title: Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions.
abstract: BACKGROUND
  The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity.
  
  
  RESULTS
  A software tool that identifies the genes encoded within a defined genomic neighborhood for the subject TR and its homologs was developed. The output lists of genes in the genetic neighborhoods, their annotated functions, the reactants/products, and identifies the metabolic pathway in which the encoded-proteins function. When a set of TRs of known function was analyzed, we observed that their homologs frequently had conserved genomic neighborhoods that co-located the metabolically related genes regulated by the subject TR. We postulate that TR effectors are metabolites in the identified pathways; indeed the known effectors were present. We analyzed Bxe_B3018 from Burkholderia xenovorans, a TR of unknown function and predicted that this TR was related to the glycine, threonine and serine degradation. We tested the binding of metabolites in these pathways and for those that bound, their ability to modulate TR binding to its specific DNA operator sequence. Using rtPCR, we confirmed that methylglyoxal was an effector of Bxe_3018.
  
  
  CONCLUSIONS
  These studies provide the proof of concept and validation of a systematic approach to the discovery of the biological activity for proteins of unknown function, in this case a TR. Bxe_B3018 is a methylglyoxal responsive TR that controls the expression of an operon composed of a putative efflux system.
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA. rm-a@lanl.gov.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Martí-Arbona
authors.forename: Fangping
authors.initials: F
authors.lastname: Mu
authors.forename: Kristy L
authors.initials: KL
authors.lastname: Nowak-Lovato
authors.forename: Melinda S
authors.initials: MS
authors.lastname: Wren
authors.forename: Clifford J
authors.initials: CJ
authors.lastname: Unkefer
authors.forename: Pat J
authors.initials: PJ
authors.lastname: Unkefer
mesh_terms: D019295:Computational Biology / Q000379:methods; D005786:Gene Expression Regulation; D023061:Gene Order; D056426:Genetic Loci; D016678:Genome; D023281:Genomics / Q000379:methods; D055432:Metabolomics; D011387:Prokaryotic Cells / Q000378:metabolism*; D011485:Protein Binding; D015203:Reproducibility of Results; D012984:Software; D014157:Transcription Factors; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors