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Furukawa N, Miyanaga A, Nakajima M, Taguchi H. Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria. Biochemistry 2018; 57:5388-5406. [PMID: 30149697 DOI: 10.1021/acs.biochem.8b00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
d-Lactate dehydrogenases (d-LDHs) from Fusobacterium nucleatum (FnLDH) and Escherichia coli (EcLDH) exhibit positive cooperativity in substrate binding, and the Pseudomonas aeruginosa enzyme (PaLDH) shows negatively cooperative substrate binding. The apo and ternary complex structures of FnLDH and PaLDH have been determined together with the apo-EcLDH structure. The three enzymes consistently form homotetrameric structures with three symmetric axes, the P-, Q-, and R-axes, unlike Lactobacillus d-LDHs, P-axis-related dimeric enzymes, although apo-FnLDH and EcLDH form asymmetric and distorted quaternary structures. The tetrameric structure allows apo-FnLDH and EcLDH to form wide intersubunit contact surfaces between the opened catalytic domains of the two Q-axis-related subunits in coordination with their asymmetric and distorted quaternary structures. These contact surfaces comprise intersubunit hydrogen bonds and hydrophobic interactions and likely prevent the domain closure motion during initial substrate binding. In contrast, apo-PaLDH possesses a highly symmetrical quaternary structure and partially closed catalytic domains that are favorable for initial substrate binding and forms virtually no intersubunit contact surface between the catalytic domains, which present their negatively charged surfaces to each other at the subunit interface. Complex FnLDH and PaLDH possess highly symmetrical quaternary structures with closed forms of the catalytic domains, which are separate from each other at the subunit interface. Structure-based mutations successfully converted the three enzymes to their dimeric forms, which exhibited no significant cooperativity in substrate binding. These observations indicate that the three enzymes undergo typical sequential allosteric transitions to exhibit their distinctive allosteric functions through the tetrameric structures.
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Affiliation(s)
- Nayuta Furukawa
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan.,Department of Applied Life Sciences , Niigata University of Pharmacy and Applied Life Sciences , 265-1 Higashijima , Akiha-ku, Niigata 956-8603 , Japan
| | - Akimasa Miyanaga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
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2
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The ternary complex structure of d-mandelate dehydrogenase with NADH and anilino(oxo)acetate. Biochem Biophys Res Commun 2017; 486:665-670. [PMID: 28327357 DOI: 10.1016/j.bbrc.2017.03.088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/17/2017] [Indexed: 01/08/2023]
Abstract
Enterococcus faecium NAD-dependent d-mandelate dehydrogenase (d-ManDH) belongs to a ketopantoate reductase (KPR)-related d-2-hydroxyacid dehydrogenase family, and exhibits broad substrate specificity toward bulky hydrophobic 2-ketoacids, preferring C3-branched substrates. The ternary complex structure of d-ManDH with NADH and anilino(oxo)acetate (AOA) revealed that the substrate binding induces a shear motion of the N-terminal domain along the C-terminal domain, following the hinge motion induced by the NADH binding, and allows the bound NADH molecule to form favorable interactions with a 2-ketoacid substrate. d-ManDH possesses a sufficiently wide pocket that accommodates the C3 branched side chains of substrates like KPR, but unlike the pocket of KPR, the pocket of d-ManDH comprises an entirely hydrophobic surface and an expanded space, in which the AOA benzene is accommodated. The expanded space mostly comprises a mobile loop structure, which likely modulates the shape and size of the space depending on the substrate.
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3
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Hellwig M, Börner M, Beer F, van Pée KH, Henle T. Transformation of Free and Dipeptide-Bound Glycated Amino Acids by Two Strains ofSaccharomyces cerevisiae. Chembiochem 2016; 18:266-275. [DOI: 10.1002/cbic.201600486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Michael Hellwig
- Chair of Food Chemistry; Technische Universität Dresden; Bergstrasse 66 01062 Dresden Germany
| | - Marie Börner
- Chair of Food Chemistry; Technische Universität Dresden; Bergstrasse 66 01062 Dresden Germany
| | - Falco Beer
- Chair of Food Chemistry; Technische Universität Dresden; Bergstrasse 66 01062 Dresden Germany
| | - Karl-Heinz van Pée
- Chair of Biochemistry; Technische Universität Dresden; Bergstrasse 66 01062 Dresden Germany
| | - Thomas Henle
- Chair of Food Chemistry; Technische Universität Dresden; Bergstrasse 66 01062 Dresden Germany
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Sakko M, Tjäderhane L, Sorsa T, Hietala P, Rautemaa R. Antimicrobial 2-hydroxyisocaproic acid and chlorhexidine resist inactivation by dentine. Int Endod J 2015; 49:352-60. [DOI: 10.1111/iej.12465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/30/2015] [Indexed: 11/28/2022]
Affiliation(s)
- M. Sakko
- Institute of Dentistry; University of Oulu; Oulu Finland
- Department of Oral and Maxillofacial Diseases; Helsinki University and Helsinki University Hospital; Helsinki Finland
| | - L. Tjäderhane
- Institute of Dentistry; University of Oulu; Oulu Finland
