Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development

Abstract

BackgroundSeveral Gram-negative species undergo development leading to the formation of metabolically dormant desiccation resistant cysts. Recent analysis of cyst development has revealed that ~20 % of the Rhodospirillum centenum transcriptome undergo temporal changes in expression as cells transition from vegetative to cyst forms. It has also been established that one trigger for cyst formation is the synthesis of the signaling nucleotide 3‘, 5‘- cyclic guanosine monophosphate (cGMP) that is sensed by a homolog of the catabolite repressor protein called CgrA. CgrA in the presence of cGMP initiate a cascade of gene expression leading to the development of cysts.ResultsIn this study, we have used RNA-seq and chromatin immunoprecipitation (ChIP-Seq) techniques to define the CgrA-cGMP regulon. Our results indicate that disruption of CgrA leads to altered expression of 258 genes, 131 of which have been previously reported to be involved in cyst development. ChIP-seq analysis combined with transcriptome data also demonstrates that CgrA directly regulates the expression of numerous sigma factors and transcription factors several of which are known to be involved in cyst cell development.ConclusionsThis analysis reveals the presence of CgrA binding sites upstream of many developmentally regulated genes including many transcription factors and signal transduction components. CgrA thus functions as master controller of the cyst development by initiating a hierarchal cascade of downstream transcription factors that induces temporal expression of encystment genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2248-z) contains supplementary material, which is available to authorized users.

The Vitamin B 12 -Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters

“…Finally, there are 101 called peaks for which we do not observe changes in neighboring gene expression. Similar ChIP-seq-identified “silent” binding sites have been reported for several other transcription factors such as cyclic AMP receptor protein (CRP), FnrL, fumarate and nitrate reductase (FNR), LuxR, and CgrA (5, 29–32). These silent peaks imply additional potential regulation by CrtJ that presumably do not show regulation under the assayed RNA-seq conditions due to other transcription factors that are dominant.…”

Transcriptome analysis of Azospirillum brasilense vegetative and cyst states reveals large-scale alterations in metabolic and replicative gene expression

“…In congruence with an overall reduction in protein synthesis, we also observed six genes involved in amino acid metabolism that were repressed (Data S1). Reduced protein synthesis in Azospirillum cysts is also consistent with our previous transcriptome study on R. centenum cysts [ 19 ].…”

“…A lack of general metabolic repression has also been noted by Dong et al . [ 19 ] regarding the R. centenum cyst transcriptome. Azospirillum cysts did, however, display different global patterns for several metabolic processes as compared with vegetative cells.…”

New Twists and Turns in Bacterial Locomotion and Signal Transduction

“…The development of a technique to synchronize bacterial encystation, along with whole transcriptome shotgun sequencing (RNA-Seq) of cells along this developmental trajectory, and traditional forward and reverse genetics allowed this group to dissect how a complex Che3 phosphorelay switches bacteria between vegetative growth and cyst formation. The discovery that nucleotidyl cyclase mutants interrupted encystation also allowed Bauer and colleagues to identify cyclic GMP as an activating cofactor for the transcriptional regulator CgrA, with a regulon encompassing approximately one-third of the genes involved in cyst development (67).…”