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Qian J, Fan L, Yang J, Feng J, Gao N, Cheng G, Pu W, Zhou W, Cai T, Li S, Zheng P, Sun J, Wang D, Wang Y. Directed evolution of a neutrophilic and mesophilic methanol dehydrogenase based on high-throughput and accurate measurement of formaldehyde. Synth Syst Biotechnol 2023; 8:386-395. [PMID: 37342805 PMCID: PMC10277290 DOI: 10.1016/j.synbio.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/01/2023] [Accepted: 05/21/2023] [Indexed: 06/23/2023] Open
Abstract
Methanol is a promising one-carbon feedstock for biomanufacturing, which can be sustainably produced from carbon dioxide and natural gas. However, the efficiency of methanol bioconversion is limited by the poor catalytic properties of nicotinamide adenine dinucleotide (NAD+)-dependent methanol dehydrogenase (Mdh) that oxidizes methanol to formaldehyde. Herein, the neutrophilic and mesophilic NAD+-dependent Mdh from Bacillus stearothermophilus DSM 2334 (MdhBs) was subjected to directed evolution for enhancing the catalytic activity. The combination of formaldehyde biosensor and Nash assay allowed high-throughput and accurate measurement of formaldehyde and facilitated efficient selection of desired variants. MdhBs variants with up to 6.5-fold higher Kcat/KM value for methanol were screened from random mutation libraries. The T153 residue that is spatially proximal to the substrate binding pocket has significant influence on enzyme activity. The beneficial T153P mutation changes the interaction network of this residue and breaks the α-helix important for substrate binding into two short α-helices. Reconstructing the interaction network of T153 with surrounding residues may represent a promising strategy to further improve MdhBs, and this study provides an efficient strategy for directed evolution of Mdh.
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Affiliation(s)
- Jin Qian
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Liwen Fan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jinxing Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jinhui Feng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ning Gao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guimin Cheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Cai
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ping Zheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
| | - Yu Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Xia Y, Kong Y, Nielsen PH. In situ detection of starch-hydrolyzing microorganisms in activated sludge. FEMS Microbiol Ecol 2008; 66:462-71. [DOI: 10.1111/j.1574-6941.2008.00559.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Lee Y, Brown M, Cheung H. Defined minimal media for the growth of prototrophic and auxotrophic strains ofBacillus stearothermophilus. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1982.tb04675.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wynne SA, Nicholls DJ, Scawen MD, Sundaram TK. Tetrameric malate dehydrogenase from a thermophilic Bacillus: cloning, sequence and overexpression of the gene encoding the enzyme and isolation and characterization of the recombinant enzyme. Biochem J 1996; 317 ( Pt 1):235-45. [PMID: 8694770 PMCID: PMC1217469 DOI: 10.1042/bj3170235] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The gene encoding the tetrameric malate dehydrogenase (MDH) in a thermophilic Bacillus species (BI) has been cloned in an Escherichia coli plasmid. The nucleotide sequence of the gene, the first to be elucidated for a tetrameric MDH, shows the MDH subunit to contain 312 amino acids and have a molecular mass of 33648 Da, which confirms the experimentally determined value of about 35 kDa. Like the genomic DNA of BI, the MDH gene is relatively AT-rich; this contrasts with the generally GC-rich nature of the DNA of thermophilic Bacillus species. Comparison of amino acid sequences reveals that BI MDH bears greater structural similarity to lactate dehydrogenases (LDHs) than to other (dimeric) MDHs. MDHs and LDHs resemble each other in catalytic mechanism and several other respects. However, whereas MDHs in the majority of organisms are dimers, the tetrameric structure is favoured among LDHs. The stronger structural resemblance that BI MDH has to LDHs than to the dimeric MDHs provides some explanation as to why Bacillus MDH, unlike most other MDHs, is tetrameric. A 1 kb fragment containing the BI MDH gene, produced in a PCR, has been cloned into a high-expression E. coli plasmid vector. BI MDH synthesized from this clone constitutes about 47% of the total protein in cell extracts of the E. coli strain carrying the clone. MDH purified from BI and that purified from the E. coli strain carrying the MDH gene clone appear to be identical proteins by several criteria. A number of characteristics of the MDH have been elucidated, including the molecular masses of the native enzyme and the subunit, N-terminal amino acid sequence, isoelectric point, pH optimum for activity, thermostability, stability to pH, urea and guanidinium chloride and several kinetic parameters. Whereas the MDH is a stable tetramer in the pH range 5-7, it appears to be converted into a stable dimer at pH 3.5. This suggests that the dimer is a stable intermediate in the dissociation of the tetramer to monomers at low pH.
