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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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Size and Structure of Viral Genomes01:26

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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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Nucleic Acid Structure01:25

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
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Introduction to Virus01:28

Introduction to Virus

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Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic processes, they can exhibit characteristics of life when infecting a host. Their defining feature is a nucleic acid core, composed of either DNA or RNA, encapsulated within a protein coat called a capsid. This simple structure allows them to invade host cells and use their machinery for replication efficiently.Viral Structure and...
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Viruses with RNA Genomes01:29

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
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Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification.

Robert M Sinclair1, Janne J Ravantti2, Dennis H Bamford3

  • 1Mathematical Biology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.

Journal of Virology
|January 27, 2017
PubMed
Summary
This summary is machine-generated.

Viral capsid proteins share hidden sequence similarities, supporting a structure-based classification. This finding reveals ancient evolutionary signatures in viral genomes across all domains of life.

Keywords:
cotranslational protein foldingmore sensitive orphan gene annotationsequence similarity twilight zonestructure-based viral lineages

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Area of Science:

  • Virology
  • Structural Biology
  • Bioinformatics

Background:

  • Viral capsids protect viral genomes and exhibit strong evolutionary conservation.
  • A structure-based classification of viruses has been proposed but lacked strong sequence support.
  • Structural convergence was a potential explanation for observed capsid similarities.

Purpose of the Study:

  • To investigate if undetected sequence similarities support a structure-based viral capsid classification.
  • To explore both amino acid and nucleotide sequence similarity for evolutionary insights.
  • To identify candidate genes for viral capsid proteins, such as for Pandoravirus.

Main Methods:

  • Comparative sequence analysis of viral capsid proteins.
  • Searched for both amino acid and nucleotide sequence similarities.
  • Utilized a structure-based classification framework for viral capsids.

Main Results:

  • Detected significant amino acid and nucleotide sequence similarities among viral capsid proteins.
  • Confirmed that sequence similarities strongly support the structure-based classification.
  • Identified a candidate gene for the Pandoravirus capsid protein.

Conclusions:

  • The structure-based classification of icosahedral viral capsids is supported by common descent, evidenced by sequence similarities.
  • Nucleotide sequence similarities were found across viruses infecting all three domains of life.
  • This study bridges sequence and structure analyses for understanding macromolecular function and evolution.