Biocomputional construction of a gene network under acid stress in Synechocystis sp. PCC 6803.
Acid stress is one of the most serious threats that cyanobacteria have to face, and it has an impact at all levels from genome to phenotype. However, very little is known about the detailed response mechanism to acid stress in this species. We present here a general analysis of the gene regulatory network of Synechocystis sp. PCC 6803 in response to acid stress using comparative genome analysis and biocomputational prediction. In this study, we collected 85 genes and used them as an initial template to predict new genes through co-regulation, protein-protein interactions and the phylogenetic profile, and 179 new genes were obtained to form a complete template. In addition, we found that 11 enriched pathways such as glycolysis are closely related to the acid stress response. Finally, we constructed a regulatory network for the intricate relationship of these genes and summarize the key steps in response to acid stress. This is the first time a bioinformatic approach has been taken systematically to gene interactions in cyanobacteria and the elaboration of their cell metabolism and regulatory pathways under acid stress, which is more efficient than a traditional experimental study. The results also provide theoretical support for similar research into environmental stresses in cyanobacteria and possible industrial applications.
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
Yi
Y
Li
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China. Electronic address: raonn@uestc.edu.cn.
Nini
N
Rao
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
Feng
F
Yang
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
Ying
Y
Zhang
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
Yang
Y
Yang
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
Han-ming
HM
Liu
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
Fengbiao
F
Guo
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
Jian
J
Huang
D000143:Acids / Q000633:toxicity*; D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks; D013312:Stress, Physiological; D046939:Synechocystis / Q000187:drug effects*
D000143:Acids
Acid stress; Operon; Pathway; Protein–protein interaction; Regulatory network