Genomewide expression profiling in Emphasis Type

Authors: Julia Krushkal Bin Yan Laurie N DiDonato Marko Puljic Kelly P Nevin Trevor L Woodard Ronald M Adkins Barbara A Methé Derek R Lovley

Publish Date: 2007/04/04

Volume: 7, Issue: 3, Pages: 229-255

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Abstract

RelGsu is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms These proteins are involved in the regulation of levels of guanosine 3′ 5′ bispyrophosphate ppGpp a molecule that signals slow growth and stress response under nutrient limitation in bacteria We used information obtained from genomewide expression profiling of the rel Gsu deletion mutant to identify putative regulatory sites involved in transcription networks modulated by RelGsu or ppGpp Differential gene expression in the rel Gsu deletion mutant as compared to the wild type was available from two growth conditions steady state chemostat cultures and stationary phase batch cultures Hierarchical clustering analysis of these two datasets identified several groups of operons that are likely coregulated Using a search for conserved motifs in the upstream regions of these coregulated operons we identified sequences similar to Fur and RpoSregulated sites These findings suggest that Fur and RpoSdependent gene expression in G sulfurreducens is affected by RelGsumediated signalingWe are grateful to Drs C Núñez Instituto de Biotecnología/UNAM Cuernavaca Mexico C Leang and T Ueki both of University of Massachusetts Amherst for critical reading of this manuscript and helpful comments We also thank R Glaven University of Massachusetts Amherst for helpful discussions and J Peeples University of Tennessee Memphis for editorial assistance

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