- Department of Oral and Maxillofacial Diseases; Helsinki University and Helsinki University Hospital; Helsinki Finland
- Medical Research Center Oulu; Oulu University Hospital and University of Oulu; Oulu Finland
| | - T. Sorsa
- Department of Oral and Maxillofacial Diseases; Helsinki University and Helsinki University Hospital; Helsinki Finland
- Division of Periodontology; Department of Dental Medicine; Karolinska Institutet; Huddinge Sweden
| | | | - R. Rautemaa
- Manchester Academic Health Science Centre; Institute of Inflammation and Repair; University Hospital of South Manchester; University of Manchester; Manchester UK
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Furukawa N, Miyanaga A, Togawa M, Nakajima M, Taguchi H. Diverse allosteric and catalytic functions of tetrameric d-lactate dehydrogenases from three Gram-negative bacteria. AMB Express 2014; 4:76. [PMID: 25401076 PMCID: PMC4230899 DOI: 10.1186/s13568-014-0076-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
Abstract
NAD-dependent d-lactate dehydrogenases (d-LDHs) reduce pyruvate into d-lactate with oxidation of NADH into NAD+. Although non-allosteric d-LDHs from Lactobacilli have been extensively studied, the catalytic properties of allosteric d-LDHs from Gram-negative bacteria except for Escherichia coli remain unknown. We characterized the catalytic properties of d-LDHs from three Gram-negative bacteria, Fusobacterium nucleatum (FNLDH), Pseudomonas aeruginosa (PALDH), and E. coli (ECLDH) to gain an insight into allosteric mechanism of d-LDHs. While PALDH and ECLDH exhibited narrow substrate specificities toward pyruvate like usual d-LDHs, FNLDH exhibited a broad substrate specificity toward hydrophobic 2-ketoacids such as 2-ketobutyrate and 2-ketovalerate, the former of which gave a 2-fold higher kcat/S0.5 value than pyruvate. Whereas the three enzymes consistently showed hyperbolic shaped pyruvate saturation curves below pH 6.5, FNLDH and ECLDH, and PALDH showed marked positive and negative cooperativity, respectively, in the pyruvate saturation curves above pH 7.5. Oxamate inhibited the catalytic reactions of FNLDH competitively with pyruvate, and the PALDH reaction in a mixed manner at pH 7.0, but markedly enhanced the reactions of the two enzymes at low concentration through canceling of the apparent homotropic cooperativity at pH 8.0, although it constantly inhibited the ECLDH reaction. Fructose 1,6-bisphosphate and certain divalent metal ions such as Mg2+ also markedly enhanced the reactions of FNLDH and PALDH, but none of them enhanced the reaction of ECLDH. Thus, our study demonstrates that bacterial d-LDHs have highly divergent allosteric and catalytic properties.
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A New Family ofD-2-Hydroxyacid Dehydrogenases That ComprisesD-Mandelate Dehydrogenases and 2-Ketopantoate Reductases. Biosci Biotechnol Biochem 2014; 72:1087-94. [DOI: 10.1271/bbb.70827] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Miyanaga A, Fujisawa S, Furukawa N, Arai K, Nakajima M, Taguchi H. The crystal structure of d-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase. Biochem Biophys Res Commun 2013; 439:109-14. [DOI: 10.1016/j.bbrc.2013.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 11/26/2022]
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Wang X, Zheng Z, Dou P, Qin J, Wang X, Ma C, Tang H, Xu P. Cloning, expression, purification, and activity assay of proteins related to D-lactic acid formation in Lactobacillus rhamnosus. Appl Microbiol Biotechnol 2010; 87:2117-23. [DOI: 10.1007/s00253-010-2704-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 05/26/2010] [Accepted: 05/29/2010] [Indexed: 05/26/2023]
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Biocatalytic racemization of α-hydroxycarboxylic acids using a stereo-complementary pair of α-hydroxycarboxylic acid dehydrogenases. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.06.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Ishikura Y, Tsuzuki S, Takahashi O, Tokuda C, Nakanishi R, Shinoda T, Taguchi H. Recognition site for the side chain of 2-ketoacid substrate in d-lactate dehydrogenase. J Biochem 2009; 138:741-9. [PMID: 16428303 DOI: 10.1093/jb/mvi170] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Replacement of Tyr52 with Val or Ala in Lactobacillus pentosus d-lactate dehydrogenase induced high activity and preference for large aliphatic 2-ketoacids and phenylpyruvate. On the other hand, replacements with Arg, Thr or Asp severely reduced the enzyme activity, and the Tyr52Arg enzyme, the only one that exhibited significant enzyme activity, showed a similar substrate preference to the Tyr52Val and Tyr52Ala enzymes. Replacement of Phe299 with Gly or Ser greatly reduced the enzyme activity with less marked change in the substrate preference. Except for the Phe299Ser enzyme, these mutant enzymes with low catalytic activity consistently stimulated NADH oxidation in the absence of 2-ketoacid substrates. However, the double mutant enzymes, Tyr52Arg/Phe299Gly and Tyr52Thr/Phe299Ser, did not exhibit synergically decreased enzyme activity or the substrate-independent NADH oxidation, but rather increased activities toward certain 2-ketoacid substrates. These results indicate that the coordinative combination of amino acid residues at two positions is pivotal in both the functional recognition of the 2-ketoacid side chain and the protection of the bound NADH molecule from the solvent. Multiplicity in such combinations appears to provide d-LDH-related 2-hydroxyacid dehydrogenases with a great variety of catalytic and physiological functions.
