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Special Issue "Structure-Function Relationships in Viral Polymerases"

A special issue of Viruses (ISSN 1999-4915).

Deadline for manuscript submissions: closed (15 October 2017)

Special Issue Editor

Guest Editor
Dr. Olve Peersen

Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
Website | E-Mail
Interests: RNA virus replication complexes; polymerase fidelity; structural biology; enzyme kinetics

Special Issue Information

Dear Colleague,

Over the past decade our structural biology knowledge of viral polymerases and the detailed molecular interactions involved in viral genome replication has increased dramatically. We are well poised for a global comparison of these structures that highlights both commonalities among and within virus families and the unique and important aspects of individual structures. Thus, this Special Issue of Viruses is focused on viral polymerase structures and our understanding of their molecular mechanisms. The manuscripts will embrace structural biology, but they need not be strictly structure based; for example, a biochemically oriented research or review paper that leans more toward the function side of structure-function studies would be welcome.

This issue will be accompanied by an extensive collection of on-line materials in the form of movies that illustrate key elements of individual polymerase structures and comparisons of multiple structures. This is perhaps the most effective way to instil an appreciation for structure, especially for a more general virologist audience. As editor, I will work closely with the authors to develop a consistent set of molecular representations that facilitate comparisons of different polymerases. Examples of common themes to be highlighted are downstream and upstream nucleic acid interactions, strand separation mechanisms, initiation mechanisms, active site interactions and dynamics during catalysis, nucleotide selectivity, and translocation events. Suggestions for additional themes are welcome.
Guidelines for manuscript submission are shown below and authors specifically interested in partaking in the multimedia aspects of this Special Issue should contact the guest editor directly (Olve.Peersen@ColoState.edu) for initial guidance about manuscript sections and organization.

Dr. Olve Peersen
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • polymerase structure
  • replication

Published Papers (5 papers)

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Review

Open AccessReview RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution
Viruses 2018, 10(2), 76; https://doi.org/10.3390/v10020076
Received: 27 November 2017 / Revised: 30 January 2018 / Accepted: 3 February 2018 / Published: 10 February 2018
PDF Full-text (3015 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences.
[...] Read more.
RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals. In this article, we provide an overview of the structural aspects of RdRps and their complexes from the Group III, IV and V viruses and their structure-based phylogeny. Full article
(This article belongs to the Special Issue Structure-Function Relationships in Viral Polymerases)
Figures

Figure 1a

Open AccessReview Structural and Functional Basis of the Fidelity of Nucleotide Selection by Flavivirus RNA-Dependent RNA Polymerases
Viruses 2018, 10(2), 59; https://doi.org/10.3390/v10020059
Received: 9 January 2018 / Revised: 25 January 2018 / Accepted: 27 January 2018 / Published: 30 January 2018
PDF Full-text (5188 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Viral RNA-dependent RNA polymerases (RdRps) play a central role not only in viral replication, but also in the genetic evolution of viral RNAs. After binding to an RNA template and selecting 5′-triphosphate ribonucleosides, viral RdRps synthesize an RNA copy according to Watson-Crick base-pairing
[...] Read more.
Viral RNA-dependent RNA polymerases (RdRps) play a central role not only in viral replication, but also in the genetic evolution of viral RNAs. After binding to an RNA template and selecting 5′-triphosphate ribonucleosides, viral RdRps synthesize an RNA copy according to Watson-Crick base-pairing rules. The copy process sometimes deviates from both the base-pairing rules specified by the template and the natural ribose selectivity and, thus, the process is error-prone due to the intrinsic (in)fidelity of viral RdRps. These enzymes share a number of conserved amino-acid sequence strings, called motifs A–G, which can be defined from a structural and functional point-of-view. A co-relation is gradually emerging between mutations in these motifs and viral genome evolution or observed mutation rates. Here, we review our current knowledge on these motifs and their role on the structural and mechanistic basis of the fidelity of nucleotide selection and RNA synthesis by Flavivirus RdRps. Full article
(This article belongs to the Special Issue Structure-Function Relationships in Viral Polymerases)
Figures

Figure 1

Open AccessReview Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase
Viruses 2018, 10(1), 24; https://doi.org/10.3390/v10010024
Received: 21 October 2017 / Revised: 2 January 2018 / Accepted: 3 January 2018 / Published: 4 January 2018
PDF Full-text (1090 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Viral RNA-dependent RNA polymerases (RdRPs) are a class of nucleic acid polymerases bearing unique features from global architecture to catalytic mechanisms. In recent years, numerous viral RdRP crystal structures have improved the understanding of these molecular machines, in particular, for how they carry
[...] Read more.
Viral RNA-dependent RNA polymerases (RdRPs) are a class of nucleic acid polymerases bearing unique features from global architecture to catalytic mechanisms. In recent years, numerous viral RdRP crystal structures have improved the understanding of these molecular machines, in particular, for how they carry out each nucleotide addition cycle (NAC) as directed by the RNA template. This review focuses on a visual introduction of viral RdRP NAC mechanisms through a combination of static pictures of structural models, a user-friendly software-based assembly of the structural models, and two videos illustrating key conformational changes in the NAC. Full article
(This article belongs to the Special Issue Structure-Function Relationships in Viral Polymerases)
Figures

Figure 1

Open AccessReview Structure and Function of Caliciviral RNA Polymerases
Viruses 2017, 9(11), 329; https://doi.org/10.3390/v9110329
Received: 15 September 2017 / Revised: 26 October 2017 / Accepted: 2 November 2017 / Published: 6 November 2017
Cited by 2 | PDF Full-text (3322 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Caliciviruses are a leading agent of human and animal gastroenteritis and respiratory tract infections, which are growing concerns in immunocompromised individuals. However, no vaccines or therapeutics are yet available. Since the rapid rate of genetic evolution of caliciviruses is mainly due to the
[...] Read more.
Caliciviruses are a leading agent of human and animal gastroenteritis and respiratory tract infections, which are growing concerns in immunocompromised individuals. However, no vaccines or therapeutics are yet available. Since the rapid rate of genetic evolution of caliciviruses is mainly due to the error-prone nature of RNA-dependent RNA polymerase (RdRp), this article focuses on recent studies of the structures and functions of RdRp from caliciviruses. It also provides recent advances in the interactions of RdRp with virion protein genome-linked (VPg) and RNA and the structural and functional features of its precursor. Full article
(This article belongs to the Special Issue Structure-Function Relationships in Viral Polymerases)
Figures

Graphical abstract

Open AccessReview The Battle of RNA Synthesis: Virus versus Host
Viruses 2017, 9(10), 309; https://doi.org/10.3390/v9100309
Received: 15 September 2017 / Revised: 19 October 2017 / Accepted: 20 October 2017 / Published: 21 October 2017
Cited by 2 | PDF Full-text (969 KB) | HTML Full-text | XML Full-text
Abstract
Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to
[...] Read more.
Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage. Full article
(This article belongs to the Special Issue Structure-Function Relationships in Viral Polymerases)
Figures

Figure 1

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