@article {3118,
	title = {Proteome of Geobacter sulfurreducens in the presence of U(VI).},
	journal = {Microbiology (Reading)},
	volume = {160},
	year = {2014},
	month = {2014 Dec},
	pages = {2607-2617},
	abstract = {<p>Geobacter species often play an important role in the in situ bioremediation of uranium-contaminated groundwater, but little is known about how these microbes avoid uranium toxicity. To evaluate this further, the proteome of Geobacter sulfurreducens exposed to 100 {\textmu}M U(VI) acetate was compared to control cells not exposed to U(VI). Of the 1363 proteins detected from these cultures, 203 proteins had higher abundance during exposure to U(VI) compared with the control cells and 148 proteins had lower abundance. U(VI)-exposed cultures expressed lower levels of proteins involved in growth, protein and amino acid biosynthesis, as well as key central metabolism enzymes as a result of the deleterious effect of U(VI) on the growth of G. sulfurreducens. In contrast, proteins involved in detoxification, such as several efflux pumps belonging to the RND (resistance-nodulation-cell division) family, and membrane protection, and other proteins, such as chaperones and proteins involved in secretion systems, were found in higher abundance in cells exposed to U(VI). Exposing G. sulfurreducens to U(VI) resulted in a higher abundance of many proteins associated with the oxidative stress response, such as superoxide dismutase and superoxide reductase. A strain in which the gene for superoxide dismutase was deleted grew more slowly than the WT strain in the presence of U(VI), but not in its absence. The results suggested that there is no specific mechanism for uranium detoxification. Rather, multiple general stress responses are induced, which presumably enable Geobacter species to tolerate high uranium concentrations.</p>},
	keywords = {Bacterial Proteins, Gene Expression Regulation, Bacterial, Geobacter, Organometallic Compounds, Proteome},
	issn = {1465-2080},
	doi = {10.1099/mic.0.081398-0},
	author = {Orellana, Roberto and Hixson, Kim K and Murphy, Sean and Mester, T{\"u}nde and Sharma, Manju L and Lipton, Mary S and Lovley, Derek R}
}
@article {457,
	title = {Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.},
	journal = {Appl Environ Microbiol},
	volume = {75},
	year = {2009},
	month = {2009 Oct},
	pages = {6591-9},
	abstract = {Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Biodegradation, Environmental, Genomics, Geobacter, Molecular Sequence Data, Oxidation-Reduction, Peptide Mapping, Plankton, Proteomics, Uranium, Water Microbiology, Water Pollutants, Radioactive},
	issn = {1098-5336},
	doi = {10.1128/AEM.01064-09},
	author = {Wilkins, Michael J and VerBerkmoes, Nathan C and Williams, Kenneth H and Callister, Stephen J and Mouser, Paula J and Elifantz, Hila and N{\textquoteright}guessan, Lucie A and Thomas, Brian C and Nicora, Carrie D and Shah, Manesh B and Abraham, Paul and Lipton, Mary S and Lovley, Derek R and Hettich, Robert L and Long, Philip E and Banfield, Jillian F}
}
@article {477,
	title = {Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor.},
	journal = {Biochim Biophys Acta},
	volume = {1784},
	year = {2008},
	month = {2008 Dec},
	pages = {1935-41},
	abstract = {The mechanisms for Fe(III) oxide reduction in Geobacter species are of interest because Fe(III) oxides are the most abundant form of Fe(III) in many soils and sediments and Geobacter species are prevalent Fe(III)-reducing microorganisms in many of these environments. Protein abundance in G. sulfurreducens grown on poorly crystalline Fe(III) oxide or on soluble Fe(III) citrate was compared with a global accurate mass and time tag proteomic approach in order to identify proteins that might be specifically associated with Fe(III) oxide reduction. A total of 2991 proteins were detected in G. sulfurreducens grown with acetate as the electron donor and either Fe(III) oxide or soluble Fe(III) citrate as the electron acceptor, resulting in 86\% recovery of the genes predicted to encode proteins. Of the total