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Affiliation(s)
- S A Wynne
- Department of Biochemistry and Applied Molecular Biology, UMIST, Manchester, UK
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Characterization of a new Bacillus stearothermophilus isolate: a highly thermostable α-amylase-producing strain. Appl Microbiol Biotechnol 1994. [DOI: 10.1007/bf00186953] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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White D, Sharp RJ, Priest FG. A polyphasic taxonomic study of thermophilic bacilli from a wide geographical area. Antonie Van Leeuwenhoek 1994; 64:357-86. [PMID: 8085796 DOI: 10.1007/bf00873093] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Two hundred and thirty-four thermophilic Bacillus strains isolated from geographically widespread locations were examined by phenotypic characterisation followed by numerical analysis. The strains were distributed between eighteen cluster-groups which were subsequently evaluated in DNA base composition and DNA sequence homology studies. The inclusion of type and reference strains unambiguously identified strains related to B. licheniformis, B. pallidus, B. smithii, B. stearothermophilus, B. thermocloacae and B. thermoglucosidasius. Other reference strains included in distinctive groups were 'B. caldotenax', together with 'B. caldovelox' and 'B. caldolyticus', B. kaustophilus and 'B. thermodenitrificans'. An emended description of B. kaustophilus is provided. It is proposed that 'B. caldotenax' and 'B. thermodenitrificans' should be accepted as validly described species. Members of other clusters that appeared to have distinctive characteristics, including beta-glucanase production and the ability to degrade tyrosine, may provide the nuclei of further novel species.
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Affiliation(s)
- D White
- Department of Plant and Soil Science, University of Aberdeen, UK
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Buurman ET, Pennock J, Tempest DW, Teixeira de Mattos MJ, Neijssel OM. Replacement of potassium ions by ammonium ions in different micro-organisms grown in potassium-limited chemostat culture. Arch Microbiol 1989; 152:58-63. [PMID: 2669673 DOI: 10.1007/bf00447012] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The biomass concentration extant in potassium-limited cultures of either Klebsiella pneumoniae or Bacillus stearothermophilus (when growing at a fixed temperature and dilution rate in a glucose/ammonium salts medium) increased progressively as the medium pH value was raised step-wise from 7.0 to 8.5. Because the macromolecular composition of the organisms did not vary significantly, this increase in biomass could not be attributed to an accumulation of storage-type polymers but appeared to reflect a pH-dependent decrease in the cells' minimum K+ requirement. Significantly, this effect of pH was not evident with cultures in which no ammonium salts were present and in which either glutamate or nitrate was added as the sole nitrogen source; however, it was again manifest when various concentrations of NH4Cl were added to the glutamate-containing medium. This suggested a functional replacement of K+ by NH4+, a proposition consistent with the close similarity of the ionic radii of the potassium ion (1.33 A) and the ammonium ion (1.43 A). At pH 8.0, and with a medium containing both glutamate (30 mM) and NH4Cl (100 mM), cultures of B. stearothermophilus would grow without added potassium at a maximum rate of 0.7 h-1. Under these conditions the cells contained maximally 0.1% (w/w) potassium (derived from contaminating amounts of this element in the medium constituents), a value which should be compared with one of 1.4% (w/w) for cells growing in a potassium-limited medium containing initially 0.5 mM K+.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- E T Buurman
- Department of Microbiology, University of Amsterdam, The Netherlands
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Edlin JD, Sundaram TK. Isocitrate dehydrogenase from thermophilic and mesophilic bacteria. Isolation and some characteristics. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1989; 21:1203-10. [PMID: 2515075 DOI: 10.1016/0020-711x(89)90004-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
1. Simple methods incorporating the principle of selective enzyme elution from a triazinyl dye adsorbent with a mixture of NADP+ and isocitrate are described for isolating NADP+-linked isocitrate dehydrogenase in pure state from several mesophilic and thermophilic bacteria. 2. Several characteristics of the isocitrate dehydrogenases have been examined, viz. molecular size, amino acid composition including the content of sulphydryl groups, thermostability and structural homology by the criterion of immunological cross-section.
