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      Non-encapsidation activities of the capsid proteins of positive-strand RNA viruses

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          Abstract

          Viral capsid proteins (CPs) are characterized by their role in forming protective shells around viral genomes. However, CPs have additional and important roles in the virus infection cycles and in the cellular responses to infection. These activities involve CP binding to RNAs in both sequence-specific and nonspecific manners as well as association with other proteins. This review focuses on CPs of both plant and animal-infecting viruses with positive-strand RNA genomes. We summarize the structural features of CPs and describe their modulatory roles in viral translation, RNA-dependent RNA synthesis, and host defense responses.

          Highlights

          • We review regulatory activities of the capsid proteins of (+)-strand RNA viruses.

          • Activities of capsid proteins due to RNA binding and protein binding.

          • Effects of capsid proteins on viral processes.

          • Effects of capsid proteins on cellular processes.

          • Regulatory activities of the capsid proteins are affected by capsid concentrations.

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          Most cited references147

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          Flexible nets. The roles of intrinsic disorder in protein interaction networks.

          Proteins participate in complex sets of interactions that represent the mechanistic foundation for much of the physiology and function of the cell. These protein-protein interactions are organized into exquisitely complex networks. The architecture of protein-protein interaction networks was recently proposed to be scale-free, with most of the proteins having only one or two connections but with relatively fewer 'hubs' possessing tens, hundreds or more links. The high level of hub connectivity must somehow be reflected in protein structure. What structural quality of hub proteins enables them to interact with large numbers of diverse targets? One possibility would be to employ binding regions that have the ability to bind multiple, structurally diverse partners. This trait can be imparted by the incorporation of intrinsic disorder in one or both partners. To illustrate the value of such contributions, this review examines the roles of intrinsic disorder in protein network architecture. We show that there are three general ways that intrinsic disorder can contribute: First, intrinsic disorder can serve as the structural basis for hub protein promiscuity; secondly, intrinsically disordered proteins can bind to structured hub proteins; and thirdly, intrinsic disorder can provide flexible linkers between functional domains with the linkers enabling mechanisms that facilitate binding diversity. An important research direction will be to determine what fraction of protein-protein interaction in regulatory networks relies on intrinsic disorder.
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            RNA-based antiviral immunity.

            In eukaryotic RNA-based antiviral immunity, viral double-stranded RNA is recognized as a pathogen-associated molecular pattern and processed into small interfering RNAs (siRNAs) by the host ribonuclease Dicer. After amplification by host RNA-dependent RNA polymerases in some cases, these virus-derived siRNAs guide specific antiviral immunity through RNA interference and related RNA silencing effector mechanisms. Here, I review recent studies on the features of viral siRNAs and other virus-derived small RNAs from virus-infected fungi, plants, insects, nematodes and vertebrates and discuss the innate and adaptive properties of RNA-based antiviral immunity.
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              Function and structure of inherently disordered proteins.

              The application of bioinformatics methodologies to proteins inherently lacking 3D structure has brought increased attention to these macromolecules. Here topics concerning these proteins are discussed, including their prediction from amino acid sequence, their enrichment in eukaryotes compared to prokaryotes, their more rapid evolution compared to structured proteins, their organization into specific groups, their structural preferences, their half-lives in cells, their contributions to signaling diversity (via high contents of multiple-partner binding sites, post-translational modifications, and alternative splicing), their distinct functional repertoire compared to that of structured proteins, and their involvement in diseases.
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                Author and article information

                Contributors
                Journal
                Virology
                Virology
                Virology
                Elsevier Inc.
                0042-6822
                1096-0341
                27 August 2013
                November 2013
                27 August 2013
                : 446
                : 1
                : 123-132
                Affiliations
                [0005]Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
                Author notes
                [* ]Corresponding author. ckao@ 123456indiana.edu
                Article
                S0042-6822(13)00443-1
                10.1016/j.virol.2013.07.023
                3818703
                24074574
                a96e4b93-222a-4a88-adbd-be15de28c0f2
                Copyright © 2013 Elsevier Inc.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 26 March 2013
                : 11 July 2013
                : 20 July 2013
                Categories
                Article

                Microbiology & Virology
                capsid protein,positive-strand rna virus,protein–rna interaction,protein–protein interaction,regulation of viral infection,review

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