A novel role for poly(C) binding proteins in programmed ribosomal frameshifting

Napthine, Sawsan; Treffers, Emmely E.; Bell, Susanne; Goodfellow, Ian; Fāng, Yīng; Firth, Andrew E.; Snijder, Eric J.; Brierley, Ian

doi:10.1093/nar/gkw480

Cited by 50 publications

(77 citation statements)

References 59 publications

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“…Deviations in the downstream element were rare and did not involve more than one nucleotide, while observed sizes of Ϫ2TF domains were comparable (with the exception of LDV L13298.1 47 aa -2TF domain) to the experimentally verified size of the Ϫ2TF domain of PRRSV (Table 4). These results suggest that the observed variations in PRF motifs in our large virus data set (Table 4) may be compatible with their function despite the detrimental effects of some of these variations artificially introduced into PRRSV-2 (33,35).…”

Section: Resultssupporting

confidence: 58%

“…Their generation involves Ϫ1 and Ϫ2 PRFs in the nsp2 genome region encoding the HVR-TM1 junction and is directed by a slippery sequence and a downstream C-rich element conserved in several arteriviruses but not EAV (33,34). PRFs are transactivated by a complex of viral nsp1b and host poly(C) binding protein (PCBP) that binds to the downstream C-rich element (34,35).…”

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confidence: 99%

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Domain Organization and Evolution of the Highly Divergent 5′ Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus

Gulyaeva

Dunowska

Hoogendoorn

et al. 2017

J Virol

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In five experimentally characterized arterivirus species, the 5=-end genome coding region encodes the most divergent nonstructural proteins (nsp's), nsp1 and nsp2, which include papain-like proteases (PLPs) and other poorly characterized domains. These are involved in regulation of transcription, polyprotein processing, and virus-host interaction. Here we present results of a bioinformatics analysis of this region of 14 arterivirus species, including that of the most distantly related virus, wobbly possum disease virus (WPDV), determined by a modified 5= rapid amplification of cDNA ends (RACE) protocol. By combining profile-profile comparisons and phylogeny reconstruction, we identified an association of the four distinct domain layouts of nsp1-nsp2 with major phylogenetic lineages, implicating domain gain, including duplication, and loss in the early nsp1 evolution. Specifically, WPDV encodes highly divergent homologs of PLP1a, PLP1b, PLP1c, and PLP2, with PLP1a lacking the catalytic Cys residue, but does not encode nsp1 Zn finger (ZnF) and "nuclease" domains, which are conserved in other arteriviruses. Unexpectedly, our analysis revealed that the only catalytically active nsp1 PLP of equine arteritis virus (EAV), known as PLP1b, is most similar to PLP1c and thus is likely to be a PLP1b paralog. In all non-WPDV arteriviruses, PLP1b/c and PLP1a show contrasting patterns of conservation, with the N-and C-terminal subdomains, respectively, being enriched with conserved residues, which is indicative of different functional specializations. The least conserved domain of nsp2, the hypervariable region (HVR), has its size varied 5-fold and includes up to four copies of a novel PxPxPR motif that is potentially recognized by SH3 domain-containing proteins. Apparently, only EAV lacks the signal that directs Ϫ2 ribosomal frameshifting in the nsp2 coding region.IMPORTANCE Arteriviruses comprise a family of mammalian enveloped positivestrand RNA viruses that include some of the most economically important pathogens of swine. Most of our knowledge about this family has been obtained through characterization of viruses from five species: Equine arteritis virus, Simian hemorrhagic fever virus, Lactate dehydrogenase-elevating virus, Porcine respiratory and reproductive syndrome virus 1, and Porcine respiratory and reproductive syndrome virus 2. Here we present the results of comparative genomics analyses of viruses from all known 14 arterivirus species, including the most distantly related virus, WPDV, whose genome sequence was completed in this study. Our analysis focused on the multifunctional 5=-end genome coding region that encodes multidomain nonstructural proteins 1 and 2. Using diverse bioinformatics techniques, we identified many patterns of evolutionary conservation that are specific to members of distinct arterivirus species, both characterized and novel, or their groups. They are likely associated with struc-

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Section: Resultssupporting

confidence: 58%

mentioning

confidence: 99%

Domain Organization and Evolution of the Highly Divergent 5′ Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus

