Replication mode and landscape topology differentially affect RNA virus mutational load and robustness

Regardless of genome polarity, intermediaries of complementary sense must be synthesized and used as templates for the production of new genomic strands. Depending on whether these new genomic strands become themselves templates for producing extra antigenomic ones, thus giving rise to geometric gro...

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Detalles Bibliográficos
Autores: Sardanyés, Josep, Solé, Ricard V., Elena, Santiago F.
Tipo de recurso: artículo
Fecha de publicación:2009
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/18457
Acceso en línea:http://hdl.handle.net/10261/18457
Access Level:acceso abierto
Palabra clave:virus evolution
systems biology
replication
fitness landscapes
deleterious mutations
robustness
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spelling Replication mode and landscape topology differentially affect RNA virus mutational load and robustnessSardanyés, JosepSolé, Ricard V.Elena, Santiago F.virus evolutionsystems biologyreplicationfitness landscapesdeleterious mutationsrobustnessRegardless of genome polarity, intermediaries of complementary sense must be synthesized and used as templates for the production of new genomic strands. Depending on whether these new genomic strands become themselves templates for producing extra antigenomic ones, thus giving rise to geometric growth, or only the firstly synthesized antigenomic strands can be used to this end, thus following Luria's stamping machine model, the abundances and distributions of mutant genomes will be different. Here we propose mathematical and bit string models that allow distinguishing between stamping machine and geometric replication. We have observed that, regardless the topology of the fitness landscape, the critical mutation rate at which the master sequence disappears increases as the mechanism of replication switches from purely geometric to stamping machine. We also found that, for a wide range of mutation rates, large-effect mutations do not accumulate regardless the scheme of replication. However, mild mutations accumulate more in the geometric model. Furthermore, at high mutation rates, geometric growth leads to a population collapse for intermediate values of mutational effects at which the stamping machine still produces master genomes. We observed that the critical mutation rate was weakly dependent on the strength of antagonistic epistasis but strongly dependent on synergistic epistasis. In conclusion, we have shown that RNA viruses may increase their robustness against the accumulation of deleterious mutations by replicating as stamping machines and that the magnitude of this benefit depends on the topology of the fitness landscape assumed.Peer reviewedAmerican Society for Microbiology200920092009info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_65012898758 bytesapplication/pdfhttp://hdl.handle.net/10261/18457reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglésjvi.asm.org/cgi/content/full/83/23/12579?view=long&pmid=19776117info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/184572026-05-22T06:33:51Z
dc.title.none.fl_str_mv Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
title Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
spellingShingle Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
Sardanyés, Josep
virus evolution
systems biology
replication
fitness landscapes
deleterious mutations
robustness
title_short Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
title_full Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
title_fullStr Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
title_full_unstemmed Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
title_sort Replication mode and landscape topology differentially affect RNA virus mutational load and robustness
dc.creator.none.fl_str_mv Sardanyés, Josep
Solé, Ricard V.
Elena, Santiago F.
author Sardanyés, Josep
author_facet Sardanyés, Josep
Solé, Ricard V.
Elena, Santiago F.
author_role author
author2 Solé, Ricard V.
Elena, Santiago F.
author2_role author
author
dc.subject.none.fl_str_mv virus evolution
systems biology
replication
fitness landscapes
deleterious mutations
robustness
topic virus evolution
systems biology
replication
fitness landscapes
deleterious mutations
robustness
description Regardless of genome polarity, intermediaries of complementary sense must be synthesized and used as templates for the production of new genomic strands. Depending on whether these new genomic strands become themselves templates for producing extra antigenomic ones, thus giving rise to geometric growth, or only the firstly synthesized antigenomic strands can be used to this end, thus following Luria's stamping machine model, the abundances and distributions of mutant genomes will be different. Here we propose mathematical and bit string models that allow distinguishing between stamping machine and geometric replication. We have observed that, regardless the topology of the fitness landscape, the critical mutation rate at which the master sequence disappears increases as the mechanism of replication switches from purely geometric to stamping machine. We also found that, for a wide range of mutation rates, large-effect mutations do not accumulate regardless the scheme of replication. However, mild mutations accumulate more in the geometric model. Furthermore, at high mutation rates, geometric growth leads to a population collapse for intermediate values of mutational effects at which the stamping machine still produces master genomes. We observed that the critical mutation rate was weakly dependent on the strength of antagonistic epistasis but strongly dependent on synergistic epistasis. In conclusion, we have shown that RNA viruses may increase their robustness against the accumulation of deleterious mutations by replicating as stamping machines and that the magnitude of this benefit depends on the topology of the fitness landscape assumed.
publishDate 2009
dc.date.none.fl_str_mv 2009
2009
2009
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/18457
url http://hdl.handle.net/10261/18457
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv jvi.asm.org/cgi/content/full/83/23/12579?view=long&pmid=19776117
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 2898758 bytes
application/pdf
dc.publisher.none.fl_str_mv American Society for Microbiology
publisher.none.fl_str_mv American Society for Microbiology
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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