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Affiliation(s)
- J D Edlin
- Department of Biochemistry, University of Manchester Institute of Science & Technology, England
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Metabolic and energetic aspects of the growth of Bacillus stearothermophilus in glucose-limited and glucose-sufficient chemostat culture. Arch Microbiol 1988. [DOI: 10.1007/bf00422286] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Dowds BC, Sheehan MC, Bailey CJ, McConnell DJ. Cloning and characterization of the gene for a methanol-utilising alcohol dehydrogenase from Bacillus stearothermophilus. Gene X 1988; 68:11-22. [PMID: 2851486 DOI: 10.1016/0378-1119(88)90594-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cloning and characterization of the alcohol dehydrogenase (ADH) gene (adh) from Bacillus stearothermophilus strain DSM2334, an obligate aerobe, are described. The clone directed the synthesis of ADH as judged on Western blots, activity gels and tetrazolium plates. It specified an enzyme that oxidised methanol as well as ethanol. The enzyme was found to be encoded by a single gene in B. stearothermophilus which did not cross-hybridize to adh clones from Escherichia coli, yeast or maize. The cloned gene was expressed in E. coli but activity was not detected in Bacillus subtilis, despite stable maintenance of the recombinant plasmid in this host. The gene is catabolite-repressed in DSM2334.
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Affiliation(s)
- B C Dowds
- Department of Genetics, Trinity College, Dublin, Ireland
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Sheehan MC, Bailey CJ, Dowds BC, McConnell DJ. A new alcohol dehydrogenase, reactive towards methanol, from Bacillus stearothermophilus. Biochem J 1988; 252:661-6. [PMID: 3421916 PMCID: PMC1149199 DOI: 10.1042/bj2520661] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
An NAD+-dependent alcohol dehydrogenase (ADH) was purified to homogeneity from an aerobic strain of Bacillus stearothermophilus, DSM 2334 (ADH 2334), and compared with the ADH from B. stearothermophilus NCA 1503 (ADH 1503). When an antibody raised against ADH 2334 was used, no cross-reactivity with ADH 1503 was observed on Western blots; by means of an enzyme-linked-immunoabsorbent-assay ('e.l.i.s.a.') procedure, it was found that ADH 1503 had less than 6% of the antigenic activity of ADH 2334. Amino acid analyses detected very small differences in composition, equivalent to about 40 sequence changes, between the two enzymes. The new enzyme has the same six-amino-acid N-terminal sequence as ADH 1503. ADH 2334, but not ADH 1503, is reactive towards methanol; both enzymes can oxidize ethanol, propan-1-ol, butan-1-ol and butan-2-ol. The new enzyme has a distinctive pH optimum at pH 5.5-6 and has significantly lower KEthanolm and kEthanolcat. values than those of ADH 1503. From steady-state kinetic parameters of the reaction with ethanol, propan-1-ol and butan-1-ol, it was shown that ADH 2334 has an ordered mechanism in both directions, with NAD+ being the compulsory first substrate in alcohol oxidation and NADH release being the rate-limiting step. ADH 1503 has an ordered addition of NAD+ and alcohol, but NADH release is not rate-limiting.
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Affiliation(s)
- M C Sheehan
- Department of Biochemistry, Trinity College, Dublin, Ireland
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Bacquet C, Twumasi DY. A homogeneous enzyme immunoassay with avidin-ligand conjugate as the enzyme-modulator. Anal Biochem 1984; 136:487-90. [PMID: 6372543 DOI: 10.1016/0003-2697(84)90248-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A homogeneous enzyme immunoassay (EIA) based on the immunomodulation of an avidin-ligand conjugate and the inhibition of pyruvate carboxylase is described. The conjugation of the ligand, 5,5-diphenylhydantoin (DPH), to avidin does not affect avidin's capacity to bind biotin or inhibit pyruvate carboxylase. The DPH-avidin conjugate and free DPH were shown to compete for a limited number of antibody sites. The interaction of anti-DPH with the DPH-avidin conjugate sterically inhibited enzyme inactivation. Enzyme activity was correlated with DPH concentrations in the therapeutic range found in serum.
