Genome-wide analysis of protein–protein interactions and involvement of viral proteins in SARS-CoV-2 replication

Abstract Background Analysis of viral protein–protein interactions is an essential step to uncover the viral protein functions and the molecular mechanism for the assembly of a viral protein complex. We employed a mammalian two-hybrid system to screen all the viral proteins of SARS-CoV-2 for the protein–protein interactions. Results Our study detected 48 interactions, 14 of which were firstly reported here. Unlike Nsp1 of SARS-CoV, Nsp1 of SARS-CoV-2 has the most interacting partners among all the viral proteins and likely functions as a hub for the viral proteins. Five self-interactions were confirmed, and five interactions, Nsp1/Nsp3.1, Nsp3.1/N, Nsp3.2/Nsp12, Nsp10/Nsp14, and Nsp10/Nsp16, were determined to be positive bidirectionally. Using the replicon reporter system of SARS-CoV-2, we screened all viral Nsps for their impacts on the viral replication and revealed Nsp3.1, the N-terminus of Nsp3, significantly inhibited the replicon reporter gene expression. We found Nsp3 interacted with N through its acidic region at N-terminus, while N interacted with Nsp3 through its NTD, which is rich in the basic amino acids. Furthermore, using purified truncated N and Nsp3 proteins, we determined the direct interactions between Nsp3 and N protein. Conclusions Our findings provided a basis for understanding the functions of coronavirus proteins and supported the potential of interactions as the target for antiviral drug development.

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Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV-2 replication

10.21203/rs.3.rs-337427/v1 ◽

2021 ◽

Author(s):

Yiling Jiang ◽

Kuijie Tong ◽

Roubin Yao ◽

Yuanze Zhou ◽

Hanwen Lin ◽

...

Keyword(s):

Protein Interactions ◽

Viral Protein ◽

Antiviral Drug ◽

Viral Proteins ◽

Protein Protein Interactions ◽

Reporter System ◽

N Protein ◽

Genome Wide ◽

N Terminus ◽

Protein Functions

Abstract Analysis of viral protein-protein interactions is an essential step to uncover the viral protein functions and the molecular mechanism for the assembly of a viral protein complex. We employed a mammalian two-hybrid system to screen all the viral proteins of SARS-CoV-2 for the protein-protein interactions. Our study detected 48 interactions, 14 of which were firstly reported here. Unlike Nsp1 of SARS-CoV, Nsp1 of SARS-CoV-2 has the most interacting partners among all the viral proteins and likely functions as a hub for the viral proteins. Five self-interactions were confirmed, and five interactions, Nsp1/Nsp3.1, Nsp3.1/N, Nsp3.2/Nsp12, Nsp10/Nsp14, and Nsp10/Nsp16, were determined to be positive bidirectionally. Using the replicon reporter system of SARS-CoV-2, we screened all viral proteins for their impacts on the viral replication and revealed Nsp3.1, the N-terminus of Nsp3, significantly inhibited the replicon reporter gene expression. We found Nsp3 interacted with N through its acidic region at N-terminus, while N interacted with Nsp3 through its NTD, which is rich in the basic amino acids. Furthermore, using purified truncated N and Nsp3 proteins, we determined the direct interactions between Nsp3 and N protein. In summary, our findings provided a basis for understanding the functions of coronavirus proteins and supported the potential of interactions as the target for antiviral drug development.

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Role of Viral Protein-Protein Interactions and Possible Targets for New Therapeutics

NUST Journal of Natural Sciences ◽

10.53992/njns.v2i2.36 ◽

2021 ◽

Vol 2 (2) ◽

pp. 1-15

Author(s):

Rehan Zafar Paracha ◽

Fahed Parvaiz ◽

Babar Aslam ◽

Ayesha Obaid ◽

Sidra Qureshi ◽

...

