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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization
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Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization

机译：基因组重建Shewanella oneidensis MR-1代谢揭示了乳酸利用的先前未知的机制

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摘要

The ability to use lactate as a sole source of carbon and energy is one of the key metabolic signatures of Shewanellae, a diverse group of dissimilatory metal-reducing bacteria commonly found in aquatic and sedimentary environments. Nonetheless, homology searches failed to recognize orthologs of previously described bacterial d- or L-lactate oxidizing enzymes (Escherichia coli genes dld and lldD) in any of the 13 analyzed genomes of Shewanella spp. By using comparative genomic techniques, we identified a conserved chromosomal gene cluster in Shewanella oneidensis MR-1 (locus tag: SO_1522-SO_1518) containing lactate permease and* candidate genes for both d- and L-lactate dehydrogenase enzymes. The predicted d-LDH gene (dld-ll, SO_1521) is a distant homolog of FAD-dependent lactate dehydrogenase from yeast, whereas the predicted l-LDH is encoded by 3 genes with previously unknown functions (IIdEGF, SO_1520-SO_1518). Through a combination of genetic and biochemical techniques, we experimentally confirmed the predicted physiological role of these novel genes in 5. Oneidensis MR-1 and carried out successful functional validation studies in Escherichia coli and Bacillus subtilis. We conclusively showed that dld-ll and lldEFG encode fully functional D-and l-LDH enzymes, which catalyze the oxidation of the respective lactate stereoiso-mers to pyruvate. Notably, the S. Oneidensis MR-1 LldEFG enzyme is a previously uncharacterized example of a multisubunit lactate oxidase. Comparative analysis of >400 bacterial species revealed the presence of LldEFG and Dld-ll in a broad range of diverse species accentuating the potential importance of these previously unknown proteins in microbial metabolism.
机译：利用乳酸作为碳和能量的唯一来源的能力是希瓦氏菌（Shewanellae）的关键代谢特征之一，希瓦氏菌是在水生和沉积环境中常见的多种减少异化金属的细菌。但是，同源搜索未能在希瓦氏菌的13个分析基因组中的任何一个中识别先前描述的细菌d-或L-乳酸氧化酶的直系同源物（大肠杆菌基因dld和lldD）。通过使用比较基因组学技术，我们在Shewanella oneidensis MR-1（基因标签：SO_1522-SO_1518）中鉴定了一个保守的染色体基因簇，其中含有乳酸通透酶和d和L-乳酸脱氢酶的候选基因。预测的d-LDH基因（dld-II，SO_1521）是来自酵母的FAD依赖性乳酸脱氢酶的遥远同源物，而预测的1-LDH由3个功能未知的基因编码（IIdEGF，SO_1520-SO_1518）。通过遗传和生化技术的结合，我们实验证实了这些新基因在5的Oneidensis MR-1中的预期生理作用。并在大肠杆菌和枯草芽孢杆菌中进行了成功的功能验证研究。我们结论性地表明，dld-II和lldEFG编码功能齐全的D-和1-LDH酶，它们催化相应的乳酸立体异构体氧化为丙酮酸。值得注意的是，S。Oneidensis MR-1 LldEFG酶是多亚单位乳酸氧化酶的先前未表征的实例。对> 400个细菌物种的比较分析显示，LldEFG和Dld-II在多种多样的物种中均存在，从而突显了这些以前未知的蛋白在微生物代谢中的潜在重要性。

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  • 作者

    Grigory E. Pinchuk; Dmitry A. Rodionov; Chen Yang; Xiaoqing Li; Andrei L. Osterman; Etienne Dervyn; Oleg V. Geydebrekht; Samantha B. Reed; Margaret F. Romine; Frank R. Collart; James H. Scott; Jim K. Fredrickson; Alexander S. Beliaev;

  • 作者单位

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352;

    Bumham Institute for Medical Research, La Jolla, CA 92037 Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia;

    Bumham Institute for Medical Research, La Jolla, CA 92037 Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China;

    Bumham Institute for Medical Research, La Jolla, CA 92037;

    Bumham Institute for Medical Research, La Jolla, CA 92037 Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527;

    Genetique Microbienne, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas, France;

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352;

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352;

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352;

    Biosciences Division, Argonne National Laboratory, Argonne, IL 60439;

    Department of Earth Sciences, Dartmouth College, Hanover, NH 03755;

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352;

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
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  • 关键词

    central carbon metabolism; genome context analysis; lactate dehydrogenase;

    机译：中央碳代谢基因组背景分析;乳酸脱氢酶;

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