Gene and Protein Expression Profiles of<i>Shewanella oneidensis</i>during Anaerobic Growth with Different Electron Acceptors

Beliaev, Alex; Thompson, Danielle; Khare, Tripti; Lim, H.; Brandt, Craig C.; Li, Guangshan; Murray, Alison E.; Heidelberg, John F.; Giometti, Carol S.; Yates, John R.; Nealson, Kenneth H.; Tiedje, James M.; Zhou, Jizhong

doi:10.1089/15362310252780834

Cited by 91 publications

(94 citation statements)

References 74 publications

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“…This study focused on S. oneidensis strain MR-1 that has recently begun serving as a model microorganism for determining the genetic basis of the metabolic respiratory versatility in metal-reducing Shewanella (3,4,14,16,17,23). Transcriptome and proteome analyses resulted in the identification of 538 hypothetical genes as expressed in S. oneidensis cells (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Bioflow model 110 fermentors (New Brunswick Scientific), either in fed-batch or in continuous-feed modes, were used for the aerobic and suboxic conditions, in which cells were grown in a modified defined medium M1 (15). Sample processing for the transcriptome analysis (16) as well as the experimental protocol are described in Supporting Materials. The same S. oneidensis arrays, consisting of Ϸ95% of the predicted genes (17), were used for all gene expression analyses.…”

Section: Methodsmentioning

confidence: 99%

“…Several parallel proteomic approaches were implemented in this study (Supporting Materials) to analyze S. oneidensis protein expression: (i) liquid chromatography (LC) coupled to tandem MS (MS͞MS) as described in refs. 11 and 19-24; (ii) LC coupled to Fourier transform ion cyclotron resonance MS (25,26); (iii) LC coupled to quadruple-TOF MS (27); and (iv) 2D gel electrophoresis followed by LC-MS͞MS (16,23). Common approaches used in different proteome analyses included: LC-MS͞MS implemented by using the LCQ platform (Thermo Electron, San Jose, CA), standard sample processing (Supporting Materials), standard top-down data-dependent ion selection (11,(19)(20)(21)(22)(23)(24), use of the TURBO-SEQUEST (Thermo Electron) search engine, and use of the recently developed standard mixtures for proteome studies (24).…”

Section: Methodsmentioning

confidence: 99%

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Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations

Kolker

Picone

Galperin

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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114

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The ␥-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other sequenced organisms, Ϸ40% of the predicted ORFs in the S. oneidensis genome were annotated as uncharacterized ''hypothetical'' genes. We implemented an integrative approach by using experimental and computational analyses to provide more detailed insight into gene function. Global expression profiles were determined for cells after UV irradiation and under aerobic and suboxic growth conditions. Transcriptomic and proteomic analyses confidently identified 538 hypothetical genes as expressed in S. oneidensis cells both as mRNAs and proteins (33% of all predicted hypothetical proteins). Publicly available analysis tools and databases and the expression data were applied to improve the annotation of these genes. The annotation results were scored by using a seven-category schema that ranked both confidence and precision of the functional assignment. We were able to identify homologs for nearly all of these hypothetical proteins (97%), but could confidently assign exact biochemical functions for only 16 proteins (category 1; 3%). Altogether, computational and experimental evidence provided functional assignments or insights for 240 more genes (categories 2-5; 45%). These functional annotations advance our understanding of genes involved in vital cellular processes, including energy conversion, ion transport, secondary metabolism, and signal transduction. We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome.computational biology ͉ expression analysis ͉ microarrays ͉ proteomics ͉ integrative microbiology

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations

Kolker

Picone

Galperin

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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114

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“…The purified PCR products were visualized by gel electrophoresis in the presence of ethidium bromide, and their respective sizes were verified by comparison to the expected product length, yielding a collection of 2,976 distinct ORFs. Microarray fabrication, hybridization, probe labeling, image acquisition, and processing were carried out as described (18,19). Because nonirradiated ESP DEIRA cells inoculated into fresh medium yield a fully grown culture in the time taken by the 15 kGy-induced growth lag, our expression analyses compared total RNA derived from recovering DEIRA with total RNA from nonirradiated control cells.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Liu

Zhou

Omelchenko

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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358

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Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering Ϸ94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.T he Gram-positive aerobic bacterium Deinococcus radiodurans R1 (DEIRA) has an extraordinary resistance to ␥-radiation and a wide range of other DNA-damaging conditions, including desiccation and oxidizing agents (1, 2). Ionizing radiation induces DNA double-stranded breaks (DSBs) that are the most lethal form of DNA damage (3). After acute exposures to 10 kGy, early stationary phase (ESP) DEIRA can reassemble its 3.285-Mbp genome, which consists of four haploid genomic copies per cell (4), from hundreds of DNA DSB fragments without lethality or induced mutagenesis (5, 6). Also remarkable is DEIRA's ability to grow at 60 Gy͞h without any discernable effect on its growth rate (7). Because most organisms, generally, can tolerate so few DSBs (8), radiationinduced DSBs and their repair have been difficult to study. In DEIRA, however, there are so many DSBs in fully viable irradiated cells after high-dose irradiation that the steps in DSB repair can be monitored directly in mass culture (5, 9-11). This characteristic has been exploited and used to examine the timing of DNA recombination (5, 10, 12) after high-dose irradiation and has revealed the sequential action of RecA-independent and -dependent pathways during repair (11).Comparative genomic and experimental analyses support the view that DEIRA's extreme radiation resistance phenotype is complex, likely determined collectively by an assortment o...

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“…Transcripts of hcp and the Hcp protein were also more abundant in Shewanella when Fe(III) was provided as an electron acceptor than when oxygen was provided (Beliaev et al, 2002).…”

Section: Electron Transport Genes Only Upregulated In Fe(iii) Oxide-gmentioning

confidence: 99%

Proteins involved in electron transfer to Fe(III) and Mn(IV) oxides by Geobacter sulfurreducens and Geobacter uraniireducens

et al. 2013

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Gene and Protein Expression Profiles ofShewanella oneidensisduring Anaerobic Growth with Different Electron Acceptors

Cited by 91 publications

References 74 publications

Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations

Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Proteins involved in electron transfer to Fe(III) and Mn(IV) oxides by Geobacter sulfurreducens and Geobacter uraniireducens

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