A second open reading frame in human enterovirus determines viral replication in intestinal epithelial cells

Guo, Hao; Li, Yan; Liu, Guanchen; Jiang, Yunhe; Shen, Siyu; Bi, R.; Huang, Honglan; Cheng, Tong; Wang, Handong; Wei, Wei

doi:10.1038/s41467-019-12040-9

Cited by 41 publications

(37 citation statements)

References 46 publications

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“…There have been various studies outlining the impacts of picornavirus 5' UTR mutations on IRES-mediated translation efficiency. While some picornaviruses have been determined to have multiple start codons, this is not the case for EV-D68 [61,62].There has been substantial evolution in the EV-D68 5' UTR since its initial discovery in 1962. Comparing the genetic composition, there is 83% 5' UTR sequence homology between our representative historic and contemporary strains and these differences do impact the overall predicted secondary structure ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Numerous studies have identified 5' UTR mutations that impact IRES-mediated translation efficiency, which can be linked to temperature sensitivity, and neurotropism [57,59,60]. While some picornaviruses have been determined to have multiple open reading frames with an additional start codon in the 5' UTR, this is not the case for EV-D68 [61,62]. There has been substantial evolution in the EV-D68 5' UTR since its initial discovery in 1962, most notably in the form of heightened variability and large deletions in the spacer region flanking the AUG start codon [63,64].…”

Section: Introductionmentioning

confidence: 99%

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Contemporary Enterovirus D68 strains show enhanced replication and translation at 37°C

Smith

Pekosz

2020

Preprint

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Enterovirus D68 (EV-D68) emerged in 2014 as an important pathogen linked to severe lower respiratory disease and acute flaccid myelitis outbreaks. Historically associated with mild common-cold-like symptoms, clusters of severe disease attributed to EV-D68 appeared during a series of outbreaks in 2014, 2016, and 2018. Previous studies of historic EV-D68 strains demonstrated attenuated replication at temperatures of the lower respiratory tract (37°C), when compared to the upper respiratory tract (32°C). By testing a panel of historic and contemporary EV-D68 strains at 32°C and 37°C, we demonstrate that contemporary strains of EV-D68 undergo little to no attenuation at increased temperatures. Contemporary strains produced higher levels of viral proteins at 32°C and 37°C than historic strains, although both strains infected similar numbers of cells and had comparable amounts of replication complexes. IRES activity assays with dual-luciferase reporter plasmids demonstrated enhanced translation in recent EV-D68 strains mapped to regions of variability in the 5' UTR found only in contemporary strains. Using an infectious clone system, we demonstrate that the translation advantage dictated by the 5' UTR does not solely mediate temperature sensitivity. The strain-dependent effects of temperature on the EV-D68 life cycle gives insight into the susceptibility of the lower respiratory system to contemporary strains. IMPORTANCEEnterovirus-D68 (EV-D68) emerged in 2014 as a causative agent of biannual severe pediatric respiratory disease and acute flaccid myelitis (AFM). We show that recent EV-D68 viruses have gained the ability to replicate at 37⁰C. Enhanced virus protein translation seemed to correlate with enhanced virus replication at 37⁰C but other genetic factors are also contributing to this phenotype. An enhanced ability to replicate at core body temperature may have allowed EV-D68 to penetrate both lower in the respiratory tract and into the central nervous system, explaining the recent surge in severe disease associated with virus infection.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Contemporary Enterovirus D68 strains show enhanced replication and translation at 37°C

Smith

Pekosz

2020

Preprint

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“…The functions of these are unknown. Moreover, in the Picornaviridae family, enteroviruses produce a short protein that is important for viral infection from an ORF partially overlapping with the viral polyprotein region at the +2 frame [46,47], and Foot-and-Mouth Disease Virus produces two alternative forms of the L protein, a peptidase, which is initiated at two in-frame AUGs [48] in an IRES-dependent mechanism.…”

Section: Discussionmentioning

confidence: 99%

“…We have previously shown that the integrity of the first two stem-loops SL47 (nt 388-423) and SL87 (nt 427-507) is important for the translation of the viral polyprotein but not for viral RNA stability, using the JFH1 infectious clone [40,41] in cell culture and in mice xenografted with human hepatocytes [42]. These data prompted us to investigate the possibility of the presence, in this region, of a genetic element regulating core+1/S translation, by analogy to other RNA viruses [43][44][45][46][47][48].…”

