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Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses

Begomovirus (genus Begomovirus, family Geminiviridae) infection is devastating to a wide variety of agricultural crops including tomato, squash, and cassava. Thus, understanding the replication and adaptation of begomoviruses has important translational value in alleviating substantial economic loss...

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Autores principales: Ho, Eric S., Kuchie, Joan, Duffy, Siobain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226511/
https://www.ncbi.nlm.nih.gov/pubmed/25383632
http://dx.doi.org/10.1371/journal.pone.0111957
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author Ho, Eric S.
Kuchie, Joan
Duffy, Siobain
author_facet Ho, Eric S.
Kuchie, Joan
Duffy, Siobain
author_sort Ho, Eric S.
collection PubMed
description Begomovirus (genus Begomovirus, family Geminiviridae) infection is devastating to a wide variety of agricultural crops including tomato, squash, and cassava. Thus, understanding the replication and adaptation of begomoviruses has important translational value in alleviating substantial economic loss, particularly in developing countries. The bipartite genome of begomoviruses prevalent in the New World and their counterparts in the Old World share a high degree of genome homology except for a partially overlapping reading frame encoding the pre-coat protein (PCP, or AV2). PCP contributes to the essential functions of intercellular movement and suppression of host RNA silencing, but it is only present in the Old World viruses. In this study, we analyzed a set of non-redundant bipartite begomovirus genomes originating from the Old World (N = 28) and the New World (N = 65). Our bioinformatic analysis suggests ∼120 nucleotides were deleted from PCP’s proximal promoter region that may have contributed to its loss in the New World viruses. Consequently, genomes of the New World viruses are smaller than the Old World counterparts, possibly compensating for the loss of the intercellular movement functions of PCP. Additionally, we detected substantial purifying selection on a portion of the New World DNA-B movement protein (MP, or BC1). Further analysis of the New World MP gene revealed the emergence of a putative tyrosine phosphorylation site, which likely explains the increased purifying selection in that region. These findings provide important information about the strategies adopted by bipartite begomoviruses in adapting to new environment and suggest future in planta experiments.
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spelling pubmed-42265112014-11-13 Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses Ho, Eric S. Kuchie, Joan Duffy, Siobain PLoS One Research Article Begomovirus (genus Begomovirus, family Geminiviridae) infection is devastating to a wide variety of agricultural crops including tomato, squash, and cassava. Thus, understanding the replication and adaptation of begomoviruses has important translational value in alleviating substantial economic loss, particularly in developing countries. The bipartite genome of begomoviruses prevalent in the New World and their counterparts in the Old World share a high degree of genome homology except for a partially overlapping reading frame encoding the pre-coat protein (PCP, or AV2). PCP contributes to the essential functions of intercellular movement and suppression of host RNA silencing, but it is only present in the Old World viruses. In this study, we analyzed a set of non-redundant bipartite begomovirus genomes originating from the Old World (N = 28) and the New World (N = 65). Our bioinformatic analysis suggests ∼120 nucleotides were deleted from PCP’s proximal promoter region that may have contributed to its loss in the New World viruses. Consequently, genomes of the New World viruses are smaller than the Old World counterparts, possibly compensating for the loss of the intercellular movement functions of PCP. Additionally, we detected substantial purifying selection on a portion of the New World DNA-B movement protein (MP, or BC1). Further analysis of the New World MP gene revealed the emergence of a putative tyrosine phosphorylation site, which likely explains the increased purifying selection in that region. These findings provide important information about the strategies adopted by bipartite begomoviruses in adapting to new environment and suggest future in planta experiments. Public Library of Science 2014-11-10 /pmc/articles/PMC4226511/ /pubmed/25383632 http://dx.doi.org/10.1371/journal.pone.0111957 Text en © 2014 Ho et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Ho, Eric S.
Kuchie, Joan
Duffy, Siobain
Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses
title Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses
title_full Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses
title_fullStr Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses
title_full_unstemmed Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses
title_short Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses
title_sort bioinformatic analysis reveals genome size reduction and the emergence of tyrosine phosphorylation site in the movement protein of new world bipartite begomoviruses
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226511/
https://www.ncbi.nlm.nih.gov/pubmed/25383632
http://dx.doi.org/10.1371/journal.pone.0111957
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