title: Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development.
abstract: BACKGROUND
  Several 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. dong3@umail.iu.edu.
authors.forename: Qian
authors.initials: Q
authors.lastname: Dong
authors.affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. fangm@umail.iu.edu.
authors.forename: Mingxu
authors.initials: M
authors.lastname: Fang
authors.affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. suroycho@umail.iu.edu.|Present address: Owensboro Cancer Research Program, University of Louisville James Graham Brown Cancer Center, Owensboro, KY, 42303, USA. suroycho@umail.iu.edu.
authors.forename: Sugata
authors.initials: S
authors.lastname: Roychowdhury
authors.affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. bauer@indiana.edu.|Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S. Hawthorne Drive, Bloomington, IN, 47405-7003, USA. bauer@indiana.edu.
authors.forename: Carl E
authors.initials: CE
authors.lastname: Bauer
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional; D018085:Regulon; D042182:Rhodospirillum centenum / Q000502:physiology*; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins