title: Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannitol.
abstract: Bacterial degradation of xylose is sequentially mediated by two enzymes - an isomerase (XutA) and a xylulokinase (XutB) - with xylulose as an intermediate. Pseudomonas fluorescens SBW25, though capable of growth on xylose as a sole carbon source, encodes only one degradative enzyme XutA at the xylose utilization (xut) locus. Here, using site-directed mutagenesis and transcriptional assays, we have identified two functional xylulokinase-encoding genes (xutB1 and xutB2) and further show that expression of xutB1 is specifically induced by xylose. Surprisingly, xylose-induced xutB1 expression is mediated by the mannitol-responsive regulator MtlR, using xylulose rather than xylose as the direct inducer. In contrast, expression of the xutA operon is regulated by XutR - a transcriptional activator of the AraC family - in a xylose-, xylulose- and ribose-dependent manner. Detailed genetic and biochemical analyses of XutR, including DNase I footprinting assays, suggest an unconventional model of XutR regulation that does not involve DNA-looping, a mechanism typically found for AraC-type regulators from enteric bacteria. XutR functions as a dimer and recognizes two inverted repeat sequences, but binding to one half site is weak thus requiring an inducer molecule such as xylose for activation.
authors.affiliation: Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0745, New Zealand.|NZ Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand.
authors.forename: Yunhao
authors.initials: Y
authors.lastname: Liu
authors.affiliation: NZ Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand.|Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Rainey
authors.affiliation: Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0745, New Zealand.
authors.forename: Xue-Xian
authors.initials: XX
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008353:Mannitol / Q000378:metabolism*; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009876:Operon; D010429:Pentoses / Q000378:metabolism*; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000235:genetics / Q000378:metabolism; D011551:Pseudomonas fluorescens / Q000235:genetics* / Q000378:metabolism*; D012266:Ribose / Q000378:metabolism; D014994:Xylose / Q000378:metabolism; D014996:Xylulose / Q000378:metabolism
chemical_list: D010429:Pentoses; D008353:Mannitol; D014996:Xylulose; D012266:Ribose; D014994:Xylose; D017853:Phosphotransferases (Alcohol Group Acceptor); C032700:xylulokinase