Growth-phase dependent differential gene expression in Synechocystis sp. strain PCC 6803 and regulation by a group 2 sig
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ORIGINAL PAPER
Growth-phase dependent differential gene expression in Synechocystis sp. strain PCC 6803 and regulation by a group 2 sigma factor Jamie S. Foster Æ Abhay K. Singh Æ Lynn J. Rothschild Æ Louis A. Sherman
Received: 7 July 2006 / Revised: 25 October 2006 / Accepted: 6 November 2006 / Published online: 12 December 2006 Springer-Verlag 2006
Abstract 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. Keywords Cyanobacteria Light-limited growth Sigma factors Gene regulation Microarrays IsiA phrA
Introduction Electronic supplementary material Supplementary material is available in the online version of this article at http://dx.doi.org/ 10.1007/s00203-006-0193-6 and is accessible for authorized users. J. S. Foster Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Kennedy Space Center, FL 32899, USA J. S. Foster L. J. Rothschild NASA Ames Research Center, Ecosystem, Science and Technology Branch, Moffett Field, CA 94035, USA J. S. Foster A. K. Singh L. A. Sherman (&) Department of Biological Sciences, Purdue University, 1392 Lilly Hall of Life Sciences, West Lafayette, IN 47907, USA e-mail: [email protected] Present Address: A. K. Singh Department of Biology, Washington University, St. Louis, MO 63130, USA
Cyanobacteria are a physiologically and ecologically diverse group of microbes that occupy a wide range of habitats (Potts 1999; Taton et al. 2003). The competitive success of these dominant phototrophs depends heavily on continuous fine-tuning of growth rate in order to exploit the changing nutritional environment. To cope with depleted nutrients and exploit those that are plentiful, microbes undergo transitions from exponential to arithmetic (linear) growth into nongrowth physiological states (Gerhardt and Drew 1994). As a required nutrient becomes exhaust
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