title: Discovery of DNA operators for TetR and MarR family transcription factors from Burkholderia xenovorans.
abstract: Determining transcription factor (TF) recognition motifs or operator sites is central to understanding gene regulation, yet few operators have been characterized. In this study, we used a protein-binding microarray (PBM) to discover the DNA recognition sites and putative regulons for three TetR and one MarR family TFs derived from Burkholderia xenovorans, which are common to the genus Burkholderia. We also describe the development and application of a more streamlined version of the PBM technology that significantly reduced the experimental time. Despite the genus containing many pathogenically important species, only a handful of TF operator sites have been experimentally characterized for Burkholderia to date. Our study provides a significant addition to this knowledge base and illustrates some general challenges of discovering operators on a large scale for prokaryotes.
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Tuhin Subhra
authors: TS
authors: Maity
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Devin W
authors: DW
authors: Close
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Yolanda E
authors: YE
authors: Valdez
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Kristy
authors: K
authors: Nowak-Lovato
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Ricardo
authors: R
authors: Marti-Arbona
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Tinh T
authors: TT
authors: Nguyen
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Pat J
authors: PJ
authors: Unkefer
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Elizabeth
authors: E
authors: Hong-Geller
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: Andrew R M
authors: ARM
authors: Bradbury
authors: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors: John
authors: J
authors: Dunbar
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D019117:Burkholderia / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D005810:Multigene Family; D009875:Operator Regions, Genetic; D010802:Phylogeny; D011485:Protein Binding; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D014157:Transcription Factors