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PMID: 15576789 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis.

Journal of bacteriology ·Vol. 186 ·No. 24 ·2004-12-00 ·Pages 8385-400

Wan XF, Verberkmoes NC, McCue LA, Stanek D, Connelly H, Hauser LJ, Wu L, Liu X, Yan T, Leaphart A, Hettich RL, Zhou J, Thompson DK

Abstract

The availability of the complete genome sequence for Shewanella oneidensis MR-1 has permitted a comprehensive characterization of the ferric uptake regulator (Fur) modulon in this dissimilatory metal-reducing bacterium. We have employed targeted gene mutagenesis, DNA microarrays, proteomic analysis using liquid chromatography-mass spectrometry, and computational motif discovery tools to define the S. oneidensis Fur regulon. Using this integrated approach, we identified nine probable operons (containing 24 genes) and 15 individual open reading frames (ORFs), either with unknown functions or encoding products annotated as transport or binding proteins, that are predicted to be direct targets of Fur-mediated repression. This study suggested, for the first time, possible roles for four operons and eight ORFs with unknown functions in iron metabolism or iron transport-related functions. Proteomic analysis clearly identified a number of transporters, binding proteins, and receptors related to iron uptake that were up-regulated in response to a fur deletion and verified the expression of nine genes originally annotated as pseudogenes. Comparison of the transcriptome and proteome data revealed strong correlation for genes shown to be undergoing large changes at the transcript level. A number of genes encoding components of the electron transport system were also differentially expressed in a fur deletion mutant. The gene omcA (SO1779), which encodes a decaheme cytochrome c, exhibited significant decreases in both mRNA and protein abundance in the fur mutant and possessed a strong candidate Fur-binding site in its upstream region, thus suggesting that omcA may be a direct target of Fur activation.

MeSH Terms
Bacterial Proteins/chemistry,genetics,metabolism Base Sequence Chromatography, High Pressure Liquid Computational Biology/methods Gene Expression Profiling Gene Expression Regulation, Bacterial Iron/metabolism Mass Spectrometry/methods Molecular Sequence Data Oligonucleotide Array Sequence Analysis Oxidation-Reduction Proteome Regulon Repressor Proteins/genetics,metabolism Shewanella/genetics,growth & development,metabolism Transcription, Genetic
Chemicals
Bacterial Proteins Proteome Repressor Proteins ferric uptake regulating proteins, bacterial Iron
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Wan Xiu-Feng
Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6038, USA.
Verberkmoes Nathan C
McCue Lee Ann
Stanek Dawn
Connelly Heather
Hauser Loren J
Wu Liyou
Liu Xueduan
Yan Tingfen
Leaphart Adam
Hettich Robert L
Zhou Jizhong
Thompson Dorothea K
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Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/JB.186.24.8385-8400.2004
Published
2004-12-00
Pages
8385-400
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC532403
Subset
IM
Databases
RefSeq
NC_004347, NC_004349
External Links
PubMed source DOI: 10.1128/JB.186.24.8385-8400.2004 PMC Full Text View journal details
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