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Journal of Bacteriology, July 2002, p. 3671-3681, Vol. 184, No. 13
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.13.3671-3681.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Genome-Wide Dynamic Transcriptional Profiling of the Light-to-Dark Transition in Synechocystis sp. Strain PCC 6803

Ryan T. Gill,1 Eva Katsoulakis,1 William Schmitt,1 Gaspar Taroncher-Oldenburg,2 Jatin Misra,1 and Gregory Stephanopoulos1*

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,1 Princeton Environmental Institute, Princeton University, Princeton, New Jersey 085442

Received 11 October 2001/ Accepted 29 March 2002

We report the results of whole-genome transcriptional profiling of the light-to-dark transition with the model photosynthetic prokaryote Synechocystis sp. strain PCC 6803 (Synechocystis). Experiments were conducted by growing Synechocystis cultures to mid-exponential phase and then exposing them to two cycles of light/dark conditions, during which RNA samples were obtained. These samples were probed with a full-genome DNA microarray (3,169 genes, 20 samples) as well as a partial-genome microarray (88 genes, 29 samples). We concluded that (i) 30-min sampling intervals accurately captured transcriptional dynamics throughout the light/dark transition, (ii) 25% of the Synechocystis genes (783 genes) responded positively to the presence of light, and (iii) the response dynamics varied greatly for individual genes, with a delay of up to 120 to 150 min for some genes. Four classes of genes were identified on the basis of their dynamic gene expression profiles: class I (108 genes, 30-min response time), class II (279 genes, 60 to 90 min), class III (258 genes, 120 to 150 min), and class IV (138 genes, 180 min). The dynamics of several transcripts from genes involved in photosynthesis and primary energy generation are discussed. Finally, we applied Fisher discriminant analysis to better visualize the progression of the overall transcriptional program throughout the light/dark transition and to determine those genes most indicative of the lighting conditions during growth.

* Corresponding author. Mailing address: Department of Chemical Engineering, Room 56-469, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139. Phone: (617) 253-4583. Fax: (617) 253-3122. E-mail: gregstep{at}mit.edu.

Journal of Bacteriology, July 2002, p. 3671-3681, Vol. 184, No. 13
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.13.3671-3681.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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