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Related Concept Videos

Viral Structure00:56

Viral Structure

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Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Small population sizes put a species at extreme risk of extinction due to a lack of variation, and a consequent decrease in adaptability. This weakens the chances of survival under pressures such as climate change, competition from other species, or new diseases. Large populations are more likely to survive pressures such as these, as such populations are more likely to harbor individuals that have genetic variants that are adaptive under new stresses. Small populations are much less...
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Conserved Secondary Structures in Viral mRNAs.

Michael Kiening1, Roman Ochsenreiter2, Hans-Jörg Hellinger3

  • 1Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany. m.kiening@wzw.tum.de.

Viruses
|May 1, 2019
PubMed
Summary

This study presents the first comprehensive catalog of conserved RNA structures within viral protein-coding regions. These identified RNA structures, organized into subVOGs, offer insights into viral regulation and replication.

Keywords:
RNA structuremRNA familiesmRNA structuresecondary structurestructurally homogenousstructurally relatedstructure databasesubVOGviral mRNA

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Area of Science:

  • Virology
  • Computational Biology
  • RNA Biology

Background:

  • RNA secondary structures in untranslated and coding regions are crucial for gene regulation and viral replication.
  • While non-coding RNA structures are well-studied, a comprehensive overview of viral coding mRNA structures is missing.
  • Predicting secondary structures for long RNA molecules like viral mRNAs is computationally challenging due to combinatorial complexity.

Purpose of the Study:

  • To develop and apply a computational pipeline for predicting functional conserved RNA secondary structures in viral coding regions.
  • To create the first comprehensive compilation of such structures across the entire RefSeq viral database.
  • To make these findings accessible via a dedicated web resource.

Main Methods:

  • A structure prediction pipeline was applied to Viral Orthologous Groups (VOGs).
  • The pipeline identifies potentially structured regions and assesses their functional significance.
  • Orthologous groups were segmented into structurally homogeneous subgroups termed subVOGs.

Main Results:

  • Successfully recovered known RNA structural elements within viral coding sequences.
  • Discovered numerous novel structured regions previously uncharacterized.
  • Generated a comprehensive catalog of conserved RNA structures in viral coding regions, covering the complete RefSeq viral database.

Conclusions:

  • The study provides the first extensive resource (subVOGs) of conserved RNA structures in viral coding regions.
  • These findings enhance understanding of RNA's role in viral regulatory processes and replication.
  • The RNASIV web resource (http://rnasiv.bio.wzw.tum.de) offers access to these novel structural insights.