Characterization and functional interrogation of the SARS-CoV-2 RNA interactome

Labeau, Athena; Fery-Simonian, Luc; Lefèvre‐Utile, Alain; Pourcelot, Marie; Bonnet-Madin, Lucie; Soumelis, Vassili; Lotteau, Vincent; Vidalain, Pierre‐Olivier; Amara, Ali; Meertens, Laurent

doi:10.1016/j.celrep.2022.110744

Cited by 40 publications

(37 citation statements)

References 74 publications

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“…Taking SRSF1 protein as an example (described in Figure 3 ), it interacted with the RNAs of six different SARS-CoV-2 strains (not only the France/IDF-220-95 one, but also the remaining five strains: Argentina/INEI104133, Zimbabwe/CERI-KRISP, Namibia/N17380, IPBCAMS-YL01 and Wuhan-Hu-1). This suggested that the IVRHP between SARS-CoV-2′s RNA region and host SRSF1 protein was greatly conserved despite the viral evolution ( 25 , 26 , 34 , 37 , 72 ). Moreover, some other host proteins were found to selectively interact with specific virus strains.…”

Section: Factual Content and Data Retrievalmentioning

confidence: 99%

“…Moreover, some other host proteins were found to selectively interact with specific virus strains. Taking the CCAR2 protein as another example, it only interacted with the RNA region from France/IDF-220–95 stain of SARS-CoV-2 ( 34 ). That is to say, the corresponding interactions between virus RNA region and host CCAR2 protein were deprived during the virus evolution from the France strain to others.…”

Section: Factual Content and Data Retrievalmentioning

confidence: 99%

“…Compared with the interactions above (VHPPIs, VHRRIs and VPHRIs), the interactions between virus RNA and host protein (IVRHPs, highlighted using blue & bold font in Figure 1 ) are unique in representing not only the virus’ attempts to accelerate their translation and replication ( 24–26 ), but also the host's endeavor to combat virus pathogenicity ( 27–29 ). With the recent technological breakthrough in detecting such invaluable interactions ( 30–33 ), the discovery of new IVRHP has attracted broad attention from the research community and a huge number of IVRHP data have thus been accumulated ( 34–38 ). Particularly, some of these newly discovered IVRHPs are reported to promote the translation/replication of virus ( pro-virus ( 39 , 40 )), while some others are found to suppress the infection ( anti-virus ( 41–43 )).…”

Section: Introductionmentioning

confidence: 99%

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CovInter: interaction data between coronavirus RNAs and host proteins

Amahong

Zhang

Zhou

et al. 2022

Nucleic Acids Research

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Coronavirus has brought about three massive outbreaks in the past two decades. Each step of its life cycle invariably depends on the interactions among virus and host molecules. The interaction between virus RNA and host protein (IVRHP) is unique compared to other virus–host molecular interactions and represents not only an attempt by viruses to promote their translation/replication, but also the host's endeavor to combat viral pathogenicity. In other words, there is an urgent need to develop a database for providing such IVRHP data. In this study, a new database was therefore constructed to describe the interactions between coronavirus RNAs and host proteins (CovInter). This database is unique in (a) unambiguously characterizing the interactions between virus RNA and host protein, (b) comprehensively providing experimentally validated biological function for hundreds of host proteins key in viral infection and (c) systematically quantifying the differential expression patterns (before and after infection) of these key proteins. Given the devastating and persistent threat of coronaviruses, CovInter is highly expected to fill the gap in the whole process of the ‘molecular arms race’ between viruses and their hosts, which will then aid in the discovery of new antiviral therapies. It's now free and publicly accessible at: https://idrblab.org/covinter/

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Section: Factual Content and Data Retrievalmentioning

confidence: 99%

Section: Factual Content and Data Retrievalmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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CovInter: interaction data between coronavirus RNAs and host proteins

Amahong

Zhang

Zhou

et al. 2022

Nucleic Acids Research

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“…20 PSF/SFPQ has recently been shown to bind to SARS-CoV-2 RNA and promote its replication. 21 Human PSF exhibits the highest binding affinity for poly(U) in vitro. 1 We report here the characterization of a truncated PSF form (sPSF, consisting of residues 214−598) to bind to the promoter region of a proto-oncogene, a 60 bp region from GAGE6 DNA, followed by its release by a 30mer from VL30-1, and then report the crystal structure of the sPSF-RNA complex.…”

Section: ■ Introductionmentioning

confidence: 96%

“…The presence of PUN is a major immunosensor for detection of invasion of coronaviruses, including SARS-CoV-2 . PSF/SFPQ has recently been shown to bind to SARS-CoV-2 RNA and promote its replication . Human PSF exhibits the highest binding affinity for poly(U) in vitro .…”

Section: Introductionmentioning

confidence: 99%

Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript-1

et al. 2022

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Human polypyrimidine-binding splicing factor (PSF/SFPQ) is a tumor suppressor protein that regulates the gene expression of several proto-oncogenes and binds to the 5′-polyuridine negative-sense template (5′-PUN) of some RNA viruses. The activity of PSF is negatively regulated by long-noncoding RNAs, human metastasis associated in lung adenocarcinoma transcript-1 and murine virus-like 30S transcript-1 (VL30-1). PSF is a 707-amino acid protein that has a DNA-binding domain and two RNA recognition motifs (RRMs). Although the structure of the apo-truncated PSF is known, how PSF recognizes RNA remains elusive. Here, we report the 2.8 Å and 3.5 Å resolution crystal structures of a biologically active truncated construct of PSF (sPSF, consisting of residues 214–598) alone and in a complex with a 30mer fragment of VL30-1 RNA, respectively. The structure of the complex reveals how the 30mer RNA is recognized at two U-specific induced-fit binding pockets, located at the previously unrecognized domain-swapped, inter-subunit RRM1 (of the first subunit)-RRM2 (of the second subunit) interfaces that do not exist in the apo structure. Thus, the sPSF dimer appears to have two conformations in solution: one in a low-affinity state for RNA binding, as seen in the apo-structure, and the other in a high-affinity state for RNA binding, as seen in the sPSF-RNA complex. PSF undergoes an all or nothing transition between having two or no RNA-binding pockets. We predict that the RNA binds with a high degree of positive cooperativity. These structures provide an insight into a new regulatory mechanism that is likely involved in promoting malignancies and other human diseases.

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Viral RNA Is a Hub for Critical Host–Virus Interactions

Castello,

Iselin

2023

Subcellular Biochemistry

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Characterization and functional interrogation of the SARS-CoV-2 RNA interactome

Cited by 40 publications

References 74 publications

CovInter: interaction data between coronavirus RNAs and host proteins

CovInter: interaction data between coronavirus RNAs and host proteins

Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript-1

Viral RNA Is a Hub for Critical Host–Virus Interactions

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