Gulyaeva

Dunowska

Hoogendoorn

et al. 2017

J Virol

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“…We can now confirm that this effect is mediated at the translational level, and depends on protein-stimulated PRF rather than ribosomal drop-off at StopGo or at other sites during polyprotein synthesis. Together with À 2 PRF for nsp2TF expression in members of the family Arteriviridae, where we recently demonstrated that PRF is critically dependent on the arteriviral protein nsp1b and host poly(C) binding proteins interacting with a 3 0 C-rich motif separated from the frameshift site by a 10-nt spacer 27 , this is one of only two known cases of protein-stimulated PRF. As 2A and nsp1b are viral proteins, they cannot be utilized for normal cellular gene expression.…”

Section: Discussionmentioning

confidence: 89%

Protein-directed ribosomal frameshifting temporally regulates gene expression

et al. 2017

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Programmed −1 ribosomal frameshifting is a mechanism of gene expression, whereby specific signals within messenger RNAs direct a proportion of translating ribosomes to shift −1 nt and continue translating in the new reading frame. Such frameshifting normally occurs at a set ratio and is utilized in the expression of many viral genes and a number of cellular genes. An open question is whether proteins might function as trans-acting switches to turn frameshifting on or off in response to cellular conditions. Here we show that frameshifting in a model RNA virus, encephalomyocarditis virus, is trans-activated by viral protein 2A. As a result, the frameshifting efficiency increases from 0 to 70% (one of the highest known in a mammalian system) over the course of infection, temporally regulating the expression levels of the viral structural and enzymatic proteins.

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“…Some RNA viruses naturally employ viral and cellular encoded proteins to regulate PRF during viral replica-tion cycles. For example, a novel Ϫ1/Ϫ2 PRF mechanism is stimulated in the absence of any apparent downstream RNA structural element in porcine reproductive and respiratory syndrome virus (23,24). Both Ϫ1 and Ϫ2 PRF events are stimulated by the binding of a trans-acting protein complex composed of the virus-encoded nsP1␤ replicase subunit and the cellular poly(C)-binding protein.…”

Section: Employing Trans-acting Modulators To Make Variable Resistorsmentioning

confidence: 99%

Translational recoding signals: Expanding the synthetic biology toolbox

Dinman

2019

Journal of Biological Chemistry

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Innovation follows discovery. If the 20th century was a golden age of discovery in the biomolecular biosciences, the current century may be remembered by the explosion of beneficial devices and therapies conceived by the bioengineers of the era. Much as the development of solid-state electronic components made possible the information revolution, the rational combining of millions of basic molecular control modules will enable the development of highly sophisticated biomachines that will make today's smartphones appear rudimentary. The molecular toolbox is already well-stocked, particularly in our ability to manipulate DNA, control transcription, generate functionally novel hybrid proteins, and expand the genetic code to include unnatural amino acids. This review focuses on how RNA-based regulatory modules that direct alternative readings of the genetic code can be employed as basic circuit components to expand our ability to control gene expression.Since the elucidation of the genetic code in the early 1960s (1), the common perception has been that 1) all codons encode identical information in all organisms, and 2) coding sequences are "fixed" (i.e. ribosomes must maintain translational reading frame to faithfully decode all of the information contained in mRNAs). Shortly thereafter, however, bacteriophage geneticists identified bacterial mutants capable of suppressing stop codons in viral mRNAs (2), which led to the discovery of tRNAs (called suppressor tRNAs) in both bacteria (3) and eukaryotes (4) that are capable of reassigning the meaning of "stop codons" to encode specific amino acids. In the next decade, there were additional discoveries of cis-acting mRNA elements that direct ribosomes to reassign the meanings of codons or induce ribosomes to shift into alternative reading frames. This general phenomenon is collectively referred to as "translational recoding," which is defined as instances in which "the rules for decoding are temporarily altered through the action of specific signals built into the mRNA sequences" (5).In a unique and thought-provoking research article, Anzalone et al. (6) exploited RNA recoding elements to create a gene expression control circuit. They employed a directed evolutionary approach in vitro to identify RNA aptamers that stim-ulated the activity of a translational recoding element. These aptamers were then exploited to construct single-mRNA logic gates that were applied to control a new module governing cell death. This work marked a seminal milestone in the effort to integrate translational reprogramming modules into the synthetic biology toolbox. Importantly, these synthetic elements enabled manipulation of gene expression during the elongation phase of translation, thus addressing a critical gap in the synthetic biology toolbox for regulating gene expression in synthetic biology.

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A novel role for poly(C) binding proteins in programmed ribosomal frameshifting

Cited by 50 publications

References 59 publications

Domain Organization and Evolution of the Highly Divergent 5′ Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus

Domain Organization and Evolution of the Highly Divergent 5′ Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus

Protein-directed ribosomal frameshifting temporally regulates gene expression

Translational recoding signals: Expanding the synthetic biology toolbox

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