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Affiliation(s)
- Yoshirou Ishikura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
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11
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The D-2-hydroxyacid dehydrogenase incorrectly annotated PanE is the sole reduction system for branched-chain 2-keto acids in Lactococcus lactis. J Bacteriol 2008; 191:873-81. [PMID: 19047348 DOI: 10.1128/jb.01114-08] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydroxyacid dehydrogenases of lactic acid bacteria, which catalyze the stereospecific reduction of branched-chain 2-keto acids to 2-hydroxyacids, are of interest in a variety of fields, including cheese flavor formation via amino acid catabolism. In this study, we used both targeted and random mutagenesis to identify the genes responsible for the reduction of 2-keto acids derived from amino acids in Lactococcus lactis. The gene panE, whose inactivation suppressed hydroxyisocaproate dehydrogenase activity, was cloned and overexpressed in Escherichia coli, and the recombinant His-tagged fusion protein was purified and characterized. The gene annotated panE was the sole gene responsible for the reduction of the 2-keto acids derived from leucine, isoleucine, and valine, while ldh, encoding L-lactate dehydrogenase, was responsible for the reduction of the 2-keto acids derived from phenylalanine and methionine. The kinetic parameters of the His-tagged PanE showed the highest catalytic efficiencies with 2-ketoisocaproate, 2-ketomethylvalerate, 2-ketoisovalerate, and benzoylformate (V(max)/K(m) ratios of 6,640, 4,180, 3,300, and 2,050 U/mg/mM, respectively), with NADH as the exclusive coenzyme. For the reverse reaction, the enzyme accepted d-2-hydroxyacids but not l-2-hydroxyacids. Although PanE showed the highest degrees of identity to putative NADP-dependent 2-ketopantoate reductases (KPRs), it did not exhibit KPR activity. Sequence homology analysis revealed that, together with the d-mandelate dehydrogenase of Enterococcus faecium and probably other putative KPRs, PanE belongs to a new family of D-2-hydroxyacid dehydrogenases which is unrelated to the well-described D-2-hydroxyisocaproate dehydrogenase family. Its probable physiological role is to regenerate the NAD(+) necessary to catabolize branched-chain amino acids, leading to the production of ATP and aroma compounds.
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Abstract
Lactic acid bacteria (LAB) constitute a diverse group of Gram positive obligately fermentative microorganisms which include both beneficial and pathogenic strains. LAB generally have complex nutritional requirements and therefore they are usually associated with nutrient-rich environments such as animal bodies, plants and foodstuffs. Amino acids represent an important resource for LAB and their utilization serves a number of physiological roles such as intracellular pH control, generation of metabolic energy or redox power, and resistance to stress. As a consequence, the regulation of amino acid catabolism involves a wide set of both general and specific regulators and shows significant differences among LAB. Moreover, due to their fermentative metabolism, LAB amino acid catabolic pathways in some cases differ significantly from those described in best studied prokaryotic model organisms such as Escherichia coli or Bacillus subtilis. Thus, LAB amino acid catabolism constitutes an interesting case for the study of metabolic pathways. Furthermore, LAB are involved in the production of a great variety of fermented products so that the products of amino acid catabolism are also relevant for the safety and the quality of fermented products.
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Affiliation(s)
- María Fernández
- Instituto de Productos Lácteos de Asturias CSIC, Crta de Infiesto s/n, Villaviciosa, Asturias, Spain
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13
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Liu M, Nauta A, Francke C, Siezen RJ. Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. Appl Environ Microbiol 2008; 74:4590-600. [PMID: 18539796 PMCID: PMC2519355 DOI: 10.1128/aem.00150-08] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mengjin Liu
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
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14
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Analysis of ldh genes in Lactobacillus casei BL23: role on lactic acid production. J Ind Microbiol Biotechnol 2008; 35:579-86. [PMID: 18231816 DOI: 10.1007/s10295-008-0319-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 01/13/2008] [Indexed: 10/22/2022]
Abstract
Lactobacillus casei is a lactic acid bacterium that produces L-lactate as the main product of sugar fermentation via L-lactate dehydrogenase (Ldh1) activity. In addition, small amounts of the D-lactate isomer are produced by the activity of a D-hydroxycaproate dehydrogenase (HicD). Ldh1 is the main L-lactate producing enzyme, but mutation of its gene does not eliminate L-lactate synthesis. A survey of the L. casei BL23 draft genome sequence revealed the presence of three additional genes encoding Ldh paralogs. In order to study the contribution of these genes to the global lactate production in this organism, individual, as well as double mutants (ldh1 ldh2, ldh1 ldh3, ldh1 ldh4 and ldh1 hicD) were constructed and lactic acid production was assessed in culture supernatants. ldh2, ldh3 and ldh4 genes play a minor role in lactate production, as their single mutation or a mutation in combination with an ldh1 deletion had a low impact on L-lactate synthesis. A Deltaldh1 mutant displayed an increased production of D-lactate, which was probably synthesized via the activity of HicD, as it was abolished in a Deltaldh1 hicD double mutant. Contrarily to HicD, no Ldh1, Ldh2, Ldh3 or Ldh4 activities could be detected by zymogram assays. In addition, these assays revealed the presence of extra bands exhibiting D-/L-lactate dehydrogenase activity, which could not be attributed to any of the described genes. These results suggest that L. casei BL23 possesses a complex enzymatic system able to reduce pyruvic to lactic acid.
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Rintala E, Pitkänen JP, Vehkomäki ML, Penttilä M, Ruohonen L. The ORF YNL274c (GOR1) codes for glyoxylate reductase in Saccharomyces cerevisiae. Yeast 2007; 24:129-36. [PMID: 17173333 DOI: 10.1002/yea.1434] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme glyoxylate reductase reversibly reduces glyoxylate to glycolate, or alternatively hydroxypyruvate to D-glycerate, using either NADPH or NADH as a co-factor. The enzyme has multiple metabolic roles in different organisms. In this paper we show that GOR1 (ORF YNL274c) encodes a glyoxylate reductase and not a hydroxyisocaproate dehydrogenase in Saccharomyces cerevisiae, even though it also has minor activity on alpha-ketoisocaproate. In addition, we show that deletion of the glyoxylate reductase-encoding gene leads to higher biomass concentration after diauxic shift.
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Affiliation(s)
- Eija Rintala
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland.
