The membrane proteome of <b><i>Halobacterium salinarum</i></b>

Klein, Christian; Garcia-Rizo, Carolina; Bisle, Birgit; Scheffer, Beatrix; Zischka, Hans; Pfeiffer, Friedhelm; Siedler, Frank; Oesterhelt, Dieter

doi:10.1002/pmic.200400943

Cited by 96 publications

(104 citation statements)

References 57 publications

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“…salinarum have been reported (e.g. Karadzic & Maupin-Furlow, 2005;Klein et al, 2005;Tebbe et al, 2005). It was shown that proteome analysis can also be used to improve genome annotation in halophiles.…”

Section: Genetics and Functional Genomicsmentioning

confidence: 99%

From genomes to function: haloarchaea as model organisms

Soppa

2006

Microbiology

123

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Haloarchaea are adapted to high-salt environments and accumulate equally high salt concentrations in the cytoplasm. The genomes of representatives of six haloarchaeal genera have been fully or partially sequenced, allowing the analysis of haloarchaeal properties in silico. Transcriptome and proteome analyses have been established for Halobacterium salinarum and Haloferax volcanii. Genetic systems are available including methods that allow the fast in-frame deletion or modification of chromosomal genes. The high-efficiency transformation system of Hf. volcanii allows the isolation of genes essential for a biological process by complementation of loss-of-function mutants. For the analysis of haloarchaeal biology many molecular genetic, biochemical, structural and cell biological methods have been adapted to application at high salt concentrations. Recently it has become clear that several different mechanisms allow the adaptation of proteins to the high salt concentration of the cytoplasm. Taken together, the wealth of techniques available make haloarchaea excellent archaeal model species.

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Section: Genetics and Functional Genomicsmentioning

confidence: 99%

From genomes to function: haloarchaea as model organisms

Soppa

2006

Microbiology

123

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“…NRC-1 (2,17,34,35). A total of 972 (P Ͼ 0.9) unique proteins have been identified in this and our previous (17) proteome analyses.…”

Section: Figmentioning

confidence: 52%

“…Using a ProteinProphet probability of 0.9 as the cutoff, most of the proteins (89 of 162 membrane, 218 of 226 soluble, and 26 of 29 membrane/soluble fraction proteins) found in our previous analysis were also identified in this study. The proteome analysis of a closely related strain, H. salinarium, resulted in the identification of 802 proteins in the soluble proteome (34) and 141 proteins in purified membrane (35). The H. salinarium proteome analyses detected ϳ680 unique proteins classified as reliable or trusted identifications.…”

Section: Figmentioning

confidence: 99%

Proteome Analysis of Halobacterium sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter

Gan

Chiu

et al. 2006

Molecular & Cellular Proteomics

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To better understand the extremely halophilic archaeon Halobacterium species NRC-1, we analyzed its soluble proteome by two-dimensional liquid chromatography coupled to electrospray ionization tandem mass spectrometry. A total of 888 unique proteins were identified with a ProteinProphet probability (P) between 0.9 and 1.0. To evaluate the biochemical activities of the organism, the proteomic data were subjected to a biological network analysis using our BMSorter software. This allowed us to examine the proteins expressed in different biomodules and study the interactions between pertinent biomodules. Interestingly an integrated analysis of the enzymes in the amino acid metabolism and citrate cycle networks suggested that up to eight amino acids may be converted to oxaloacetate, fumarate, or oxoglutarate in the citrate cycle for energy production. In addition, glutamate and aspartate may be interconverted from other amino acids or synthesized from citrate cycle intermediates to meet the high demand for the acidic amino acids that are required to build the highly acidic proteome of the organism. Thus this study demonstrated that proteome analysis can provide useful information and help systems analyses of organisms. Halobacterium species NRC-1 is an extremely halophilic archaeon containing a highly acidic proteome with a median pI of 4.9, a property that is essential to the maintenance of the solubility and function of the proteins in a high salinity environment of about 5 M salts (1, 2). Genome sequence analysis has revealed 2,630 putative protein-coding genes in the 2,571,010-bp genome (2). Among the predicted proteins, 1,658 can be matched to sequences in public databases. Of the matches, 1,067 are proteins of known or predicted function, and 591 are proteins of unknown function. The possession of a relatively small and completely sequenced genome, the availability of a full arsenal of genetic manipulation tools, and the relative ease of culture make Halobacterium sp. NRC-1 an attractive systems biology model organism of the domain Archaea (3-6).The genomes of Halobacterium species are extremely unstable (7-9). Early studies of Halobacterium sp. NRC-1 (also known as Halobacterium halobium) and the closely related Halobacterium salinarium discovered unusually high spontaneous mutation frequencies of 0.01% for the production of bacteriorhodopsin-or bacterioruberin-deficient phenotypes and a more striking 1% for partial or total gas vesicle-deficient phenotypes. The species is also noteworthy for the large number of insertion sequence elements that are harbored in this unstable genome. Molecular genetic analysis of the bacteriorhodopsin-and gas vesicle-deficient mutants established a relationship between transposable insertion sequence-mediated insertional inactivation or deletions of structural or regulatory genes and the high mutant rates (10 -16). Upon the completion of the genome sequence, DNA analysis revealed the presence of 91 copies of insertion sequence elements belonging to 12 families in the Halobacteri...

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“…The flow-through was collected. A step-wise elution was performed using 20 μL of 30% acetonitrile in different concentrations of NH4FA (20,30,40,50, 60 and 120 mM, pH 3). All fractions were dried in vacuo and resuspended in 5% formic acid to allow analysis by nanoLC-MS/MS.…”

Section: Separation Of Peptides By Strong Cation Exchange Chromatographymentioning

confidence: 99%

“…enterica (previous S. typhimurium) (28), 14 from Klebsiella pneumoniae (27), and 15 from green-sulfur bacterium Chlorobium tepidum (1). Using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS), 114 integral membrane proteins were identified in Halobacterium salinarum (20) and 79 membrane proteins were detected in Mycobacterium tuberculosis (14). Emerging gelfree proteomic approaches have provided powerful tools for the analysis of complex mixtures and have made membrane proteins accessible for mass spectrometric proteomic analysis (43).…”

mentioning

confidence: 99%

Identification of Salt-Tolerant Sinorhizobium sp. Strain BL3 Membrane Proteins Based on Proteomics

et al. 2010

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Sinorhizobium sp. BL3 is a salt-tolerant strain that can fix atmospheric nitrogen in symbiosis with leguminous host plants under salt-stress conditions. Since cell membranes are the first barrier to environmental change, it is interesting to explore the membrane proteins within this protective barrier under salt stress. The protein contents of membraneenriched fractions obtained from BL3 were analyzed by nanoflow liquid chromatography interfaced with electrospray ionization tandem mass spectrometry. A total of 105 membrane proteins were identified. These proteins could be classified into 17 functional categories, the two biggest of which were energy production and conversion, and proteins not in clusters of orthologous groups (COGS). In addition, a comparative analysis of membrane proteins between salt-stressed and non-stressed BL3 cells was conducted using a membrane enrichment method and off-line SCX fractionation coupled to nanoLC-MS/MS. These techniques would be useful for further comparative analysis of membrane proteins that function in the response to environmental stress.

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The membrane proteome of Halobacterium salinarum

Cited by 96 publications

References 57 publications

From genomes to function: haloarchaea as model organisms

From genomes to function: haloarchaea as model organisms

Proteome Analysis of Halobacterium sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter

Identification of Salt-Tolerant Sinorhizobium sp. Strain BL3 Membrane Proteins Based on Proteomics

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