Section: Introductionmentioning

confidence: 99%

A Novel Cis-Acting RNA Structural Element Embedded in the Core Coding Region of the Hepatitis C Virus Genome Directs Internal Translation Initiation of the Overlapping Core+1 ORF

Vassilaki

Frakolaki

Kalliampakou

et al. 2020

IJMS

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Hepatitis C virus (HCV) genome translation is initiated via an internal ribosome entry site (IRES) embedded in the 5′-untranslated region (5′UTR). We have earlier shown that the conserved RNA stem-loops (SL) SL47 and SL87 of the HCV core-encoding region are important for viral genome translation in cell culture and in vivo. Moreover, we have reported that an open reading frame overlapping the core gene in the +1 frame (core+1 ORF) encodes alternative translation products, including a protein initiated at the internal AUG codons 85/87 of this frame (nt 597–599 and 603–605), downstream of SL87, which is designated core+1/Short (core+1/S). Here, we provide evidence for SL47 and SL87 possessing a novel cis-acting element that directs the internal translation initiation of core+1/S. Firstly, using a bicistronic dual luciferase reporter system and RNA-transfection experiments, we found that nucleotides 344–596 of the HCV genotype-1a and -2a genomes support translation initiation at the core+1 frame AUG codons 85/87, when present in the sense but not the opposite orientation. Secondly, site-directed mutagenesis combined with an analysis of ribosome–HCV RNA association elucidated that SL47 and SL87 are essential for this alternative translation mechanism. Finally, experiments using cells transfected with JFH1 replicons or infected with virus-like particles showed that core+1/S expression is independent from the 5′UTR IRES and does not utilize the polyprotein initiation codon, but it requires intact SL47 and SL87 structures. Thus, SL47 and SL87, apart from their role in viral polyprotein translation, are necessary elements for mediating the internal translation initiation of the alternative core+1/S ORF.

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“…Enteroviral genome has a principal ORF encoding a long and single monocistronic autocatalytic polyprotein of ≈250 kDa resulting in viral capsid proteins and non-structural proteins. Moreover, a second upstream ORF (uORF) of the principal has been recently identified and could encode for a protein promoting the viral growth in initial viral replication sites (human epithelial cells) and facilitating viral particle release [13,31]. These two ORFs are flanked by 5 and 3 NCRs, also called untranslated regions (UTR).…”

Section: Functional Organization Of 5 Terminal Ev-b Rna Secondary Strmentioning

confidence: 99%

Structures and Functions of Viral 5′ Non-Coding Genomic RNA Domain-I in Group-B Enterovirus Infections

Glenet

Heng

Callon

et al. 2020

Viruses

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Group-B enteroviruses (EV-B) are ubiquitous naked single-stranded positive RNA viral pathogens that are responsible for common acute or persistent human infections. Their genome is composed in the 5′ end by a non-coding region, which is crucial for the initiation of the viral replication and translation processes. RNA domain-I secondary structures can interact with viral or cellular proteins to form viral ribonucleoprotein (RNP) complexes regulating viral genomic replication, whereas RNA domains-II to -VII (internal ribosome entry site, IRES) are known to interact with cellular ribosomal subunits to initiate the viral translation process. Natural 5′ terminally deleted viral forms lacking some genomic RNA domain-I secondary structures have been described in EV-B induced murine or human infections. Recent in vitro studies have evidenced that the loss of some viral RNP complexes in the RNA domain-I can modulate the viral replication and infectivity levels in EV-B infections. Moreover, the disruption of secondary structures of RNA domain-I could impair viral RNA sensing by RIG-I (Retinoic acid inducible gene I) or MDA5 (melanoma differentiation-associated protein 5) receptors, a way to overcome antiviral innate immune response. Overall, natural 5′ terminally deleted viral genomes resulting in the loss of various structures in the RNA domain-I could be major key players of host–cell interactions driving the development of acute or persistent EV-B infections.

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A second open reading frame in human enterovirus determines viral replication in intestinal epithelial cells

Cited by 41 publications

References 46 publications

Contemporary Enterovirus D68 strains show enhanced replication and translation at 37°C

Contemporary Enterovirus D68 strains show enhanced replication and translation at 37°C

A Novel Cis-Acting RNA Structural Element Embedded in the Core Coding Region of the Hepatitis C Virus Genome Directs Internal Translation Initiation of the Overlapping Core+1 ORF

Structures and Functions of Viral 5′ Non-Coding Genomic RNA Domain-I in Group-B Enterovirus Infections

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