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D. Models of Regulation During Light-Dark Transitions and of a Sigma Factor Network

We have devoted a great deal of effort to understanding the way in which the group 2 sigma factors function in Synechocystis, and especially during the light and dark periods.  The results have been published in a series of papers Singh et al. (2006), Foster et al. (2007) and Summerfield and Sherman (2007).  This has provided a great deal of information and much of this has been summarized in models presented in Summerfield and Sherman (2007).

Our results indicate the importance of the group 2 sigma factors, SigB, SigD and SigE, in global regulation of transcription in Synechocystis sp. PCC6803.  But, why are so many genes affected when one of these factors is deleted?  The results can best be explained using the σ cycle paradigm and particularly the stochastic release model as described in Mooney et al. (2005).  In this model, a pool of σ factors competes for binding to the core RNA polymerase to form an open complex.  The stochastic release model states that the affinity of σ for the RNA polymerase decreases in the elongation complex, but that release of the σ factor occurs stochastically after the RNA polymerase has initiated transcription.  Thus, sigma release occurs during each transcription cycle and sigma competition for rebinding of the RNA polymerase is permitted.  Mooney et al. (2005) have summarized the evidence for and against a half dozen different possible models of sigma action and conclude that stochastic release best describes all of the data.  Therefore, control of global transcription will be based on the amount of the various sigmas present and able to bind to the RNA polymerase.

The model described in Figure 2 is based on our transcription data as well as the levels of the nine sigma factors in the light and dark as calculated by Imamura et al. (2003).  In the wild type, the transition from growth in the light to the dark generated an increase in SigB and a decrease in SigE.  The major impact of this transition on global regulation was a decrease of the transcript levels of genes encoding ribosomal proteins and photosynthesis proteins.  At the same time, genes encoding enzymes involved in energy metabolism, biosynthesis of various cofactors and prosthetic groups, regulatory functions, and transport and binding proteins tended to increase.  This pattern was reversed as the cells go back into the light where SigB decreases two-fold SigD and SigE increase two-fold.  When SigB is absent, there’s very little effect in the light.  However, in the dark, many more genes show enhanced transcript levels relative to the wild type, especially in genes encoding ribosomal proteins and many hypothetical proteins.  It is striking that the major effect of removing SigB is to up-regulate at least some genes in many different categories.  Thus, the absence of SigB in the dark permits other sigma factors to preferentially bind to the RNA polymerase and to transcribe selected genes—especially the major operon encoding ribosomal proteins.

The absence of SigD has a more profound impact on global regulation of transcription.  SigD represented a larger proportion of sigma factors available in both the light and the dark, but especially during light growth.  In accordance with the stochastic release model, our results clearly demonstrated a much greater influence of SigD removal in the light than in the dark.  In the light, many genes demonstrated differential transcription in DsigD compared to the wild type and many of them were up-regulated.  When SigD was absent, photosynthesis genes demonstrated numerous changes, especially in the light where the SigD concentration would be the highest.  The absence of SigD leads to an increase in approximately two-thirds of the differentially regulated genes in the light, whereas only approximately half of the genes are up-regulated in the dark.  Taken together, the result with both mutants indicate that SigB is much more important in the dark, whereas SigD has a much greater influence on global transcription in the light.