsid protein expression levels by using constructs with or without ORF3 or the 3UTR revealed that the 3UTR increased the levels of VP1 RNA, whereas the presence of VP2 resulted in increased levels of VP1. Furthermore, VP2 increased VP1 stability and protected VP1 from disassembly and protease degradation. The increase in VP1 expression levels caused by the presence of VP2 in cis was also observed in mammalian cells.The Norwalk virus (NV) is a member of the genus Norovirus in the family Caliciviridae. The recent accessibility of molecular diagnostic assays has demonstrated that noroviruses are the leading cause of outbreaks of nonbacterial gastroenteritis worldwide (17). In addition, caliciviruses have been recently classified as category B biodefense pathogens (http://www.niaid .nih.gov/biodefense/). The NV 7.7-kb positive-strand RNA genome is organized into a 5Ј untranslated region (UTR), three open reading frames (ORFs), a 3ЈUTR, and a poly(A) tail (19). The NV predicted subgenomic RNA contains ORF2, ORF3, and the 3ЈUTR. ORF2 and ORF3 code for the major capsid protein (VP1) and a small basic structural protein (VP2), respectively. The ORF3 protein (VP2) has been detected in NV virions and virus-like particles (VLPs) (15). VP2 or a VP2-equivalent protein has been detected in the virions of other members of the Caliciviridae family such as the rabbit hemorrhagic disease virus (RHDV) (34) and feline calicivirus (FCV) (54). VP2 is not essential for the formation of NV VLPs because baculovirus recombinants expressing VP1 alone are able to produce NV VLPs (5, 58). The highly basic VP2 may serve a function similar to the basic N terminus of plant virus capsid proteins, which are involved in RNA binding, since the N terminus of NV VP1 is acidic and is not thought to ...

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“…However, they hardly occupy extended RNA regions and therefore could not make a significant contribution to the observed difference in the rates of evolution of VP1 and 2AB. On the other hand, the importance of RNA secondary structure may be related not only to certain conserved domains but also to the rule "fold as you please, but fold you must" (2). Implementation of this rule may result in negative selection of certain synonymous substitutions and hence in retardation of the evolutionary rate.…”

Section: Discussionmentioning

confidence: 99%

Evolution of Circulating Wild Poliovirus and of Vaccine-Derived Poliovirus in an Immunodeficient Patient: a Unifying Model

Gavrilin

Cherkasova

Lipskaya

et al. 2000

J Virol

132

122

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We determined nucleotide sequences of the VP1 and 2AB genes and portions of the 2C and 3D genes of two evolving poliovirus lineages: circulating wild viruses of T geotype and Sabin vaccine-derived isolates from an immunodeficient patient. Different regions of the viral RNA were found to evolve nonsynchronously, and the rate of evolution of the 2AB region in the vaccine-derived population was not constant throughout its history. Synonymous replacements occurred not completely randomly, suggesting the need for conservation of certain rare codons (possibly to control translation elongation) and the existence of unidentified constraints in the viral RNA structure. Nevertheless the major contribution to the evolution of the two lineages came from linear accumulation of synonymous substitutions. Therefore, in agreement with current theories of viral evolution, we suggest that the majority of the mutations in both lineages were fixed as a result of successive sampling, from the heterogeneous populations, of random portions containing predominantly neutral and possibly adverse mutations. As a result of such a mode of evolution, the virus fitness may be maintained at a more or less constant level or may decrease unless more-fit variants are stochastically generated. The proposed unifying model of natural poliovirus evolution has important implications for the epidemiology of poliomyelitis.Analysis of polioviruses isolated either during a given outbreak of poliomyelitis (30,35,51) or from sequential fecal samples from infected individuals (29, 31, 34) has revealed rapid changes in the nucleotide sequence of the viral 7.5-kb RNA. Oligonucleotide fingerprinting (51) and genome sequencing (30, 34) suggested that, during the epidemic, the nucleotide substitutions ranged from 1 to 2% per year. The molecular basis of such genetic instability, common to all RNA viruses, resides in a high error rate of the viral RNA-dependent RNA polymerases, estimated to be, for poliovirus, on the order of 10 Ϫ4 to 10 Ϫ5 substitutions per base per replication (12,70,71), and the absence of proofreading mechanisms for the correction of the errors made. The combination of these properties results in a high heterogeneity (the "quasispecies" nature) of all populations of the virus (8,10,11,63).Less understood, however, are the rules governing the fixation of specific mutations upon passages of a viral population. Generally speaking, a mutation may decrease or increase the level of virus fitness for a particular ecological niche or leave it unchanged. Nucleotide substitutions associated with changes in the "sense" of codons (nonsynonymous mutations) are less likely to be neutral than substitutions resulting in no change of the codon meaning (synonymous mutations). Fixation of mutations conferring a selective advantage is readily understood in the framework of positive Darwinian selection. Adverse mutations may be eliminated by negative selection.The likelihood of fixation of a mutation depends not only on the associated changes in virus fitness but, ...

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cis-Acting Elements within an RNA Coliphage Genome: Fold as You Please, but Fold You Must!!

Cited by 29 publications

References 0 publications

Translational activation in coliphage qβ: on a polycistronic messenger RNA, repression of one gene can activate translation of another 1 1Edited by M. Gottesman

Translational activation in coliphage qβ: on a polycistronic messenger RNA, repression of one gene can activate translation of another 1 1Edited by M. Gottesman

The 3′ End of Norwalk Virus mRNA Contains Determinants That Regulate the Expression and Stability of the Viral Capsid Protein VP1: a Novel Function for the VP2 Protein

Evolution of Circulating Wild Poliovirus and of Vaccine-Derived Poliovirus in an Immunodeficient Patient: a Unifying Model

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