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Journal of Bacteriology, March 2004, p. 1448-1461, Vol. 186, No. 5
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.5.1448-1461.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media

Alison K. Hottes,1,2 Maliwan Meewan,2 Desiree Yang,3,{dagger} Naomi Arana,3,{ddagger} Pedro Romero,4 Harley H. McAdams,2 and Craig Stephens3*

Departments of Electrical Engineering,1 Developmental Biology, Stanford University, Stanford, California 94305,2 Biology Department, Santa Clara University, Santa Clara, California 95053,3 Bioinformatics Research Group, SRI International, Menlo Park, California 940254

Received 14 August 2003/ Accepted 12 November 2003

Microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium Caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (PYE) and minimal salts medium with glucose or xylose as the carbon source. Nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. The differentially expressed genes included many encoding transport systems, most notably diverse TonB-dependent outer membrane channels of unknown substrate specificity. Amino acid degradation pathways constituted the largest class of genes induced in PYE. In contrast, many of the genes upregulated in minimal media encoded enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induced expression of genes encoding enzymes of the Entner-Doudoroff pathway, which was demonstrated here through mutational analysis to be essential in C. crescentus for growth on glucose. Xylose induced expression of genes encoding several hydrolytic exoenzymes as well as an operon that may encode a novel pathway for xylose catabolism. A conserved DNA motif upstream of many xylose-induced genes was identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggest that in addition to serving as a carbon source for growth of C. crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation.

* Corresponding author. Mailing address: Biology Department, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053. Phone: (408) 551-1898. Fax: (408) 554-2710. E-mail: cstephens{at}scu.edu.

{dagger} Present address: Department of Microbiology and Immunology, University of California-San Francisco, San Francisco, CA 94143.

{ddagger} Present address: Department of Developmental Biology, Stanford University, Stanford, CA 94305.

Journal of Bacteriology, March 2004, p. 1448-1461, Vol. 186, No. 5
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.5.1448-1461.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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