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Chicken E, Spode JA, Jones CW. Respiration-linked proton translocation in the moderate thermophileBacillus stearothermophilus. FEMS Microbiol Lett 1981. [DOI: 10.1111/j.1574-6968.1981.tb06959.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Energiestoffwechsel des thermophilen Bakteriums Bacillus stearothermophilus während kontinuierlicher Kultur im Phauxostat. FERMENTATION 1981. [DOI: 10.1007/978-3-7091-8634-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Váli Z, Kilár F, Lakatos S, Venyaminov SA, Závodszky P. L-alanine dehydrogenase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 615:34-47. [PMID: 6775703 DOI: 10.1016/0005-2744(80)90006-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A heat-stable L-alanine dehydrogenase was isolated and purified from the extremely thermophilic microorganism, Thermus thermophilus, by affinity chromatography. The enzyme has a molecular weight of 290 000, as determined by the sedimentation equilibrium method, and is composed of six subunits of identical molecular weight as concluded from sodium dodecyl sulphate gel electrophoresis. The enzyme has been characterized in terms of pH- and substrate concentration-dependence of activity, substrate specificity, inhibition by D-alanine and D-cysteine and amino acid composition. The parameters obtained are very similar to those reported for L-alanine dehydrogenase from the mesophilic microorganism, Bacillus subtilis (Yoshida, A. and Freese, E. (1965) Biochim. Biophys. Acta 96, 248--262). The thermal stability of the T. thermophilus enzyme is much greater than that of the B. subtilis enzyme. Activation free energy (delta G), activation enthalpy (delta H) and activation entropy (delta S) values were determined for both the alanine deamination and for the heat inactivation reactions of the thermophilic and mesophilic enzymes. The values obtained for the catalytic reaction were practically equal. However, the two enzymes differed significantly in these parameters determined for the enzyme inactivation, which indicates that the factors ensuring the thermoresistance of the enzyme from T. thermophilus do not affect enzyme activity.
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Stenesh J, Madison JB. Stability of bacterial messenger RNA in mesophiles and thermophiles. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 565:154-60. [PMID: 508760 DOI: 10.1016/0005-2787(79)90091-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The decay of [3H]uridine-labeled mRNA was measured in the mesophile, Bacillus licheniformis (grown at 37 degrees C and 46 degrees C), and in the thermophile, Bacillus stearothermophilus (grown at 46 degrees C and 55 degrees C). For each organism, the half-life of the mRNA decreased as the growth temperature was increased. The stability index (half-life of mRNA/doubling time of cells), however, was remarkably constant for each organism regardless of the growth temperature. It is concluded that these results support the concept that kinetic considerations play a significant role in the explanation of thermophily.
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Ashare E, Wentworth R, Wise D. Fuel gas production from animal residue part II. an economic assessment. ACTA ACUST UNITED AC 1979. [DOI: 10.1016/0304-3967(79)90022-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wright IP, Sundaram TK. Simple efficient methods for the isolation of malate dehydrogenase from thermophilic and mesophilic bacteria. Biochem J 1979; 177:441-8. [PMID: 435244 PMCID: PMC1186393 DOI: 10.1042/bj1770441] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Malate dehydrogenase from a number of bacteria drawn from several genera and representing the mesophilic, moderately thermophilic and extremely thermophilic classes was isolated by procedures which involve only a small number of steps (in most cases only two), of which the key one is affinity chromatography on 5'-AMP--Sepharose and/or on NAD+--hexane--agarose. Electrophoretic analysis of the native enzymes in polyacrylamide gel and of the denaturated enzymes in sodium dodecyl sulphate/polyacrylamide gel revealed no significant protein impurity in the purified preparations. The yields ranged from about 40% to over 80%. The malate dehydrogenases from the extreme thermophiles and from some of the moderate thermophiles are appreciably less efficient catalytically than their mesophilic homologues.
