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An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum

October 2007 , Volume 20 , Number  10
Pages  1,298 - 1,307

Woo-Suk Chang,1,2 William L. Franck,1,2 Eddie Cytryn,3 Sooyoung Jeong,4 Trupti Joshi,1,5,6 David W. Emerich,4 Michael J. Sadowsky,3,7 Dong Xu,1,5,6 and Gary Stacey1,2,4,5,8

1National Center for Soybean Biotechnology and 2Division of Plant Sciences, University of Missouri, Columbia 65211, U.S.A.; 3Department of Soil, Water, and Climate, University of Minnesota, St. Paul 55108, U.S.A.; 4 Division of Biochemistry, 5Christopher S. Bond Life Sciences Center, and 6Department of Computer Science, University of Missouri; 7BioTechnology Institute, University of Minnesota; 8Department of Molecular Microbiology and Immunology, University of Missouri

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Accepted 18 June 2007.

A DNA microarray, comprising 70-mer oligonucleotides, representing 8,453 open reading frames (ORFs), was constructed based on the Bradyrhizobium japonicum strain USDA110 genomic sequence. New annotation predicted 199 additional genes, which were added to the microarray and were shown to be transcribed. These arrays were used to profile transcription in cells under a variety of conditions, including growth in minimal versus rich medium, osmotic stress, and free-living cells versus bacteroids. Increased expression was seen for genes involved in translation, motility, and cell envelope synthesis in rich medium whereas expression increased in minimal medium for genes involved in vitamin biosynthesis and stress responses. Treatment with 50 mM NaCl activated stress-inducible genes but repressed genes involved in chemotaxis and motility. Strikingly, no known transport systems for accumulation of compatible solutes or osmoprotectants were induced in response to osmotic stress. A number of nif, fix, and hup genes, but not all, were upregulated in bacteroids. The B. japonicum type III secretion system, known to be important in early nodulation, was downregulated in bacteroids. The availability of a reliable, low-cost B. japonicum microarray provides a useful tool for functional genomic studies of one of the most agriculturally important bacteria.

Additional keywords: transcriptomics.

© 2007 The American Phytopathological Society