Virus-Host Coevolution: Common Patterns of Nucleotide Motif Usage in Flaviviridae and Their Hosts

被引:147
作者
Lobo, Francisco P.
Mota, Bruno E. F.
Pena, Sergio D. J.
Azevedo, Vasco
Macedo, Andrea M.
Tauch, Andreas
Machado, Carlos R.
Franco, Gloria R.
机构
[1] Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais
[2] Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais
[3] Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais
[4] Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld
来源
PLOS ONE | 2009年 / 4卷 / 07期
关键词
HEPATITIS-C VIRUS; SWINE-FEVER VIRUS; ANTIVIRAL RESPONSE; PHYLOGENETIC-RELATIONSHIPS; CYTOSINE METHYLATION; DISEASE ASSOCIATION; CODON USAGE; IN-VITRO; RNASE-L; INTERFERON;
D O I
10.1371/journal.pone.0006282
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Virus-host biological interaction is a continuous coevolutionary process involving both host immune system and viral escape mechanisms. Flaviviridae family is composed of fast evolving RNA viruses that infects vertebrate (mammals and birds) and/or invertebrate (ticks and mosquitoes) organisms. These host groups are very distinct life forms separated by a long evolutionary time, so lineage-specific anti-viral mechanisms are likely to have evolved. Flaviviridae viruses which infect a single host lineage would be subjected to specific host-induced pressures and, therefore, selected by them. In this work we compare the genomic evolutionary patterns of Flaviviridae viruses and their hosts in an attempt to uncover coevolutionary processes inducing common features in such disparate groups. Especially, we have analyzed dinucleotide and codon usage patterns in the coding regions of vertebrate and invertebrate organisms as well as in Flaviviridae viruses which specifically infect one or both host types. The two host groups possess very distinctive dinucleotide and codon usage patterns. A pronounced CpG under-representation was found in the vertebrate group, possibly induced by the methylation-deamination process, as well as a prominent TpA decrease. The invertebrate group displayed only a TpA frequency reduction bias. Flaviviridae viruses mimicked host nucleotide motif usage in a host-specific manner. Vertebrate-infecting viruses possessed under-representation of CpG and TpA, and insect-only viruses displayed only a TpA under-representation bias. Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively) were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae. We demonstrated that vertebrates and mosquitoes genomes are under very distinct lineage-specific constraints, and Flaviviridae viruses which specifically infect these lineages appear to be subject to the same evolutionary pressures that shaped their host coding regions, evidencing the lineage-specific coevolutionary processes between the viral and host groups.
引用
收藏
页数:14
相关论文
共 92 条
[1]   Modulation of toll-like receptor 9 responses through synthetic immunostimulatory motifs of DNA [J].
Agrawal, S ;
Kandimalla, ER .
THERAPEUTIC OLIGONUCLEOTIDES: ANTISENSE, RNAI, TRIPLE-HELIX, GENE REPAIR, ENHANCER DECOYS, CPG AND DNA CHIPS, 2003, 1002 :30-42
[2]   Pattern recognition receptors: From the cell surface to intracellular dynamics [J].
Altenbach, Denise ;
Robatzek, Silke .
MOLECULAR PLANT-MICROBE INTERACTIONS, 2007, 20 (09) :1031-1039
[3]  
[Anonymous], CURR PROTOC BIOINFOR
[4]   Classical swine fever virus Npro interacts with interferon regulatory factor 3 and induces its proteasomal degradation [J].
Bauhofer, Oliver ;
Summerfield, Artur ;
Sakoda, Yoshihiro ;
Tratschin, Jon-Duri ;
Hofmann, Martin A. ;
Ruggli, Nicolas .
JOURNAL OF VIROLOGY, 2007, 81 (07) :3087-3096
[5]   The RNA Virus Database [J].
Belshaw, Robert ;
de Oliveira, Tulio ;
Markowitz, Sidney ;
Rambaut, Andrew .
NUCLEIC ACIDS RESEARCH, 2009, 37 :D431-D435
[6]  
BENSON DA, 2008, NUCL ACIDS RES
[7]   Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector [J].
Billoir, F ;
de Chesse, R ;
Tolou, H ;
de Micco, P ;
Gould, EA ;
de Lamballerie, X .
JOURNAL OF GENERAL VIROLOGY, 2000, 81 :781-790
[8]   Perceptions of epigenetics [J].
Bird, Adrian .
NATURE, 2007, 447 (7143) :396-398
[9]   DNA METHYLATION AND THE FREQUENCY OF CPG IN ANIMAL DNA [J].
BIRD, AP .
NUCLEIC ACIDS RESEARCH, 1980, 8 (07) :1499-1504
[10]   Diverse functions of RNase L and implications in pathology [J].
Bisbal, Catherine ;
Silverman, Robert H. .
BIOCHIMIE, 2007, 89 (6-7) :789-798