Tags

Type your tag names separated by a space and hit enter

A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process.
J Virol. 2019 12 01; 93(23)JV

Abstract

Pandoraviridae is a rapidly growing family of giant viruses, all of which have been isolated using laboratory strains of Acanthamoeba The genomes of 10 distinct strains have been fully characterized, reaching up to 2.5 Mb in size. These double-stranded DNA genomes encode the largest of all known viral proteomes and are propagated in oblate virions that are among the largest ever described (1.2 μm long and 0.5 μm wide). The evolutionary origin of these atypical viruses is the object of numerous speculations. Applying the chaos game representation to the pandoravirus genome sequences, we discovered that the tetranucleotide (4-mer) "AGCT" is totally absent from the genomes of 2 strains (Pandoravirus dulcis and Pandoravirus quercus) and strongly underrepresented in others. Given the amazingly low probability of such an observation in the corresponding randomized sequences, we investigated its biological significance through a comprehensive study of the 4-mer compositions of all viral genomes. Our results indicate that AGCT was specifically eliminated during the evolution of the Pandoraviridae and that none of the previously proposed host-virus antagonistic relationships could explain this phenomenon. Unlike the three other families of giant viruses (Mimiviridae, Pithoviridae, and Molliviridae) infecting the same Acanthamoeba host, the pandoraviruses exhibit a puzzling genomic anomaly suggesting a highly specific DNA editing in response to a new kind of strong evolutionary pressure.IMPORTANCE Recent years have seen the discovery of several families of giant DNA viruses infecting the ubiquitous amoebozoa of the genus Acanthamoeba With double-stranded DNA (dsDNA) genomes reaching 2.5 Mb in length packaged in oblate particles the size of a bacterium, the pandoraviruses are currently the most complex and largest viruses known. In addition to their spectacular dimensions, the pandoraviruses encode the largest proportion of proteins without homologs in other organisms, which is thought to result from a de novo gene creation process. While using comparative genomics to investigate the evolutionary forces responsible for the emergence of such an unusual giant virus family, we discovered a unique bias in the tetranucleotide composition of the pandoravirus genomes that can result only from an undescribed evolutionary process not encountered in any other microorganism.

Authors+Show Affiliations

Aix Marseille University, CNRS, IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Marseille, France olivier.poirot@igs.cnrs-mrs.fr jean-michel.claverie@univ-amu.fr.Aix Marseille University, CNRS, IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Marseille, France.Aix Marseille University, CNRS, IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Marseille, France.Aix Marseille University, CNRS, IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Marseille, France olivier.poirot@igs.cnrs-mrs.fr jean-michel.claverie@univ-amu.fr.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

31534042

Citation

Poirot, Olivier, et al. "A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process." Journal of Virology, vol. 93, no. 23, 2019.
Poirot O, Jeudy S, Abergel C, et al. A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. J Virol. 2019;93(23).
Poirot, O., Jeudy, S., Abergel, C., & Claverie, J. M. (2019). A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. Journal of Virology, 93(23). https://doi.org/10.1128/JVI.01206-19
Poirot O, et al. A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. J Virol. 2019 12 1;93(23) PubMed PMID: 31534042.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. AU - Poirot,Olivier, AU - Jeudy,Sandra, AU - Abergel,Chantal, AU - Claverie,Jean-Michel, Y1 - 2019/11/13/ PY - 2019/07/19/received PY - 2019/09/10/accepted PY - 2019/9/20/pubmed PY - 2020/6/17/medline PY - 2019/9/20/entrez KW - 4-mer statistics KW - DNA editing KW - Pandoravirus KW - chaos game representation KW - genome composition KW - giant viruses KW - host-virus relationship JF - Journal of virology JO - J Virol VL - 93 IS - 23 N2 - Pandoraviridae is a rapidly growing family of giant viruses, all of which have been isolated using laboratory strains of Acanthamoeba The genomes of 10 distinct strains have been fully characterized, reaching up to 2.5 Mb in size. These double-stranded DNA genomes encode the largest of all known viral proteomes and are propagated in oblate virions that are among the largest ever described (1.2 μm long and 0.5 μm wide). The evolutionary origin of these atypical viruses is the object of numerous speculations. Applying the chaos game representation to the pandoravirus genome sequences, we discovered that the tetranucleotide (4-mer) "AGCT" is totally absent from the genomes of 2 strains (Pandoravirus dulcis and Pandoravirus quercus) and strongly underrepresented in others. Given the amazingly low probability of such an observation in the corresponding randomized sequences, we investigated its biological significance through a comprehensive study of the 4-mer compositions of all viral genomes. Our results indicate that AGCT was specifically eliminated during the evolution of the Pandoraviridae and that none of the previously proposed host-virus antagonistic relationships could explain this phenomenon. Unlike the three other families of giant viruses (Mimiviridae, Pithoviridae, and Molliviridae) infecting the same Acanthamoeba host, the pandoraviruses exhibit a puzzling genomic anomaly suggesting a highly specific DNA editing in response to a new kind of strong evolutionary pressure.IMPORTANCE Recent years have seen the discovery of several families of giant DNA viruses infecting the ubiquitous amoebozoa of the genus Acanthamoeba With double-stranded DNA (dsDNA) genomes reaching 2.5 Mb in length packaged in oblate particles the size of a bacterium, the pandoraviruses are currently the most complex and largest viruses known. In addition to their spectacular dimensions, the pandoraviruses encode the largest proportion of proteins without homologs in other organisms, which is thought to result from a de novo gene creation process. While using comparative genomics to investigate the evolutionary forces responsible for the emergence of such an unusual giant virus family, we discovered a unique bias in the tetranucleotide composition of the pandoravirus genomes that can result only from an undescribed evolutionary process not encountered in any other microorganism. SN - 1098-5514 UR - https://www.unboundmedicine.com/medline/citation/31534042/A_Puzzling_Anomaly_in_the_4_Mer_Composition_of_the_Giant_Pandoravirus_Genomes_Reveals_a_Stringent_New_Evolutionary_Selection_Process_ L2 - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31534042/ DB - PRIME DP - Unbound Medicine ER -