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16
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Booth MPS, Conners R, Rumsby G, Brady RL. Structural basis of substrate specificity in human glyoxylate reductase/hydroxypyruvate reductase. J Mol Biol 2006; 360:178-89. [PMID: 16756993 DOI: 10.1016/j.jmb.2006.05.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 05/04/2006] [Accepted: 05/08/2006] [Indexed: 11/18/2022]
Abstract
Human glyoxylate reductase/hydroxypyruvate reductase (GRHPR) is a D-2-hydroxy-acid dehydrogenase that plays a critical role in the removal of the metabolic by-product glyoxylate from within the liver. Deficiency of this enzyme is the underlying cause of primary hyperoxaluria type 2 (PH2) and leads to increased urinary oxalate levels, formation of kidney stones and renal failure. Here we describe the crystal structure of human GRHPR at 2.2 A resolution. There are four copies of GRHPR in the crystallographic asymmetric unit: in each homodimer, one subunit forms a ternary (enzyme+NADPH+reduced substrate) complex, and the other a binary (enzyme+NADPH) form. The spatial arrangement of the two enzyme domains is the same in binary and ternary forms. This first crystal structure of a true ternary complex of an enzyme from this family demonstrates the relationship of substrate and catalytic residues within the active site, confirming earlier proposals of the mode of substrate binding, stereospecificity and likely catalytic mechanism for these enzymes. GRHPR has an unusual substrate specificity, preferring glyoxylate and hydroxypyruvate, but not pyruvate. A tryptophan residue (Trp141) from the neighbouring subunit of the dimer is projected into the active site region and appears to contribute to the selectivity for hydroxypyruvate. This first crystal structure of a human GRHPR enzyme also explains the deleterious effects of naturally occurring missense mutations of this enzyme that lead to PH2.
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Affiliation(s)
- Michael P S Booth
- Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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17
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Viana R, Yebra MJ, Galán JL, Monedero V, Pérez-Martínez G. Pleiotropic effects of lactate dehydrogenase inactivation in Lactobacillus casei. Res Microbiol 2005; 156:641-9. [PMID: 15882939 DOI: 10.1016/j.resmic.2005.02.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 01/21/2005] [Accepted: 02/01/2005] [Indexed: 10/25/2022]
Abstract
In lactic acid bacteria, conversion of pyruvic to lactic acid through the activity of lactate dehydrogenase (Ldh) constitutes the final step of the homofermentative pathway. Lactobacillus casei has two characterized genes encoding Ldh activities. The ldhL gene codes for an L-Ldh, which specifically catalyzes the formation of L-lactate, whereas the hicD gene codes for a D-hydroxyisocaproate dehydrogenase (HicDH), which catalyzes the conversion of pyruvate into D-lactate. In L. casei cells fermenting glucose, a mixture of L-/D-lactate with a 97:3% ratio was formed. Inactivation of hicD led to undetectable D-lactate levels after glucose fermentation, while L-lactate levels remained constant. Inactivation of ldhL did not abolish the production of L-lactate, but the lactate final concentration decreased about 25% compared to the wild type, suggesting the presence of at least a second L-Ldh. Moreover, part of the pyruvate flux was rerouted and half of the lactate produced was in the D-isomer form. ldhL inactivation in L. casei showed additional interesting effects. First, the glycolytic flux from pyruvate to lactate was redirected and other fermentation products, including acetate, acetoin, pyruvate, ethanol, diacetyl, mannitol and CO(2), were produced. Second, a lack of carbon catabolite repression of lactose metabolism and N-acetyl-glucosaminidase activity was observed. This second effect could be partly avoided by growing the cells under aeration, since NADH oxidases could account for NAD+ regeneration.
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Affiliation(s)
- Rosa Viana
- Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos, IATA-CSIC, P.O. Box 73, 46100 Burjassot, Valencia, Spain
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18
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Chatterjee S, Schoepe J, Lohmer S, Schomburg D. High level expression and single-step purification of hexahistidine-tagged L-2-hydroxyisocaproate dehydrogenase making use of a versatile expression vector set. Protein Expr Purif 2005; 39:137-43. [PMID: 15642463 DOI: 10.1016/j.pep.2004.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 07/28/2004] [Indexed: 11/21/2022]
Abstract
Affinity tags as fusions to the N- or C-terminal part of proteins are valuable tools to facilitate the production and purification of proteins. In many cases, there may be the necessity to remove the tag after protein preparation to regain activity. Removal of the tag is accomplished by insertion of a unique amino acid sequence that is recognized and cleaved by a site specific protease. Here, we report the construction of an expression vector set that combines N- or C-terminal fusion to either a hexahistidine tag or Streptag with the possibility of tag removal by factor Xa or recombinant tobacco etch virus protease (rTEV), respectively. The vector set offers the option to produce different variants of the protein of interest by cloning the corresponding gene into four different Escherichia coli expression vectors. Either immobilized metal affinity chromatography or streptactin affinity chromatography can be used for the one-step purification. Furthermore, we show the successful application of the expression vector for C-terminal hexahistidine tagging. The expression and purification of His-tagged L-2-hydroxyisocaproate dehydrogenase yields fully active enzyme. The tag removal is here accomplished by a derivative of rTEV.
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Affiliation(s)
- Shivani Chatterjee
- Institut für Biochemie, Universität zu Köln, Zülpicher Strasse 47, 50674 Cologne, Germany
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Shinoda T, Arai K, Shigematsu-Iida M, Ishikura Y, Tanaka S, Yamada T, Kimber MS, Pai EF, Fushinobu S, Taguchi H. Distinct conformation-mediated functions of an active site loop in the catalytic reactions of NAD-dependent D-lactate dehydrogenase and formate dehydrogenase. J Biol Chem 2005; 280:17068-75. [PMID: 15734738 DOI: 10.1074/jbc.m500970200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional structures of NAD-dependent D-lactate dehydrogenase (D-LDH) and formate dehydrogenase (FDH), which resemble each other, imply that the two enzymes commonly employ certain main chain atoms, which are located on corresponding loop structures in the active sites of the two enzymes, for their respective catalytic functions. These active site loops adopt different conformations in the two enzymes, a difference likely attributable to hydrogen bonds with Asn97 and Glu141, which are also located at equivalent positions in D-LDH and FDH, respectively. X-ray crystallography at 2.4-A resolution revealed that replacement of Asn97 with Asp did not markedly change the overall protein structure but markedly perturbed the conformation of the active site loop in Lactobacillus pentosus D-LDH. The Asn97-->Asp mutant D-LDH exhibited virtually the same k(cat), but about 70-fold higher K(M) value for pyruvate than the wild-type enzyme. For Paracoccus sp. 12-A FDH, in contrast, replacement of Glu141 with Gln and Asn induced only 5.5- and 4.3-fold increases in the K(M) value, but 110 and 590-fold decreases in the k(cat) values for formate, respectively. Furthermore, these mutant FDHs, particularly the Glu141-->Asn enzyme, exhibited markedly enhanced catalytic activity for glyoxylate reduction, indicating that FDH is converted to a 2-hydroxy-acid dehydrogenase on the replacement of Glu141. These results indicate that the active site loops play different roles in the catalytic reactions of D-LDH and FDH, stabilization of substrate binding and promotion of hydrogen transfer, respectively, and that Asn97 and Glu141, which stabilize suitable loop conformations, are essential elements for proper loop functioning.
