Modularity and evolutionary constraints in a baculovirus gene regulatory network

BMC Systems Biology

Paolo Marinho de Andrade Zanotto³  Atila Iamarino¹  Caio César de Melo Freire¹  Carla Torres Braconi¹  Anderson Fernandes de Brito¹  Juliana Velasco Oliveira² 

[1] Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil;Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas Caixa Postal 6170, 13083-970, Brazil;Departamento de Microbiologia, Instituto de Ciências Biomédicas - ICB II, Laboratório de Evolução Molecular e Bioinformática, Universidade de São Paulo - USP, Av. Prof. Lineu Prestes, 1374, São Paulo CEP: 05508-900, Brasil

关键词: Modularity;    Overlapping transcripts;    Gene regulatory network;    Real-time PCR;    Transcriptome;    Baculovirus;   

Others  :  1142202
DOI  :  10.1186/1752-0509-7-87

 received in 2013-02-18, accepted in 2013-08-15,  发布年份 2013

【 摘 要 】

Background

The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression.

Results

We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization.

Conclusions

Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.

【 授权许可】

   
2013 Oliveira et al.; licensee BioMed Central Ltd.

【 图 表 】

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