Keyword(s):

Protein Interactions ◽

Viral Protein ◽

Influenza A ◽

Viral Infections ◽

Treatment Options ◽

Interaction Network ◽

Viral Proteins ◽

Protein Protein Interactions ◽

Virus Influenza

Viral infections are the cause of serious infirmities in humans and kill millions of people every year. Management of viral diseases is one of the challenges faced by the whole world which needs improvement in prevention and treatment options. Complete understanding of the consequences of viral proteins interaction network on host physiology is essential. Towards this goal, deciphering viral protein-protein interactions is one of the perspective which can help in our understanding about the basis of viral pathogenesis and the development of new antivirals. Indeed, viral infection network based on viral-viral proteins will provide an elusive and investigative framework to articulate rationalize drug discovery based on proteomics scale of viruses. In this study, proteomics a collection of viral-viral protein interactions reporting different studies of Hepatitis C virus, Influenza A virus, Dengue virus and SARS Coronavirus. Our effort of protein-interactions was focused on different studies reporting interactions between viral proteins encoded by the viruses under study. The study is integrated with a broad and original literature-curated data of viral-viral protein (197 non-redundant) interactions.

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Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication

PLoS ONE ◽

10.1371/journal.pone.0003299 ◽

2008 ◽

Vol 3 (10) ◽

pp. e3299 ◽

Cited By ~ 79

Author(s):

Ji'An Pan ◽

Xiaoxue Peng ◽

Yajing Gao ◽

Zhilin Li ◽

Xiaolu Lu ◽

...

Keyword(s):

Protein Interactions ◽

Viral Proteins ◽

Protein Protein Interactions ◽

Genome Wide Analysis ◽

Genome Wide

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Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

10.1101/2021.04.19.440086 ◽

2021 ◽

Author(s):

Thomas Kruse ◽

Caroline Benz ◽

Dimitriya H Garvanska ◽

Richard Lindqvist ◽

Filip Mihalic ◽

...

Keyword(s):

Protein Interactions ◽

Large Scale ◽

Specific Interaction ◽

Viral Proteins ◽

Protein Protein Interactions ◽

N Protein ◽

Host Interactions ◽

Viral Peptide ◽

Viral Interactions ◽

Peptide Interaction

Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a scalable viral peptide discovery approach covering 229 RNA viruses that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an [FILV]xFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its [FILV]xFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction blocks SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.

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Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

Nature Communications ◽

10.1038/s41467-021-26498-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Thomas Kruse ◽

Caroline Benz ◽

Dimitriya H. Garvanska ◽

Richard Lindqvist ◽

Filip Mihalic ◽

...

Keyword(s):

Protein Interactions ◽

Large Scale ◽

Specific Interaction ◽

Viral Proteins ◽

Protein Protein Interactions ◽

N Protein ◽

Host Interactions ◽

Viral Peptide ◽

Viral Interactions ◽

Peptide Interaction

AbstractViral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.

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Roles of the 14-3-3 gene family in cotton flowering

BMC Plant Biology ◽

10.1186/s12870-021-02923-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Na Sang ◽

Hui Liu ◽

Bin Ma ◽

Xianzhong Huang ◽

Lu Zhuo ◽

...

Keyword(s):

Gene Family ◽

Protein Interactions ◽

Leucine Zipper ◽

Expression Patterns ◽

Bimolecular Fluorescence Complementation ◽

Structural Motif ◽

Virus Induced Gene Silencing ◽

Protein Protein Interactions ◽

Basic Leucine Zipper ◽

Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

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Genome-wide analysis of vaccinia virus protein-protein interactions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.080078197 ◽

2000 ◽

Vol 97 (9) ◽

pp. 4879-4884 ◽

Cited By ~ 193

Author(s):

S. McCraith ◽

T. Holtzman ◽

B. Moss ◽

S. Fields

Keyword(s):

Vaccinia Virus ◽

Protein Interactions ◽

Virus Protein ◽

Protein Protein Interactions ◽

Genome Wide Analysis ◽

Genome Wide

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Coiled-coil networking shapes cell molecular machinery

Molecular Biology of the Cell ◽

10.1091/mbc.e12-05-0396 ◽

2012 ◽

Vol 23 (19) ◽

pp. 3911-3922 ◽

Cited By ~ 44

Author(s):

Yongqiang Wang ◽

Xinlei Zhang ◽

Hong Zhang ◽

Yi Lu ◽

Haolong Huang ◽

...