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Affiliation(s)
- Takeshi Shinoda
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Broadbent JR, Gummalla S, Hughes JE, Johnson ME, Rankin SA, Drake MA. Overexpression of Lactobacillus casei D-hydroxyisocaproic acid dehydrogenase in cheddar cheese. Appl Environ Microbiol 2004; 70:4814-20. [PMID: 15294819 PMCID: PMC492331 DOI: 10.1128/aem.70.8.4814-4820.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2004] [Accepted: 05/05/2004] [Indexed: 11/20/2022] Open
Abstract
Metabolism of aromatic amino acids by lactic acid bacteria is an important source of off-flavor compounds in Cheddar cheese. Previous work has shown that alpha-keto acids produced from Trp, Tyr, and Phe by aminotransferase enzymes are chemically labile and may degrade spontaneously into a variety of off-flavor compounds. However, dairy lactobacilli can convert unstable alpha-keto acids to more-stable alpha-hydroxy acids via the action of alpha-keto acid dehydrogenases such as d-hydroxyisocaproic acid dehydrogenase. To further characterize the role of this enzyme in cheese flavor, the Lactobacillus casei d-hydroxyisocaproic acid dehydrogenase gene was cloned into the high-copy-number vector pTRKH2 and transformed into L. casei ATCC 334. Enzyme assays confirmed that alpha-keto acid dehydrogenase activity was significantly higher in pTRKH2:dhic transformants than in wild-type cells. Reduced-fat Cheddar cheeses were made with Lactococcus lactis starter only, starter plus L. casei ATCC 334, and starter plus L. casei ATCC 334 transformed with pTRKH2:dhic. After 3 months of aging, the cheese chemistry and flavor attributes were evaluated instrumentally by gas chromatography-mass spectrometry and by descriptive sensory analysis. The culture system used significantly affected the concentrations of various ketones, aldehydes, alcohols, and esters and one sulfur compound in cheese. Results further indicated that enhanced expression of d-hydroxyisocaproic acid dehydrogenase suppressed spontaneous degradation of alpha-keto acids, but sensory work indicated that this effect retarded cheese flavor development.
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Affiliation(s)
- Jeffery R Broadbent
- Western Dairy Center, Department of Nutrition and Food Sciences, Utah State University, Logan, UT 84322-8700, USA.
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Tokuda C, Ishikura Y, Shigematsu M, Mutoh H, Tsuzuki S, Nakahira Y, Tamura Y, Shinoda T, Arai K, Takahashi O, Taguchi H. Conversion of Lactobacillus pentosus D-lactate dehydrogenase to a D-hydroxyisocaproate dehydrogenase through a single amino acid replacement. J Bacteriol 2003; 185:5023-6. [PMID: 12897026 PMCID: PMC166478 DOI: 10.1128/jb.185.16.5023-5026.2003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The single amino acid replacement of Tyr52 with Leu drastically increased the activity of Lactobacillus pentosus NAD-dependent D-lactate dehydrogenase toward larger aliphatic or aromatic 2-ketoacid substrates by 3 or 4 orders of magnitude and decreased the activity toward pyruvate by about 30-fold, converting the enzyme into a highly active D-2-hydroxyisocaproate dehydrogenase.
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Affiliation(s)
- Chizuka Tokuda
- Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, Noda, Chiba 278-8510, Japan
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22
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Tamura Y, Ohkubo A, Iwai S, Wada Y, Shinoda T, Arai K, Mineki S, Iida M, Taguchi H. Two forms of NAD-dependent D-mandelate dehydrogenase in Enterococcus faecalis IAM 10071. Appl Environ Microbiol 2002; 68:947-51. [PMID: 11823242 PMCID: PMC126676 DOI: 10.1128/aem.68.2.947-951.2002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two forms of NAD-dependent D-mandelate dehydrogenase (D-ManDHs) were purified from Enterococcus faecalis IAM 10071. While these two enzymes consistently exhibited high activity toward large 2-ketoacid substrates that were branched at the C3 or C4 position, they gave distinctly different K(m) and V(max) values for these substrates and had distinct molecular weights by gel electrophoresis and gel filtration.
