H-086. Genome Wide Analysis of RNA Polymerase and σ70 Binding in Geobacter sulfurreducens

Y. Qiu1, K. Zengler1, B-K. Cho1, L. Kagan1, J. Elkins1, D. R. Lovley2, B. Ø. Palsson1;
1Univ. of California, La Jolla, CA, 2Univ. of Massachusetts, Amherst, MA.

Geobacter sulfurreducens is capable of transferring electrons to a variety of electron acceptors, including Fe(III), U(IV), and the surface of electrodes, making it the candidate of choice for bioremediation of contaminated environments and harvesting electricity from waste organic matter. In depth understanding of how G. sulfurreducens functions will have great impact on optimizing bioremediation and energy harvesting applications. A major step toward this goal is the establishment of a genome-scale transcriptional regulatory network (TRN) which allows in depth understanding of fundamental aspects of chromosome structure, DNA replication and repair, response to stress and regulation of metabolism. Towards a comprehensive understanding of the TRN in G. sulfurreducens, genome-wide binding patterns of RNA polymerase and Sigma 70 were determined by chromatin immunoprecipitation (ChIP) coupled with high-density tiling arrays (ChIP-chip). Patterns of RNA polymerase (RNAP) and Sigma 70 binding were compared from cells grown with acetate under fumarate and Fe(III)-reducing conditions. All ChIP-chip results were complemented by gene expression profiles using high-density tiling arrays. In addition promoter regions in G. sulfurreducens were determined under various growth conditions by ChIP-chip analysis of cells treated with rifampicin (rifampicin inhibits transcription elongation by RNA polymerase but not its binding to promoter region). Over 650 binding sites for RNAP were identified. We found 419 and 423 binding sites of Sigma 70 under fumarate and Fe(III)-reducing conditions, respectively. While most Sigma 70 binding sites were identical under both conditions, we identified several sites which were more strongly bound by Sigma 70 under fumarate reducing condition than under Fe(III)-reducing conditions, including Fur (ferric uptake regulator), the chemotaxis sensor mcp034 as well as NADPH-dependent ferredoxin oxidoreductase.