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Chell RM, Sundaram TK, Wilkinson AE. Isolation and characterization of isocitrate lyase from a thermophilic Bacillus sp. Biochem J 1978; 173:165-77. [PMID: 687365 PMCID: PMC1185759 DOI: 10.1042/bj1730165] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isocitrate lyase was isolated in homogeneous state from a thermophilic Bacillus. The enzyme has a mol.wt. of 180000 and a pI of 4.5 and contains threonine as the N-terminal residue. It resembles in size the cognate enzyme from the mesophilic bacterium Pseudomonas indigofera, but is smaller than the enzyme from the eukaryotic fungus Neurospora crassa. All three lyases are tetramers and similar in amino acid composition, but the thermophile enzyme is distinctive from its mesophilic coutnerparts in possessing a lower catalytic-centre activity, greater resistance to chemical and thermal denaturation and fewer thiol groups and in being strongly activated by salts. Salt activation, by 0.4M-KCl, is about 3-fold at 30 degrees C and pH 6.8 and weakens progressively as the temperature or pH is raised. The activation is probably due to a change in the enzyme conformation caused by the electrolyte modifying the interaction between charged groups or between hydrophobic groups in protein. The possible significance of the salt activation, of the relative paucity of thiol groups and of the greater resistance to chemical denaturants is discussed. Besides its effect on the Vmax., KCl produces large increases in the magnitude of several kinetic parameters. A rise in reaction temperature from 30 to 55 degrees C produces a somewhat similar result. In view of these peculiar features, the patterns of inhibition of enzyme activity by compounds such as succinate and phosphoenolpyruvate were examined at 30 and 55 degrees C in the presence and absence of KCl.
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Downey RJ, Ragno L. Peptide requirement in the biosynthesis of nitrate reductase in Bacillus stearothermophilus. FEMS Microbiol Lett 1978. [DOI: 10.1111/j.1574-6968.1978.tb01946.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Amelunxen RE, Murdock AL. Mechanisms of thermophily. CRC CRITICAL REVIEWS IN MICROBIOLOGY 1978; 6:343-93. [PMID: 365460 DOI: 10.3109/10408417809090626] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Reizer J, Epstein I, Grossowicz N. Temperature-induced metabolic alterations in a thermophilic bacillus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 77:463-70. [PMID: 891545 DOI: 10.1111/j.1432-1033.1977.tb11687.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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27
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Thalenfeld B, Epstein I, Grossowicz N. Relationship between culture density and catabolite repression of an inducible aliphatic amidase in a thermophilic bacillus. Biochim Biophys Acta Gen Subj 1977; 497:112-21. [PMID: 14704 DOI: 10.1016/0304-4165(77)90143-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A direct correlation between the absorbance of a thermophilic bacillus and specific amidase activity was observed, which was found to depend on the cell density of the culture rather than on the time of contact of the culture with the inducer. Dilution of high density cultures caused the specific amidase activity to decrease. Environmental factors such as pH, concentration of inducer or degree of aeration, and level of NH+4 and glutamate had no effect on amidase synthesis. The decrease in amidase activity upon dilution could not be ascribed to destruction by oxygen or by inactivation or decay. Several lines of evidence suggest that catabolite repression is responsible for the phenomenon described. Succinate-grown cultures gave a stronger dilution effect thatn glutamate-grown cells. The mutant strain E-21, relatively resistant to catabolite repression, did not show the characteristic dilution effect nor the direct correlation between absorbance and specific amidase activity.
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Epstein I, Grossowicz N. Regulatory control and function of alanine dehydrogenase from a thermophilic bacillus. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 445:549-57. [PMID: 9988 DOI: 10.1016/0005-2744(76)90109-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
L-alanine dehydrogenase, (L-alanine:NAD+ oxidoreductase (deaminating), EC 1.4.1.1) synthesis in a thermophilic bacillus was found to be subjected to regulatory control. Addition of L- and D-alanine and L-serine to cultures growing in the presence of either succinate or pyruvate, induced an accelerated synthesis of the alanine dehydrogenase enzyme. Synthesis of the enzyme was dependent on the presence of inducer during growth and was arrested by addition of glucose. Catabolite repression by glucose was abolished by limiting the ammonium concentration during growth. The apparent Km values of the substrates involved in alanine dehydrogenase activity are as follows (M): NH4+, 4-10(-2); pyruvate, 5-10(-4); NADH, 6-10(-5); L-alanine, 3.1-10(-3) and NAD, 2-10(-4). Alanine dehydrogenase activity was measurable at temperatures below the minimal growth temperature (at 25 degrees C) and the highest activity was found at 65 degrees C; heat denaturation occurred at 80 degrees C.