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Affiliation(s)
- Yusuke Tamura
- Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, Noda, Chiba 278-8510, Japan
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Dickert S, Pierik AJ, Linder D, Buckel W. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:3874-84. [PMID: 10849007 DOI: 10.1046/j.1432-1327.2000.01427.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phenyllactate dehydratase from Clostridium sporogenes grown anaerobically on L-phenylalanine catalyses the reversible syn-dehydration of (R)-phenyllactate to (E)-cinnamate. Purification yielded a heterotrimeric enzyme complex (130 +/- 15 kDa) composed of FldA (46 kDa), FldB (43 kDa) and FldC (40 kDa). By re-chromatography on Q-Sepharose, the major part of FldA could be separated and identified as oxygen insensitive cinnamoyl-CoA:phenyllactate CoA-transferase, whereas the transferase depleted trimeric complex retained oxygen sensitive phenyllactate dehydratase activity and contained about one [4Fe-4S] cluster. The dehydratase activity required 10 microM FAD, 0.4 mM ATP, 2.5 mM MgCl2, 0.1 mM NADH, 5 microM cinnamoyl-CoA and small amounts of cell-free extract (10 microg protein per mL) similar to that known for 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. The N-terminus of the homogenous FldA (39 amino acids) is homologous to that of CaiB (39% sequence identity) involved in carnitine metabolism in Escherichia coli. Both enzymes are members of an emerging group of CoA-transferases which exhibit high substrate specificity but apparently do not form enzyme CoA-ester intermediates. It is concluded that dehydration of (R)-phenyllactate to (E)-cinnamate proceeds in two steps, a CoA-transfer from cinnamoyl-CoA to phenyllactate, catalysed by FldA, followed by the dehydration of phenyllactyl-CoA, catalysed by FldB and FldC, whereby the noncovalently bound prosthetic group cinnamoyl-CoA is regenerated. This demonstrates the necessity of a 2-hydroxyacyl-CoA intermediate in the dehydration of 2-hydroxyacids. The transient CoA-ester formation during the dehydration of phenyllactate resembles that during citrate cleavage catalysed by bacterial citrate lyase, which contain a derivative of acetyl-CoA covalently bound to an acyl-carrier-protein (ACP).
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Affiliation(s)
- S Dickert
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
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25
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Varmanen P, Savijoki K, Avall S, Palva A, Tynkkynen S. X-prolyl dipeptidyl aminopeptidase gene (pepX) is part of the glnRA operon in Lactobacillus rhamnosus. J Bacteriol 2000; 182:146-54. [PMID: 10613874 PMCID: PMC94251 DOI: 10.1128/jb.182.1.146-154.2000] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A peptidase gene expressing X-prolyl dipeptidyl aminopeptidase (PepX) activity was cloned from Lactobacillus rhamnosus 1/6 by using the chromogenic substrate L-glycyl-L-prolyl-beta-naphthylamide for screening of a genomic library in Escherichia coli. The nucleotide sequence of a 3.5-kb HindIII fragment expressing the peptidase activity revealed one complete open reading frame (ORF) of 2,391 nucleotides. The 797-amino-acid protein encoded by this ORF was shown to be 40, 39, and 36% identical with PepXs from Lactobacillus helveticus, Lactobacillus delbrueckii, and Lactococcus lactis, respectively. By Northern analysis with a pepX-specific probe, transcripts of 4.5 and 7.0 kb were detected, indicating that pepX is part of a polycistronic operon in L. rhamnosus. Cloning and sequencing of the upstream region of pepX revealed the presence of two ORFs of 360 and 1,338 bp that were shown to be able to encode proteins with high homology to GlnR and GlnA proteins, respectively. By multiple primer extension analyses, the only functional promoter in the pepX region was located 25 nucleotides upstream of glnR. Northern analysis with glnA- and pepX-specific probes indicated that transcription from glnR promoter results in a 2.0-kb dicistronic glnR-glnA transcript and also in a longer read-through polycistronic transcript of 7.0 kb that was detected with both probes in samples from cells in exponential growth phase. The glnA gene was disrupted by a single-crossover recombinant event using a nonreplicative plasmid carrying an internal part of glnA. In the disruption mutant, glnRA-specific transcription was derepressed 10-fold compared to the wild type, but the 7.0-kb transcript was no longer detectable with either the glnA- or pepX-specific probe, demonstrating that pepX is indeed part of glnRA operon in L. rhamnosus. Reverse transcription-PCR analysis further supported this operon structure. An extended stem-loop structure was identified immediately upstream of pepX in the glnA-pepX intergenic region, a sequence that showed homology to a 23S-5S intergenic spacer and to several other L. rhamnosus-related entries in data banks.
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Affiliation(s)
- P Varmanen
- R&D, Valio Ltd., FIN-00039 Valio, Helsinki, Finland.
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26
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Hayford AE, Petersen A, Vogensen FK, Jakobsen M. Use of conserved randomly amplified polymorphic DNA (RAPD) fragments and RAPD pattern for characterization of Lactobacillus fermentum in Ghanaian fermented maize dough. Appl Environ Microbiol 1999; 65:3213-21. [PMID: 10388723 PMCID: PMC91476 DOI: 10.1128/aem.65.7.3213-3221.1999] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present work describes the use of randomly amplified polymorphic DNA (RAPD) for the characterization of 172 dominant Lactobacillus isolates from present and previous studies of Ghanaian maize fermentation. Heterofermentative lactobacilli dominate the fermentation flora, since approximately 85% of the isolates belong to this group. Cluster analysis of the RAPD profiles obtained showed the presence of two main clusters. Cluster 1 included Lactobacillus fermentum, whereas cluster 2 comprised the remaining Lactobacillus spp. The two distinct clusters emerged at the similarity level of <50%. All isolates in cluster 1 showed similarity in their RAPD profile to the reference strains of L. fermentum included in the study. These isolates, yielding two distinct bands of approximately 695 and 773 bp with the primers used, were divided into four subclusters, indicating that several strains are involved in the fermentation and remain dominant throughout the process. The two distinct RAPD fragments were cloned, sequenced, and used as probes in Southern hybridization experiments. With one exception, Lactobacillus reuteri LMG 13045, the probes hybridized only to fragments of different sizes in EcoRI-digested chromosomal DNA of L. fermentum strains, thus indicating the specificity of the probes and variation within the L. fermentum isolates.
