Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Saito, Rie; Kato, Chiaki; Nakayama, Akihiko

doi:10.2323/jgam.52.9

Cited by 8 publications

(3 citation statements)

References 30 publications

(66 reference statements)

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“…strain HTA-462 (Shirai et al 2008), Cu/Zn superoxide dismutase from the deep-sea yeast Cryptococcus liquefaciens strain N6 (Teh et al 2008), and superoxide dismutase from the deep-sea worm Alvinella pompejana (Shin et al 2009), as found for other hyperthermophilic enzymes (Vieille and Zeikus 2001). Deep-sea enzymes with unknown crystal structures generally have the same folded structures as their normal homologs in homology modeling (Purcarea et al 1997;Saito et al 2006;Kato et al 2008b;Brindley et al 2008;Xie et al 2009). Taken together, these results indicate that the tertiary structures of deep-sea enzymes are essentially the same as those of their homologs from bacteria living in ambient atmospheric pressure environments.…”

Section: Primary and Tertiary Structures Of Deep-sea Dhfrsmentioning

confidence: 97%

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

Ohmae

Gekko

Kato

2015

Subcellular Biochemistry

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In order to elucidate the molecular adaptation mechanisms of enzymes to the high hydrostatic pressure of the deep sea, we cloned, purified, and characterized more than ten dihydrofolate reductases (DHFRs) from bacteria living in deep-sea and ambient atmospheric pressure environments. The nucleotide and amino acid sequences of these DHFRs indicate the deep-sea bacteria are adapted to their environments after the differentiation of their genus from ancestors inhabiting atmospheric pressure environments. In particular, the backbone structure of the deep-sea DHFR from Moritella profunda (mpDHFR) almost overlapped with the normal homolog from Escherichia coli (ecDHFR). Thus, those of other DHFRs would also overlap on the basis of their sequence similarities. However, the structural stability of both DHFRs was quite different: compared to ecDHFR, mpDHFR was more thermally stable but less stable against urea and pressure unfolding. The smaller volume changes due to unfolding suggest that the native structure of mpDHFR has a smaller cavity and/or enhanced hydration compared to ecDHFR. High hydrostatic pressure reduced the enzymatic activity of many DHFRs, but three deep-sea DHFRs and the D27E mutant of ecDHFR exhibited pressure-dependent activation. The inverted activation volumes from positive to negative values indicate the modification of their structural dynamics, conversion of the rate-determining step of the enzymatic reaction, and different contributions of the cavity and hydration to the transition-state structure. Since the cavity and hydration depend on amino acid side chains, DHFRs would adapt to the deep-sea environment by regulating the cavity and hydration by substituting their amino acid side chains without altering their backbone structure. The results of this study clearly indicate that the cavity and hydration play important roles in the adaptation of enzymes to the deep-sea environment.

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Section: Primary and Tertiary Structures Of Deep-sea Dhfrsmentioning

confidence: 97%

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

Ohmae

Gekko

Kato

2015

Subcellular Biochemistry

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“…21.5b, the backbone structure of this enzyme (PDB ID: 3vmk) completely overlaps with that of the normal homolog from S. oneidensis strain MR-1 (PDB ID: 3vmj) , which was collected from Oneida Lake (Venkateswaran et al 1999). The sequence length, level of identity with ecDHFR, and accession numbers for the DDBJ/GenBank/EMBL sequence databases are also indicated at the end of each sequence generally have the same folded structures as their normal homologs in homology modeling (Purcarea et al 1997;Saito et al 2006;Kato et al 2008b;Brindley et al 2008;Xie et al 2009). strain HTA-462 (Shirai et al 2008), Cu/Zn superoxide dismutase from the deep-sea yeast Cryptococcus liquefaciens strain N6 (Teh et al 2008), and superoxide dismutase from the deep-sea worm Alvinella pompejana (Shin et al 2009), as found for other hyperthermophilic enzymes (Vieille and Zeikus 2001).…”

Section: Primary and Tertiary Structures Of Deep-sea Dhfrsmentioning

confidence: 99%

High Pressure Bioscience

Akasaka¹,

Matsuki²

2015

Subcellular Biochemistry

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The book series SUBCELLULAR BIOCHEMISTRY is a renowned and well recognized forum for disseminating advances of emerging topics in Cell Biology and related subjects. All volumes are edited by established scientists and the individual chapters are written by experts on the relevant topic. The individual chapters of each volume are fully citable and indexed in Medline/Pubmed to ensure maximum visibility of the work.

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“…In recent years analyses of protein structural and kinetic adaptations to high‐pressure deep‐sea environments has increased. This includes work on actin, bacterial tubulin (FtsZ), RNA polymerase, single‐stranded DNA binding protein, proteases, isopropylmalate dehydrogenases, malate dehydrogenase, and dihydrofolate reductase 36–42 …”

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confidence: 99%

Introduction to High‐Pressure Bioscience and Biotechnology

Bartlett

2010

Annals of the New York Academy of Sciences

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The manipulation of biological materials using elevated pressure is providing an ever-growing number of opportunities in both the applied and basic sciences. Manipulation of pressure is a useful parameter for enhancing food quality and shelf life; inactivating microbes, viruses, prions, and deleterious enzymes; affecting recombinant protein production; controlling DNA hybridization; and improving vaccine preparation. In biophysics and biochemistry, pressure is used as a tool to study intermediates in protein folding, enzyme kinetics, macromolecular interactions, amyloid fibrous protein aggregation, lipid structural changes, and to discern the role of solvation and void volumes in these processes. Biologists, including many microbiologists, examine the utility and basis of pressure inactivation of cells and cellular processes, and conversely seek to discover how deep-sea life has evolved a preference for high-pressure environments. This introduction and the papers that follow provide information on the nature and promise of the highly interdisciplinary field of high-pressure bioscience and biotechnology (HPBB).

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Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Cited by 8 publications

References 30 publications

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

High Pressure Bioscience

Introduction to High‐Pressure Bioscience and Biotechnology

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