Construction and validation of the Rhodobacter sphaeroides 2.4.1 DNA microarray: transcriptome flexibility at diverse growth modes

Journal of Bacteriology
Christopher T PappasMark Gomelsky

Abstract

A high-density oligonucleotide DNA microarray, a genechip, representing the 4.6-Mb genome of the facultative phototrophic proteobacterium, Rhodobacter sphaeroides 2.4.1, was custom-designed and manufactured by Affymetrix, Santa Clara, Calif. The genechip contains probe sets for 4,292 open reading frames (ORFs), 47 rRNA and tRNA genes, and 394 intergenic regions. The probe set sequences were derived from the genome annotation generated by Oak Ridge National Laboratory after extensive revision, which was based primarily upon codon usage characteristic of this GC-rich bacterium. As a result of the revision, numerous missing ORFs were uncovered, nonexistent ORFs were deleted, and misidentified start codons were corrected. To evaluate R. sphaeroides transcriptome flexibility, expression profiles for three diverse growth modes--aerobic respiration, anaerobic respiration in the dark, and anaerobic photosynthesis--were generated. Expression levels of one-fifth to one-third of the R. sphaeroides ORFs were significantly different in cells under any two growth modes. Pathways involved in energy generation and redox balance maintenance under three growth modes were reconstructed. Expression patterns of genes involved in these pathways mirr...Continue Reading

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Citations

Oct 18, 2006·Applied Microbiology and Biotechnology·Armin Ehrenreich
Oct 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Okako OmadjelaJochen Zimmer
Nov 2, 2004·Journal of Bacteriology·Stephan BraatschMark Gomelsky
Jun 7, 2005·Journal of Bacteriology·Peter S ChoiJames P Shapleigh
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