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27
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Maleret C, Lauret R, Ehrlich SD, Morel-Deville F, Zagorec M. Disruption of the sole ldhL gene in Lactobacillus sakei prevents the production of both L- and D-lactate. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 12):3327-3333. [PMID: 9884224 DOI: 10.1099/00221287-144-12-3327] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A 7 kb DNA fragment was cloned from Lactobacillus sakei which contains the IdhL gene encoding the L(+)-lactate dehydrogenase (L-LDH). Analysis of the DNA sequence, Northern experiments and primer extension experiments showed that IdhL is transcribed from a single promoter, leading to a monocistronic 1.15 kb mRNA which yields the L-LDH. A stable mutant was constructed by chromosomal integration of a chloramphenicol cassette into IdhL by a double-crossover event. Both L- and D-lactate were produced by the wild-type strain whereas only residual amounts of both isomers were produced by the mutant. This demonstrates that L. sakei possesses an L-LDH producing L-lactate and a lactate racemase able to transform it to D-lactate, but is devoid of D-LDH activity. Moreover the ability to degrade L-lactate present in the medium that was observed with the mutant strain grown aerobically suggests that an L-lactate oxidase activity is also present in L. sakei.
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Affiliation(s)
- Christine Maleret
- Laboratoire de Recherches sur la Viande and Laboratoire de Génétique Microbienne F-78352 Jouy en Josas cedex, France
| | - R Lauret
- Laboratoire de Recherches sur la Viande and Laboratoire de Génétique Microbienne F-78352 Jouy en Josas cedex, France
| | - S Dusko Ehrlich
- Institut National de la Recherche Agronomique, Domaine de Vilvert, F-78352 Jouy en Josas cedex, France
| | - Françoise Morel-Deville
- Laboratoire de Recherches sur la Viande and Laboratoire de Génétique Microbienne F-78352 Jouy en Josas cedex, France
| | - Monique Zagorec
- Laboratoire de Recherches sur la Viande and Laboratoire de Génétique Microbienne F-78352 Jouy en Josas cedex, France
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Abstract
Lactobacilli play a substantial role in food biotechnology and influence our quality of life by their fermentative and probiotic properties. Despite their obvious importance in fermentation ecology and biotechnology only recent years have brought some insight into the genetics of lactobacilli. These genetic investigations allow the elucidation of traits determinative for competitiveness and ecology and thus product safety and quality. They have concentrated only on a small selection of lactobacilli whereas others are hardly touched or remained recalcitrant to genetic analysis and manipulation. The knowledge gained on the biochemistry, physiology, ecology and especially genetics is a prerequisite for the deliberate application and improved handling of lactobacilli in traditional and novel applications. In this review, the achievements in the genetics of lactobacilli are described including detection systems, genetic elements, host vector systems, gene cloning and expression and risk assessment of genetically engineered lactobacilli.
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Affiliation(s)
- R F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising-Weihenstephan, Germany
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29
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Dickinson JR, Lanterman MM, Danner DJ, Pearson BM, Sanz P, Harrison SJ, Hewlins MJ. A 13C nuclear magnetic resonance investigation of the metabolism of leucine to isoamyl alcohol in Saccharomyces cerevisiae. J Biol Chem 1997; 272:26871-8. [PMID: 9341119 DOI: 10.1074/jbc.272.43.26871] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The metabolism of leucine to isoamyl alcohol in yeast was examined by 13C nuclear magnetic resonance spectroscopy. The product of leucine transamination, alpha-ketoisocaproate had four potential routes to isoamyl alcohol. The first, via branched-chain alpha-keto acid dehydrogenase to isovaleryl-CoA with subsequent conversion to isovalerate by acyl-CoA hydrolase operates in wild-type cells where isovalerate appears to be an end product. This pathway is not required for the synthesis of isoamyl alcohol because abolition of branched-chain alpha-keto acid dehydrogenase activity in an lpd1 disruption mutant did not prevent the formation of isoamyl alcohol. A second possible route was via pyruvate decarboxylase; however, elimination of pyruvate decarboxylase activity in a pdc1 pdc5 pdc6 triple mutant did not decrease the levels of isoamyl alcohol produced. A third route utilizes alpha-ketoisocaproate reductase (a novel activity in Saccharomyces cerevisiae) but with no role in the formation of isoamyl alcohol from alpha-hydroxyisocaproate because cell homogenates could not convert alpha-hydroxyisocaproate to isoamyl alcohol. The final possibility was that a pyruvate decarboxylase-like enzyme encoded by YDL080c appears to be the major route of decarboxylation of alpha-ketoisocaproate to isoamyl alcohol although disruption of this gene reveals that at least one other unidentified decarboxylase can substitute to a minor extent.
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Affiliation(s)
- J R Dickinson
- School of Pure & Applied Biology, University of Wales, Cardiff CF1 3TL, United Kingdom
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30
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Dengler U, Niefind K, Kiess M, Schomburg D. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. J Mol Biol 1997; 267:640-60. [PMID: 9126843 DOI: 10.1006/jmbi.1996.0864] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei is a homodimer with 333 amino acids and a molecular mass of 37 kDa per subunit. The enzyme belongs to the protein family of NAD+-dependent D-2-hydroxycarboxylate dehydrogenases and within this family to the subgroup of D-lactate dehydrogenases (D-LDHs). Compared with other D-LDHs D-HicDH is characterized by a very low specificity regarding size and chemical constitution of the accepted D-2-hydroxycarboxylates. Hexagonal crystals of recombinant D-HicDH in the presence of NAD+ and 2-oxoisocaproate (4-methyl-2-oxopentanoate) were grown with ammonium sulphate as precipitating agent. The structure of these crystals was solved by molecular replacement and refined to a final R-factor of 19.6% for all measured X-ray reflections in the resolution range (infinity to 1.86 A). Both NAD+ and 2-oxoisocaproate were identified in the electron density map; binding of the latter in the active site, however, competes with a sulphate ion, which is also defined by electron density. Additionally the final model contains 182 water molecules and a second sulphate ion. The binding of both an in vitro substrate and the natural cosubstrate in the active site provides substantial insight into the catalytic mechanism and allows us to assess previously published active site models for this enzyme family, in particular the two most controversial points, the role of the conserved Arg234 and substrate binding. Furthermore the overall topology and details of the D-HicDH structure are described, discussed against the background of homologous structures and compared with one closely and one distantly related protein.