expressed proteins 76\% were less abundant in Fe(III) oxide cultures than in Fe(III) citrate cultures, which is consistent with the overall slower rate of metabolism during growth with an insoluble electron acceptor. A total of 269 proteins were more abundant in Fe(III) oxide-grown cells than in cells grown on Fe(III) citrate. Most of these proteins were in the energy metabolism category: primarily electron transport proteins, including 13 c-type cytochromes and PilA, the structural protein for electrically conductive pili. Several of the cytochromes that were more abundant in Fe(III) oxide-grown cells were previously shown with genetic approaches to be essential for optimal Fe(III) oxide reduction. Other proteins that were more abundant during growth on Fe(III) oxide included transport and binding proteins, proteins involved in regulation and signal transduction, cell envelope proteins, and enzymes for amino acid and protein biosynthesis, among others. There were also a substantial number of proteins of unknown function that were more abundant during growth on Fe(III) oxide. These results indicate that electron transport to Fe(III) oxide requires additional and/or different proteins than electron transfer to soluble, chelated Fe(III) and suggest proteins whose functions should be further investigated in order to better understand the mechanisms of electron transfer to Fe(III) oxide in G. sulfurreducens.},
	keywords = {Bacterial Proteins, Ferric Compounds, Gene Expression Regulation, Bacterial, Geobacter, Oxidation-Reduction, Proteome},
	issn = {0006-3002},
	doi = {10.1016/j.bbapap.2008.06.011},
	author = {Ding, Yan-Huai R and Hixson, Kim K and Aklujkar, Muktak A and Lipton, Mary S and Smith, Richard D and Lovley, Derek R and Mester, T{\"u}nde}
}
@article {518,
	title = {The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions.},
	journal = {Biochim Biophys Acta},
	volume = {1764},
	year = {2006},
	month = {2006 Jul},
	pages = {1198-206},
	abstract = {The proteome of Geobacter sulfurreducens, a model for the Geobacter species that predominate in many Fe(III)-reducing subsurface environments, was characterized with ultra high-pressure liquid chromatography and mass spectrometry using accurate mass and time (AMT) tags as well as with more traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Cells were grown under six different growth conditions in order to enhance the potential that a wide range of genes would be expressed. The AMT tag approach was able to identify a much greater number of proteins than could be detected with the 2-D PAGE approach. With the AMT approach over 3,000 gene products were identified, representing about 90\% of the total predicted gene products in the genome. A high proportion of predicted proteins in most protein role categories were detected; the highest number of proteins was identified in the hypothetical protein role category. Furthermore, 91 c-type cytochromes of 111 predicted genes in the G. sulfurreducens genome were identified. Differences in the abundance of cytochromes and other proteins under different growth conditions provided information for future functional analysis of these proteins. These results demonstrate that a high percentage of the predicted proteins in the G. sulfurreducens genome are produced and that the AMT tag approach provides a rapid method for comparing differential expression of proteins under different growth conditions in this organism.},
	keywords = {Bacterial Proteins, Bacteriological Techniques, Chromatography, High Pressure Liquid, Cytochrome c Group, Electrophoresis, Gel, Two-Dimensional, Ferric Compounds, Fumarates, Geobacter, Peptide Fragments, Proteome, Spectrometry, Mass, Electrospray Ionization},
	issn = {0006-3002},
	doi = {10.1016/j.bbapap.2006.04.017},
	author = {Ding, Yan-Huai R and Hixson, Kim K and Giometti, Carol S and Stanley, Ann and Esteve-N{\'u}{\~n}ez, Abraham and Khare, Tripti and Tollaksen, Sandra L and Zhu, Wenhong and Adkins, Joshua N and Lipton, Mary S and Smith, Richard D and Mester, T{\"u}nde and Lovley, Derek R}
}