Keyword(s):

Protein Interactions ◽

Critical Role ◽

Coiled Coil ◽

Coiled Coils ◽

Protein Protein Interactions ◽

Full Spectrum ◽

Kinetochore Assembly ◽

Genome Wide ◽

Molecular Machinery ◽

Systematic Understanding

The highly abundant α-helical coiled-coil motif not only mediates crucial protein–protein interactions in the cell but is also an attractive scaffold in synthetic biology and material science and a potential target for disease intervention. Therefore a systematic understanding of the coiled-coil interactions (CCIs) at the organismal level would help unravel the full spectrum of the biological function of this interaction motif and facilitate its application in therapeutics. We report the first identified genome-wide CCI network in Saccharomyces cerevisiae, which consists of 3495 pair-wise interactions among 598 predicted coiled-coil regions. Computational analysis revealed that the CCI network is specifically and functionally organized and extensively involved in the organization of cell machinery. We further show that CCIs play a critical role in the assembly of the kinetochore, and disruption of the CCI network leads to defects in kinetochore assembly and cell division. The CCI network identified in this study is a valuable resource for systematic characterization of coiled coils in the shaping and regulation of a host of cellular machineries and provides a basis for the utilization of coiled coils as domain-based probes for network perturbation and pharmacological applications.

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Prioritization of genes associated with the pathogenesis of leukosis in cattle

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj18.451 ◽

2019 ◽

Vol 22 (8) ◽

pp. 1063-1069 ◽

Cited By ~ 1

Author(s):

N. S. Yudin ◽

N. L. Podkolodnyy ◽

T. A. Agarkova ◽

E. V. Ignatieva

Keyword(s):

Protein Interactions ◽

Genome Wide Association Study ◽

Association Studies ◽

Mammalian Species ◽

Genome Wide Association ◽

Farm Animals ◽

Genome Wide Association Studies ◽

Protein Protein Interactions ◽

Genome Wide ◽

A Genome

Selection by means of genetic markers is a promising approach to the eradication of infectious diseases in farm animals, especially in the absence of eﬀective methods of treatment and prevention. Bovine leukemia virus (BLV) is spread throughout the world and represents one of the biggest problems for the livestock production and food security in Russia. However, recent genome-wide association studies have shown that sensitivity/resistance to BLV is polygenic. The aim of this study was to create a catalog of cattle genes and genes of other mammalian species involved in the pathogenesis of BLV-induced infection and to perform gene prioritization using bioinformatics methods. Based on manually collected information from a range of open sources, a total of 446 genes were included in the catalog of cattle genes and genes of other mammals involved in the pathogenesis of BLV-induced infection. The following criteria were used to prioritize 446 genes from the catalog: (1) the gene is associated with leukemia according to a genome-wide association study; (2) the gene is associated with leukemia according to a case-control study; (3) the role of the gene in leukemia development has been studied using knockout mice; (4) protein-protein interactions exist between the gene-encoded protein and either viral particles or individual viral proteins; (5) the gene is annotated with Gene Ontology terms that are overrepresented for a given list of genes; (6) the gene participates in biological pathways from the KEGG or REACTOME databases, which are over-represented for a given list of genes; (7) the protein encoded by the gene has a high number of protein-protein interactions with proteins encoded by other genes from the catalog. Based on each criterion, a rank was assigned to each gene. Then the ranks were summarized and an overall rank was determined. Prioritization of 446 candidate genes allowed us to identify 5 genes of interest (TNF,LTB,BOLA-DQA1,BOLA-DRB3,ATF2), which can aﬀect the sensitivity/resistance of cattle to leukemia.

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