Viral RNAs are unusually compact.
A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements o...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4154850?pdf=render |
| _version_ | 1828886859177000960 |
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| author | Ajaykumar Gopal Defne E Egecioglu Aron M Yoffe Avinoam Ben-Shaul Ayala L N Rao Charles M Knobler William M Gelbart |
| author_facet | Ajaykumar Gopal Defne E Egecioglu Aron M Yoffe Avinoam Ben-Shaul Ayala L N Rao Charles M Knobler William M Gelbart |
| author_sort | Ajaykumar Gopal |
| collection | DOAJ |
| description | A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly. |
| first_indexed | 2024-12-13T11:52:41Z |
| format | Article |
| id | doaj.art-195534bbfa944771a070536efc50ad3f |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T11:52:41Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-195534bbfa944771a070536efc50ad3f2022-12-21T23:47:18ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0199e10587510.1371/journal.pone.0105875Viral RNAs are unusually compact.Ajaykumar GopalDefne E EgeciogluAron M YoffeAvinoam Ben-ShaulAyala L N RaoCharles M KnoblerWilliam M GelbartA majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly.http://europepmc.org/articles/PMC4154850?pdf=render |
| spellingShingle | Ajaykumar Gopal Defne E Egecioglu Aron M Yoffe Avinoam Ben-Shaul Ayala L N Rao Charles M Knobler William M Gelbart Viral RNAs are unusually compact. PLoS ONE |
| title | Viral RNAs are unusually compact. |
| title_full | Viral RNAs are unusually compact. |
| title_fullStr | Viral RNAs are unusually compact. |
| title_full_unstemmed | Viral RNAs are unusually compact. |
| title_short | Viral RNAs are unusually compact. |
| title_sort | viral rnas are unusually compact |
| url | http://europepmc.org/articles/PMC4154850?pdf=render |
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