Growth-phase dependent differential gene expression in Synechocystis sp. strain PCC 6803 and regulation by a group 2 sigma factor
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Cyanobacteria must continually alter their physiological growth state in response to changes in light intensity and their nutritional and physical environment. Under typical laboratory batch growth conditions, cyanobacteria grow exponentially, then transition to a light-limited stage of linear growth before finally reaching a non-growth stationary phase. In this study, we utilized DNA microarrays to profile the expression of genes in the cyanobacterium Synechocystis sp. PCC 6803 to compare exponential and linear growth. We also studied the importance of SigB, a group 2 sigma factor in this cyanobacterium, during the different growth phases. The transcription of approximately 10% of the genes in the wild type were different in the linear, compared to the exponential phase, and our results showed that: (1) many photosynthesis and regulatory genes had lowered transcript levels; (2) individual genes, such as sigH, phrA, and isiA, which encode a group 4 sigma factor, a DNA photolyase, and a Chl-binding protein, respectively, were strongly induced; and, (3) the loss of SigB significantly impacted the differential expression of genes and modulated the changes seen in the wild type in regard to photosynthesis, regulatory and the unknown genes.
KeywordsCyanobacteria Light-limited growth Sigma factors Gene regulation Microarrays IsiA phrA
We thank Dr. Lauren McIntyre, Department of Agronomy, Purdue University, for developing the ANOVA model for analysis of the microarray data and Lisa Bono for training us in its use. We also wish to thank Dr. Hong Li for her significant efforts during the initial stages of this project. This research was supported by grant DE FG02-99ER20342 from the Department of Energy. J.S.F. was supported, in part, by a National Research Service Award 5F32AI056967-02 from the National Institutes of Health.
- Asayama M, Imamura S, Yoshihara S, Miyazaki A, Yoshida N, Sazuka T, Kaneko T, Ohara O, Tabata S, Osanai T, Tanaka K, Takahashi H, Shirai M (2004) SigC, the group 2 sigma factor of RNA polymerase, contributes to the late-stage gene expression and nitrogen promoter recognition in the cyanobacterium Synechocystis sp. strain PCC 6803. Biosci Biotechnol Biochem 68:477–487PubMedCrossRefGoogle Scholar
- Gerhardt P, Drew SW (1994) Liquid culture. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. 2 nd edn. American Society for Microbiology, Washington, DC, pp 224–247Google Scholar
- Huisman GW, Siegele DA, Zambrano MA, Kolter R (1996) Morphological and physioloical changes during stationary phase. In: Neidhardt FC et al. (eds) Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, DC, pp 1672–1682Google Scholar
- Nishiwaki T, Satomi Y, Nakajima M, Lee C, Kiyohara R, Kageyama H, Kitayama Y, Temamoto M, Yamaguchi A, Hijikata A, Go M, Iwasaki H, Takao T, Kondo T (2004) Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942. Proc Natl Acad Sci USA 101:13927–13932PubMedCrossRefGoogle Scholar
- Nystrom T, Kjelleberg S (1989) Role of protein synthesis in the cell division and starvation induced resistance to autolysis of a marine Vibrio during the initial phases of starvation. J Gen Mincrobiol 135:1599–1606Google Scholar
- Rick PD, Silver RP (1996) Enterobacterial common antigen and capsular polysaccharides. In: Neidhardt FC et al. (eds) Escherichia coli and Salmonella typhimurium: cellular and molecular biology. 2 nd edn. ASM Publications, Washington, DC, pp 104–122Google Scholar
- Rippka R, Waterbury JB, Stanier RY (1981) Isolation and purification of cyanobacteria some general principles. In: Starr MP, Stolp H, Truper HG, Balows A, Schlegel HG (eds) The Prokaryotes,vol 1. Springer, Berlin Heidelberg New York, pp 212–220Google Scholar
- Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
- Singh AK, Sherman LA (2005) Pleiotropic effect of a histidine kinase on carbohydrate metabolism in Synechocystis sp. strain PCC 6803 and its requirement for heterotrophic growth. J Bacteriol 187:2368–2376Google Scholar
- Wyman M, Fay P (1987) Acclimation to the natural light climate. In: Fay P, Van Baalen C (eds) The cyanobacteria. Elsevier, Amsterdam, pp 347–376Google Scholar
- Yeremenko N, Kouril R, Ihalainen JA, D’Haene S, van Oosterwijk N, Andrizhiyevskaya EG, Keegstra W, Dekker HL, Hagemann M, Boekema EJ, Matthijs HC, Dekker JP (2004) Supramolecular organization and dual function of the IsiA chlorophyll-binding protein in cyanobacteria. Biochemistry 43:10308–10313PubMedCrossRefGoogle Scholar