Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in Rhodobacter capsulatus

Abstract

The purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in Caulobacter crescentus has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in R. capsulatus shares a high degree of sequence similarity with the C. crescentus protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and ctrA mutant cultures to identify the genes dysregulated by the loss of CtrA in R. capsulatus. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of ϳ6% of genes in the R. capsulatus genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral ctrA gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages.The purple nonsulfur bacterium Rhodobacter capsulatus is a model organism for various aspects of bacterial physiology, such as bioenergetics and N 2 fixation, and also engages in an unusual mechanism of genetic exchange, carried out by a bacteriophage-like element called the R. capsulatus gene transfer agent (RcGTA) (34, 56). The production of RcGTA is maximal in the stationary phase of growth of R. capsulatus cultures (49) and is regulated by at least 2 distinct signaling systems, one through quorum sensing of a long chain acyl-homoserine lactone (43) and the other involving the response regulator protein CtrA (30).The CtrA protein was first characterized for Caulobacter crescentus (41), where it is essential for viability and acts as a master regulator of the cell cycle (reviewed in reference 45), controlling at least 25% (144 of 553) of the genes involved in cell cycle progression (31). Despite sharing remarkable sequence identity (71%) with the CtrA protein from C. crescentus, the R. capsulatus protein has a very different role because it is not essential and does not appear to be involved in cell cycle processes. One function of CtrA in common to the two species is the regulation of expression of genes that encode the flagellum (29, 41). The ctrA genes of Sinorhizobium meliloti (3), Brucella abortus (6), and Ruegeria sp. strain TM1040 (36) have also been studied. Similarly to C. crescentus and R. capsulatus CtrA, Ruegeria CtrA controls motility (36). A search of the GenBank database reveals that convincing homologs which share Ͼ50% identity with the C. crescen...

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“…It remains to be elucidated if the various types of cell division observed here are connected through a regular cell cycle. In Rhodobacter capsulatus (Mercer et al, 2010) and Silicibacter sp. TM1040 (Belas et al, 2009) the growth rate of the culture was not affected by knockout of ctrA.…”

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Involvement of the response regulator CtrA in the extracellular DNA production of the marine bacterium <i>Rhodovulum sulfidophilum</i>

“…Similar effects of CtrA has been noted in Rhodobacter capsulatus. Mercer et al (2010) reported that a loss of the CtrA did not affect growth phase regulation in Rba. capsulatus.…”

“…CtrA of Rba. capsulatus is not essential and is not involved in the cell cycle (Mercer et al, 2010). In a previous paper, we reported that R. sulfidophilum produces GTA-like particles and that this production is controlled by the gene ctrA (Nagao et al, 2015b).…”