Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: 
overlapping genetic responses to xylose, xylulose, ribose and mannito

Liu, Yunhao; Rainey, Paul B.; Zhang, Xue-Xian

doi:10.1111/mmi.13142

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Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannito

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Rainey, Paul B.
External Scientific Member Group Experimental and Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Liu, Y., Rainey, P. B., & Zhang, X.-X. (2015). Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannito. Molecular Microbiology, in press. doi:10.1111/mmi.13142.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0028-4DAE-D

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, xyloseinduced 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