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Journal of Bacteriology, July 2008, p. 4831-4848, Vol. 190, No. 14
0021-9193/08/$08.00+0     doi:10.1128/JB.00301-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Role of the Global Transcriptional Regulator PrrA in Rhodobacter sphaeroides 2.4.1: Combined Transcriptome and Proteome Analysis{triangledown} ,{dagger}

Jesus M. Eraso,1 Jung Hyeob Roh,1 Xiaohua Zeng,1 Stephen J. Callister,2 Mary S. Lipton,2 and Samuel Kaplan1*

Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030,1 Biological Separations and Mass Spectrometry, Mail Stop K8-98, Pacific Northwest National Laboratory, Richland, Washington 993522

Received 27 February 2008/ Accepted 7 May 2008

The PrrBA two-component regulatory system is a major global regulator in Rhodobacter sphaeroides 2.4.1. Here we have compared the transcriptome and proteome profiles of the wild-type (WT) and mutant PrrA2 cells grown anaerobically in the dark with dimethyl sulfoxide as an electron acceptor. Approximately 25% of the genes present in the PrrA2 genome are regulated by PrrA at the transcriptional level, either directly or indirectly, by twofold or more relative to the WT. The genes affected are widespread throughout all COG (cluster of orthologous group) functional categories, with previously unsuspected "metabolic" genes affected in PrrA2 cells. PrrA was found to act as both an activator and a repressor of transcription, with more genes being repressed in the presence of PrrA (9:5 ratio). An analysis of the genes encoding the 1,536 peptides detected through our chromatographic study, which corresponds to 36% coverage of the genome, revealed that approximately 20% of the genes encoding these proteins were positively regulated, whereas approximately 32% were negatively regulated by PrrA, which is in excellent agreement with the percentages obtained for the whole-genome transcriptome profile. In addition, comparison of the transcriptome and proteome mean parameter values for WT and PrrA2 cells showed good qualitative agreement, indicating that transcript regulation paralleled the corresponding protein abundance, although not one for one. The microarray analysis was validated by direct mRNA measurement of randomly selected genes that were both positively and negatively regulated. lacZ transcriptional and kan translational fusions enabled us to map putative PrrA binding sites and revealed potential gene targets for indirect regulation by PrrA.

* Corresponding author. Mailing address: Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, 6431 Fannin, Houston, TX 77030. Phone: (713) 500-5505. Fax: (713) 500-5499. E-mail: Samuel.Kaplan{at}uth.tmc.edu

{triangledown} Published ahead of print on 16 May 2008.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, July 2008, p. 4831-4848, Vol. 190, No. 14
0021-9193/08/$08.00+0     doi:10.1128/JB.00301-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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