Survival of
            <i>Shewanella oneidensis</i>
            MR-1 after UV Radiation Exposure

Qiu, Xiangyun; Sundin, George W.; Chai, Benli; Tiedje, James M.

doi:10.1128/aem.70.11.6435-6443.2004

Cited by 39 publications

(53 citation statements)

References 53 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%

“…14. Sample processing for the gene expression analysis followed standard protocols with minor modifications (14) and is described in Supporting Materials, which is published as supporting information on the PNAS web site. 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).…”

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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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%

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.

Self Cite

112

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“…The dissimilatory metal ion-reducing Shewanella oneidensis strain MR-1 is extremely sensitive to IR: e.g., 90% of MR-1 cells are killed by less than one DSB in the genome (4). S. oneidensis is also one of the most UV-and desiccation-sensitive organisms reported (4,22). The IR resistance of MR-1 is about 20 times less than that of Escherichia coli and about 200 times less than that of Deinococcus radiodurans (4).…”

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confidence: 99%

“…After irradiation, the irradiated cell culture (40 ml) and nonirradiated control culture (40 ml) were each transferred to a separate 100-ml flask (without dilution into fresh medium) and incubated at 30°C on a shaker. An aliquot of cells (12 ml) from each flask was collected after 5, 20, and 60 min of incubation for RNA extraction as described previously (22,23). Three independent cell cultures and irradiation treatments were performed and served as biological replicates for gene expression experiments.…”

mentioning

confidence: 99%

“…Three independent cell cultures and irradiation treatments were performed and served as biological replicates for gene expression experiments. RNA extraction, probe labeling, microarray hybridization, image acquisition, and processing were carried out as described previously (22,23). For each time point, two technical replicates in hybridization (fluorescent dye reversal) were carried out for each biological replicate.…”

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Transcriptome Analysis Applied to Survival of Shewanella oneidensis MR-1 Exposed to Ionizing Radiation

et al. 2006

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The ionizing radiation (IR) dose that yields 20% survival (D 20 ) of Shewanella oneidensis MR-1 is lower by factors of 20 and 200 than those for Escherichia coli and Deinococcus radiodurans, respectively. Transcriptome analysis was used to identify the genes of MR-1 responding to 40 Gy (D 20 ). We observed the induction of 170 genes and repression of 87 genes in MR-1 during a 1-h recovery period after irradiation. The genomic response of MR-1 to IR is very similar to its response to UV radiation (254 nm), which included induction of systems involved in DNA repair and prophage synthesis and the absence of differential regulation of tricarboxylic acid cycle activity, which occurs in IR-irradiated D. radiodurans. Furthermore, strong induction of genes encoding antioxidant enzymes in MR-1 was observed. DNA damage may not be the principal cause of high sensitivity to IR, considering that MR-1 carries genes encoding a complex set of DNA repair systems and 40 Gy IR induces less than one double-strand break in its genome. Instead, a combination of oxidative stress, protein damage, and prophage-mediated cell lysis during irradiation and recovery might underlie this organism's great sensitivity to IR.Ionizing radiation (IR) is potentially lethal and mutagenic to all organisms. The cellular response to IR is complex due to the variety of targets in a cell. IR can damage cellular components through direct deposition of radiation energy into biomolecules and also indirectly by generating reactive oxygen species (ROS). Hydrogen peroxide (H 2 O 2 ) and hydroxyl radicals (HO·) are major oxidizing species produced by the radiolysis of water, and superoxide ions (O 2 · Ϫ ) are formed in the presence of dissolved oxygen (8,24,25,27,28).Generally, the cytotoxic and mutagenic effects induced by IR are thought to be the result of DNA damage caused during the course of irradiation, which includes single-strand breaks (SSB), double-strand breaks (DSB), base modification, abasic sites, and sugar modification (11,27). The amounts of DNA damage caused by given doses of IR for different bacteria are very similar, although the range of IR resistance levels is large. The dissimilatory metal ion-reducing Shewanella oneidensis strain MR-1 is extremely sensitive to IR: e.g., 90% of MR-1 cells are killed by less than one DSB in the genome (4). S. oneidensis is also one of the most UV-and desiccation-sensitive organisms reported (4,22). The IR resistance of MR-1 is about 20 times less than that of Escherichia coli and about 200 times less than that of Deinococcus radiodurans (4). It is unclear why S. oneidensis MR-1 is exceptionally sensitive to radiation.Since more than 80% of IR energy deposited in cells results in the ejection of electrons from water, a large amount of ROS is produced in cells exposed to IR (8,25

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Wavelength dependence of biological damage induced by UV radiation on bacteria

et al. 2012

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The biological effects of UV radiation of different wavelengths (UVA, UVB and UVC) were assessed in nine bacterial isolates displaying different UV sensitivities. Biological effects (survival and activity) and molecular markers of oxidative stress [DNA strand breakage (DSB), generation of reactive oxygen species (ROS), oxidative damage to proteins and lipids, and the activity of antioxidant enzymes catalase and superoxide dismutase] were quantified and statistically analyzed in order to identify the major determinants of cell inactivation under the different spectral regions. Survival and activity followed a clear wavelength dependence, being highest under UVA and lowest under UVC. The generation of ROS, as well as protein and lipid oxidation, followed the same pattern. DNA damage (DSB) showed the inverse trend. Multiple stepwise regression analysis revealed that survival under UVA, UVB and UVC wavelengths was best explained by DSB, oxidative damage to lipids, and intracellular ROS levels, respectively.

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Survival of Shewanella oneidensis MR-1 after UV Radiation Exposure

Cited by 39 publications

References 53 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 Analysis Applied to Survival of Shewanella oneidensis MR-1 Exposed to Ionizing Radiation

Wavelength dependence of biological damage induced by UV radiation on bacteria

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