Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis

Journal Article · Tue Jul 01 04:00:00 EDT 2008 · Journal of Bacteriology, 190(14):4831-4848

DOI:https://doi.org/10.1128/JB.00301-08· OSTI ID:943392

Eraso, Jesus M; Roh, Jung Hyeob; Zeng, Xiaohua; Callister, Stephen J; Lipton, Mary S; Kaplan, Samuel

The PrrBA two-component regulatory system is a major global regulator in Rhodobacter sphaeroides 2.4.1. In this study we have compared the transcriptome and proteome profiles of the wild type (WT) and mutant PrrA2 cells grown anaerobically, in the dark, with DMSO as electron acceptor. Approximately 25% of the genes present in the genome are PrrA-regulated, at the transcriptional level, either directly or indirectly, by ≥ 2-fold relative to wild type. The genes affected are widespread throughout all COG functional categories, with previously unsuspected “metabolic” genes affected when in the PrrA mutant background. PrrA was found to act both as 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 genomic transcriptome profile. In addition, comparison of the transcriptome and proteome mean parameter values chosen between WT and PrrA2 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, both positively and negatively regulated genes. lacZ transcriptional and kan translational fusions enabled us to map putative PrrA binding sites, as well as revealing potential gene targets for indirect regulation by PrrA.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 943392
• Report Number(s): PNNL-SA-61118; 18427; KP1501021
• Journal Information: Journal of Bacteriology, 190(14):4831-4848, Journal Name: Journal of Bacteriology, 190(14):4831-4848 Journal Issue: 14 Vol. 190; ISSN JOBAAY; ISSN 0021-9193
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ABUNDANCE
BINDING ENERGY
ELECTRONS
Environmental Molecular Sciences Laboratory
FUNCTIONALS
GENES
MUTANTS
PEPTIDES
PROTEINS
REGULATIONS
TARGETS
TRANSCRIPTION
VALENCE