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Nucleic Acids Research Advance Access published online on August 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn453
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Stringent promoter recognition and autoregulation by the group 3 {sigma}-factor SigF in the cyanobacterium Synechocystis sp. strain PCC 6803

Munehiko Asayama* and Sousuke Imamura

Laboratory of Molecular Genetics, School of Agriculture, Ibaraki University, 3-21-1 Ami, Inashiki, Ibaraki 300-0393, Japan

*To whom correspondence should be addressed. Tel./Fax: +81 29 888 8651; Email: asam{at}mx.ibaraki.ac.jp.

Received April 8, 2008. Revised June 17, 2008. Accepted June 30, 2008.

The cyanobacteirum Synechocystis sp. strain PCC 6803 possesses nine species of the sigma ({sigma})-factor gene for RNA polymerase (RNAP). Here, we identify and characterize the novel-type promoter recognized by a group 3 {sigma}-factor, SigF. SigF autoregulates its own transcription and recognizes the promoter of pilA1 that acts in pilus formation and motility in PCC 6803. The pilA1 promoter (PpilA1-54) was recognized only by SigF and not by other {sigma}-factors in PCC 6803. No PpilA1-54 activity was observed in Escherichia coli cells that possess RpoF ({sigma}28) for fragellin and motility. Studies of in vitro transcription for PpilA1-54 identified the region from –39 to –7 including an AG-rich stretch and a core promoter with TAGGC (–32 region) and GGTAA (–12 region) as important for transcription. We also confirmed the unique PpilA1-54 architecture and further identified two novel promoters, recognized by SigF, for genes encoding periplasmic and phytochrome-like phototaxis proteins. These results and a phylogenetic analysis suggest that the PCC 6803 SigF is distinct from the E. coli RpoF or RpoD ({sigma}70) type and constitutes a novel eubacterial group 3 {sigma}-factor. We discuss a model case of stringent promoter recognition by SigF. Promoter types of PCC 6803 genes are also summarized.


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