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Reizer J, Thalenfeld B, Grossowicz N. Methyl-alpha-D-glucoside uptake and splitting by a thermophilic bacillus. Nature 1976; 260:433-5. [PMID: 1256584 DOI: 10.1038/260433a0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Sundaram TK, Libor S, Chell RM. Anaplerotic enzymes of acetate and pyruvate metabolism: distinctive characteristics in Bacillus stearothermophilus. EXPERIENTIA. SUPPLEMENTUM 1976; 26:263-75. [PMID: 939275 DOI: 10.1007/978-3-0348-7675-9_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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31
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Abstract
Anaerobic digestion offers a potential means of converting organic solid waste into fuel gas and thereby provide a supplemental and readily utilizable source of energy. We are particularly interested in the use of thermophilic digestion over a mesophilic operation for it can achieve higher rates of digestion, greater conversion of waste organics to gas, faster solid-liquid separation, and minimization of bacterial and viral pathogen accumulation. Our results comparing mesophilic (37 degree C) and thermophilic (65 degree C) anaerobic digestion of domestic solid waste confirm the increased rate and conversion of waste to methane. In addition, utilizing radioactive labeling of glucose and acetic acid, we have measured the volumetric rates of volatile acid production and disappearance under both mesophilic and thermophilic conditions.
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Epstein I, Grossowicz N. Purification and properties of glutamate dehydrogenase from a thermophilic bacillus. J Bacteriol 1975; 122:1257-64. [PMID: 238942 PMCID: PMC246183 DOI: 10.1128/jb.122.3.1257-1264.1975] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A 250- to 300-fold purification of a nicotinamide adenine denucleotide phosphate (NADP)-dependent glutamate dehydrogenase (GDH, E.C. 1.4.1.4) with a yield of 60% from a thermophilic bacillus is described. More than one NADP-specific GDH was detected by polyacrylamide gel electrophoresis. The enzyme is of high molecular weight (approximately 2 X 10-6), similar to that of the beef and frog liver GDH. The pI of the thermophilic GDH is at pH 5.24. The enzyme is highly thermostable at the pH range of 5.8 to 9.0. The purified GDH, unlike the crude enzyme, was very labile at subzero temperatures. An unidentified factor(s) from the crude cell-free extract prevented the inactivation of the purified GDH at -70 C. Various reactants of the GDH system and D-glutamate also protected, to some extent, the enzyme from inactivation at -70 C. From the Michaelis constants for glutamate (1.1 X 10-2M), NADP (3 X 10-4M), ammonia (2.1 X 10-2M), alpha-ketoglutarate (1.3 X 10-3M), and reduced NADP (5.3 X 10-5M), it is suggested that the enzyme catalyzes in vivo the formation of glutamate from ammonia and alpha-ketoglutarate. The amination of alpha-ketoglutarate and deamination of glutamate by the thermophilic GDH are optimal at the pH values of 7.2 and 8.4, respectively.
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Atkinson A, Evans CG, Yeo RG. Behaviour of Bacillus stearothermophilus grown in different media. THE JOURNAL OF APPLIED BACTERIOLOGY 1975; 38:301-4. [PMID: 1141075 DOI: 10.1111/j.1365-2672.1975.tb00533.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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34
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Coultate TP, Sundaram TK. Energetics of Bacillus stearothermophilus growth: molar growth yield and temperature effects on growth efficiency. J Bacteriol 1975; 121:55-64. [PMID: 1116992 PMCID: PMC285612 DOI: 10.1128/jb.121.1.55-64.1975] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The major growth yield of a prototrophic strain of Bacillus stearothermophilus under aerobic conditions on salts medium containing ammonium nitrate as the nitrogen source and glucose or succinate as the carbon source was maximal at the lowest growth temperature employed and decreased steadily as the temperature was raised. The temperature optima for growth yield and for growth rate were thus different. The molar growth yield values of the thermophile, especially at the lower growth temperatures, were similar to those reported for aerobically grown mesophilic bacteria, both on glucose and on succinate. At the higher growth temperatures, a lower proportion of glucose carbon was incorporated into cells and a correspondingly greater proportion was left incompletely utilized in the medium, mostly as acetate. This suggests a greater inefficiency in the coordination of the nonoxidative and oxidative phases of glucose metabolism at the gigher temperatures. Another factor causing a decreased cell yield at higher temperatures was possibly an uncoupling of energy production from respiration. The rates of respiration by intact cells of the thermophile on glucose and on succinate followed the Arrhenius relationship from 55 C to 20 C, which is some 20 C below the minimal growth temperature of the organism. The Arrhenius constant was 17.1 kcal/mol for glucose oxidation and 13.5 kcal/mol for succinate oxidation. These results are comparable to those reported for some mesophiles, and they suggest that the inability of the thermophile to grow at temperatures below about 41 C is not due to an abnormally high temperature coefficient for the uptake and oxidation of the carbon source.
