Systematic characterization of hypothetical proteins in Synechocystis sp. PCC 6803 reveals proteins functionally relevant to stress responses.
We described here a global detection and functional inference of hypothetical proteins involved in stress response in Synechocystis sp. PCC 6803. In the study, we first applied an iTRAQ-LC-MS/MS based quantitative proteomics to the Synechocystis cells grown under five stress conditions. The analysis detected a total of 807 hypothetical proteins with high confidence. Among them, 480 were differentially regulated. We then applied a Weighted Gene Co-expression Network Analysis approach to construct transcriptional networks for Synechocystis under nutrient limitation and osmotic stress conditions using transcriptome datasets. The analysis showed that 305 and 467 coding genes of hypothetical proteins were functionally relevant to nutrient limitation and osmotic stress, respectively. A comparison of responsive hypothetical proteins to all stress conditions allowed identification of 22 hypothetical proteins commonly responsive to all stresses, suggesting they may be part of the core stress responses in Synechocystis. Finally, functional inference of these core stress responsive proteins using both sequence similarity and non-similarity approaches was conducted. The study provided new insights into the stress response networks in Synechocystis, and also demonstrated that a combination of experimental "OMICS" and bioinformatics methodologies could improve functional annotation for hypothetical proteins.
School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China.
Jianjun
J
Qiao
Mingyang
M
Shao
Lei
L
Chen
Jiangxin
J
Wang
Gang
G
Wu
Xiaoxu
X
Tian
Jie
J
Liu
Siqiang
S
Huang
Weiwen
W
Zhang
D001426:Bacterial Proteins / Q000378:metabolism*; D019295:Computational Biology; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial; D013058:Mass Spectrometry; D058977:Molecular Sequence Annotation; D020543:Proteome; D040901:Proteomics / Q000379:methods; D013312:Stress, Physiological / Q000235:genetics; D046939:Synechocystis / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
D001426:Bacterial Proteins; D020543:Proteome