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Eiji Aono,
Tomoya Baba,
Takeshi Ara,
Tatsunari Nishi,
Tomoko Nakamichi,
Eiji Inamoto,
Hiromi Toyonaga,
Miki Hasegawa, Yuki Takai,
Yoshiko Okumura,
Miki Baba,
Masaru Tomita,
Chiaki Kato,
Taku Oshima,
Kaoru Nakasone,
Hirotada Mori
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ABSTRACT: Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.
Molecular BioSystems 07/2010; 6(7):1216-26. · 3.53 Impact Factor
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Natsuko Yamamoto,
Kenji Nakahigashi,
Tomoko Nakamichi,
Mihoko Yoshino, Yuki Takai,
Yae Touda,
Akemi Furubayashi,
Satoko Kinjyo,
Hitomi Dose,
Miki Hasegawa,
Kirill A Datsenko,
Toru Nakayashiki,
Masaru Tomita,
Barry L Wanner,
Hirotada Mori
Molecular Systems Biology 01/2009; 5:335. · 8.63 Impact Factor
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ABSTRACT: Central carbon metabolism is a basic and exhaustively analyzed pathway. However, the intrinsic robustness of the pathway might still conceal uncharacterized reactions. To test this hypothesis, we constructed systematic multiple-knockout mutants involved in central carbon catabolism in Escherichia coli and tested their growth under 12 different nutrient conditions. Differences between in silico predictions and experimental growth indicated that unreported reactions existed within this extensively analyzed metabolic network. These putative reactions were then confirmed by metabolome analysis and in vitro enzymatic assays. Novel reactions regarding the breakdown of sedoheptulose-7-phosphate to erythrose-4-phosphate and dihydroxyacetone phosphate were observed in transaldolase-deficient mutants, without any noticeable changes in gene expression. These reactions, triggered by an accumulation of sedoheptulose-7-phosphate, were catalyzed by the universally conserved glycolytic enzymes ATP-dependent phosphofructokinase and aldolase. The emergence of an alternative pathway not requiring any changes in gene expression, but rather relying on the accumulation of an intermediate metabolite may be a novel mechanism mediating the robustness of these metabolic networks.
Molecular Systems Biology 01/2009; 5:306. · 8.63 Impact Factor
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Nobuyoshi Ishii,
Kenji Nakahigashi,
Tomoya Baba,
Martin Robert,
Tomoyoshi Soga,
Akio Kanai,
Takashi Hirasawa,
Miki Naba,
Kenta Hirai,
Aminul Hoque, [......], Yuki Takai,
Katsuyuki Yugi,
Kazuharu Arakawa,
Nayuta Iwata,
Yoshihiro Toya,
Yoichi Nakayama,
Takaaki Nishioka,
Kazuyuki Shimizu,
Hirotada Mori,
Masaru Tomita
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ABSTRACT: Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger RNA and proteins for most disruptants. Overall, metabolite levels were also stable, reflecting the rerouting of fluxes in the metabolic network. In contrast, E. coli actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate. E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations.
Science 05/2007; 316(5824):593-7. · 31.20 Impact Factor
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ABSTRACT: We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).
Molecular Systems Biology 02/2006; 2:2006.0008. · 8.63 Impact Factor