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35
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Reizer J, Grossowicz N. Properties of alpha-aminoisobutyric acid transport in a thermophilic microorganism. J Bacteriol 1974; 118:414-24. [PMID: 4828307 PMCID: PMC246773 DOI: 10.1128/jb.118.2.414-424.1974] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Uptake of alpha-aminoisobutyric acid (AIB) by a leucine-tyrosine auxotroph of a thermophilic microorganism starved for leucine was studied. AIB was taken up by the cells against a substantial concentration gradient (300:1) and was present there in a free and unchanged form. Various energy inhibitors and sulfhydryl reagents strongly inhibited the accumulation of AIB. AIB uptake obeyed saturation kinetics, and the Lineweaver-Burk plot is characterized by a biphasic curve. AIB most probably shares a common transport system(s) with alanine, serine, and glycine. A mutant defective in l-alanine uptake was isolated by using the suicide effect due to accumulation of the tritiated substrate. The mutant also exhibited impaired transport activity towards AIB, glycine, and l-serine, but not to phenylalanine or valine. The transport of AIB, glycine, l-alanine, and l-serine was induced by d-alanine (5 x 10(-3) M) during growth in a succinate- and ammonia-containing medium. De novo protein synthesis was required for the induction of AIB transport; the induction was inhibited when growth occurred in glucose-containing media. The apparent differential rate of synthesis of the AIB transport system was decreased considerably in glucose-grown cells as compared to succinate-grown cells. A common genetic basis of either the regulatory or structural nature for the transport of AIB, alanine, glycine, and serine in a thermophilic microorganism is suggested.
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36
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Griffiths MW, Sundaram TK. Isocitrate lyase from a thermophilic Bacillus: effect of salts on enzyme activity. J Bacteriol 1973; 116:1160-9. [PMID: 4584800 PMCID: PMC246470 DOI: 10.1128/jb.116.3.1160-1169.1973] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The isocitrate lyase from a thermophilic Bacillus is activated about threefold by a variety of salts. Such strong stimulation of activity is not seen with isocitrate lyase from the mesophiles, Bacillus licheniformis, Bacillus megaterium, Escherichia coli, and Aspergillus nidulans. The salt activation is markedly pH-dependent. At pH values above 8.6, salt (KCl) indeed inhibits the enzyme activity. Potassium chloride also causes a significant shift of the pH optimum of the enzyme towards the acid side. As the temperature of the enzyme reaction is raised, activation becomes progressively weaker. Potassium chloride also affords considerable protection against enzyme denaturation at 55 C. The activation and the stabilization, however, appear to be independent effects. Of six other enzymes in the thermophile that were examined, isocitrate dehydrogenase was equally strongly activated by KCl and malate synthase was less strongly, but significantly, activated; citrate synthase, malate dehydrogenase, glutamate dehydrogenase, and lactate dehydrogenase were unaffected or slightly inhibited by KCl. The property of being strongly activated by salt appears to be a peculiar characteristic of the thermophile isocitrate lyase and possibly evolved concomitantly with its thermostability.
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37
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Abstract
A prototrophic, thermophilic bacillus is in a state of biotin insufficiency when grown in medium consisting of inorganic salts and a carbon source. The effect of this biotin deficiency on the growth rate is severe only if the functioning of pyruvate carboxylase is essential for the utilization of the particular growth substrate. A mutant, PC2, of the thermophile devoid of active pyruvate carboxylase has been isolated. The properties of this mutant confirm the anaplerotic role of this enzyme in the utilization for growth of compounds like glucose and lactate which are catabolized via pyruvate. This conclusion is supported by the finding that revertants isolated from strain PC2 have regained simultaneously the ability to synthesize active pyruvate carboxylase and the ability to utilize glucose or lactate for growth. The growth of mutant PC2 on acetate, unlike that of the parent wild type, is inhibited when glucose or lactate is added to the medium. Secondary mutants obtained from PC2, which are resistant to such inhibition, still carry the original pyruvate carboxylase lesion but are derepressed for isocitrate lyase. This suggests that the inhibition of the growth of mutant PC2 is due to a block in the functioning of the glyoxylate cycle, produced by the glucose or lactate supplement.
