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, 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.
Department of Biology, Lafayette College, Easton, Pennsylvania, United States of America.
Eric S
ES
Ho
New Jersey City University, Jersey City, New Jersey, United States of America.
Joan
J
Kuchie
Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America.
Siobain
S
Duffy
D000595:Amino Acid Sequence; D053839:Begomovirus / Q000235:genetics* / Q000378:metabolism*; D001665:Binding Sites; D019295:Computational Biology; D019143:Evolution, Molecular; D059646:Genome Size; D008969:Molecular Sequence Data; D009068:Movement; D011401:Promoter Regions, Genetic; D021381:Protein Transport; D012641:Selection, Genetic; D013045:Species Specificity; D014443:Tyrosine / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
D014764:Viral Proteins; D014443:Tyrosine