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38
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Ward J, Cockson A. Studies on a thermophilic bacillus: its isolation, properties, and temperature coefficient of growth. J Bacteriol 1972; 112:1040-2. [PMID: 4565524 PMCID: PMC251528 DOI: 10.1128/jb.112.3.1040-1042.1972] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A thermophilic bacillus with minimal, optimal, and maximal growth temperatures of 40, 64.5, and 72 C, respectively, was isolated from soil. Biochemical and morphological studies place the isolate in group 1 of the classification of Walker and Wolf. After adaption to nitrate broth, the temperature coefficient for growth was found to be 20,400 cal/mol. When the temperature coefficient for growth of the isolate, psychrophilic bacteria, mesophilic bacteria, and a strain of Bacillus stearothermophilus are compared, there is no correlation with optimal temperature. The form of the Arrhenius equation, as used by some workers, is commented on.
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Cavari BZ, Arkin-Shlank H, Grossowicz N. Regulation of aspartokinase activity in a thermophilic bacterium. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 261:161-7. [PMID: 5012462 DOI: 10.1016/0304-4165(72)90325-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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40
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Cazzulo JJ, Sundaram TK, Dilks SN, Kornberg HL. Synthesis of pyruvate carboxylase from its apoenzyme and (+)-biotin in Bacillus stearothermophilus. Purification and properties of the apoenzyme and the holoenzyme synthetase. Biochem J 1971; 122:653-61. [PMID: 5129257 PMCID: PMC1176833 DOI: 10.1042/bj1220653] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
1. Methods are described for the assay and purification of pyruvate apocarboxylase and pyruvate holocarboxylase synthetase from biotin-deficient Bacillus stearothermophilus. 2. Pyruvate apocarboxylase was obtained 200-fold purified and in a nearly homogeneous state; it closely resembled the holoenzyme of the thermophile in fractionation properties, electrophoretic mobility and molecular weight (estimated to be 350000 by gel filtration). 3. Pyruvate holocarboxylase synthetase, purified more than 50-fold, was estimated to have a molecular weight of approx. 40000. 4. The conversion of the purified apoenzyme into the holoenzyme required the presence of the synthetase, ATP (K(m)3.3x10(-7)m), (+)-biotin (K(m)7.5x10(-8)m) and Mg(2+); it differed from the conversions effected by systems forming other carboxylases in mesophilic organisms in also requiring the presence of acetyl-CoA.
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Cazzulo JJ, Sundaram TK, Kornberg HL. Properties and regulation of pyruvate carboxylase from Bacillus stearothermophilus. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON. SERIES B, BIOLOGICAL SCIENCES 1970; 176:1-19. [PMID: 4394197 DOI: 10.1098/rspb.1970.0030] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pyruvate carboxylase has been purified 400-fold from the thermophile,
Bacillus stearothermophilus;
it resembles pyruvate carboxylases purified from mesophilic organisms in its general kinetic and regulatory properties. The enzyme is virtually inactive in the absence of acetylcoenzyme A ; this activating effect is antagonized by L-aspartate. Kinetic studies show that these two compounds act as allosteric effectors. ADP inhibits the enzyme activity competitively with ATP. Although the thermophile enzyme is appreciably more thermostable than similar mesophile enzymes, it is quite labile at the temperature at which the organism grows optimally, but can be stabilized by the two allosteric effectors and by some of the reactants.
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42
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Cazzulo JJ, Sundaram TK, Kornberg HL. Mechanism of pyruvate carboxylase formation from the apo-enzyme and biotin in a thermophilic bacillus. Nature 1970; 227:1103-5. [PMID: 5451101 DOI: 10.1038/2271103a0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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43
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Abstract
Protein breakdown of 5 to 7% per hr was found in nitrogen-starved cells of an unclassified prototrophic thermophilic bacillus; a similar protein-breakdown rate (6.5% per hr) was found in resting cells of Escherichia coli. In the thermophile, the rate of protein breakdown was markedly influenced by the temperature; it was maximal between 45 and 55 C, and it decreased considerably at 35 and 75 C, temperatures which are only slightly below or above the minimal and maximal growth temperatures. Growing cultures of the thermophile showed little, if any, protein breakdown, a finding similar to that of others with E. coli.
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