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Affiliation(s)
- U Dengler
- Gesellschaft fur Biotechnologische Forschung (GBF), Abteilung Molekulare Strukturforschung, Braunschweig, Germany
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31
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Alvarez JA, Gelpí JL, Johnsen K, Bernard N, Delcour J, Clarke AR, Holbrook JJ, Cortés A. D-2-hydroxy-4-methylvalerate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus. I. Kinetic mechanism and pH dependence of kinetic parameters, coenzyme binding and substrate inhibition. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:203-12. [PMID: 9063465 DOI: 10.1111/j.1432-1033.1997.00203.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The steady-state kinetics of D-2-hydroxy-4-methylvalerate dehydrogenase have been studied at pH 8.0 by initial velocity, product inhibition, and dead-end inhibition techniques. The mechanism is rapid-equilibrium ordered in the NAD+ plus D-2-hydroxy-4-methylvalerate direction, and steady-state ordered in the other direction. In both cases coenzyme is the first substrate added and both the E-NADH-D-2-hydroxy-4-methylvalerate and E-NAD+-2-oxo-4-methylvalerate give rise to abortive complexes which cause excess substrate inhibition. Steady-state measurements show that the rate-limiting step in both directions at pH 8.0 is between formation of the enzyme-coenzyme-substrate ternary complex and the release of the first product of the reaction. Transient kinetics combined with primary kinetic deuterium isotope effects show that in the NADH-->NAD+ direction there is a slow, rate-limiting rearrangement of the E-NADH-oxoacid complex while hydride transfer is very fast. The release of NAD+ at pH 8.0 is 200-times faster than Kcat (NADH-->NAD+) whereas the release of NADH is only 5-times faster than Kcat (NAD+-->NADH). The pH dependence of NADH binding depends upon the presence of two ionizable residues with a pKa of about 5.9. The pH dependence of kinetic parameters is explained by a third ionizable residue with pKa values 7.2 (in the E-NADH complex) and < or = 6.4 (in the E-NAD+ complex) which may be the proton donor and acceptor for the chemical reaction. At pH 6.5 the mechanism changes in the NADH-->NAD+ direction to be partly limited by the chemical step with a measured primary kinetic isotope effect of 5.7 and partly by an only slightly faster dissociation of NAD+. In addition the inhibition by excess oxo-4-methylvalerate is more pronounced. The mechanism implies that removing the positive charges created by the two groups which control coenzyme affinity could both enhance the catalytic rate at pH 6.5 and diminish excess substrate inhibition to provide an enzyme better suited to the bulk synthesis of D-2-hydroxyacids.
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Affiliation(s)
- J A Alvarez
- Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Spain
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Ferain T, Schanck AN, Delcour J. 13C nuclear magnetic resonance analysis of glucose and citrate end products in an ldhL-ldhD double-knockout strain of Lactobacillus plantarum. J Bacteriol 1996; 178:7311-5. [PMID: 8955418 PMCID: PMC178649 DOI: 10.1128/jb.178.24.7311-7315.1996] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have examined the metabolic consequences of knocking out the two ldh genes in Lactobacillus plantarum using 13C nuclear magnetic resonance. Unlike its wild-type isogenic progenitor, which produced lactate as the major metabolite under all conditions tested, ldh null strain TF103 mainly produced acetoin. A variety of secondary end products were also found, including organic acids (acetate, succinate, pyruvate, and lactate), ethanol, 2,3-butanediol, and mannitol.
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Affiliation(s)
- T Ferain
- Laboratoire de Génétique Moléculaire, Unité de Génétique, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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Abstract
Lactic acid bacteria are characterized by a relatively simple sugar fermentation pathway that, by definition, results in the formation of lactic acid. The extensive knowledge of traditional pathways and the accumulating genetic information on these and novel ones, allows for the rerouting of metabolic processes in lactic acid bacteria by physiological approaches, genetic methods, or a combination of these two. This review will discuss past and present examples and future possibilities of metabolic engineering of lactic acid bacteria for the production of important compounds, including lactic and other acids, flavor compounds, and exopolysaccharides.
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Affiliation(s)
- W M de Vos
- Department of Biophysical Chemistry, NIZO, Ede, The Netherlands
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Ferain T, Hobbs JN, Richardson J, Bernard N, Garmyn D, Hols P, Allen NE, Delcour J. Knockout of the two ldh genes has a major impact on peptidoglycan precursor synthesis in Lactobacillus plantarum. J Bacteriol 1996; 178:5431-7. [PMID: 8808932 PMCID: PMC178362 DOI: 10.1128/jb.178.18.5431-5437.1996] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Most bacteria synthesize muramyl-pentapeptide peptidoglycan precursors ending with a D-alanyl residue (e.g., UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala). However, it was recently demonstrated that other types of precursors, notably D-lactate-ending molecules, could be synthesized by several lactic acid bacteria. This particular feature leads to vancomycin resistance. Vancomycin is a glycopeptide antibiotic that blocks cell wall synthesis by the formation of a complex with the extremity of peptidoglycan precursors. Substitution of the terminal D-alanine by D-lactate reduces the affinity of the antibiotic for its target. Lactobacillus plantarum is a lactic acid bacterium naturally resistant to vancomycin. It converts most of the glycolytic pyruvate to L- and D-lactate by using stereospecific enzymes designated L- and D-lactate dehydrogenases, respectively. In the present study, we show that L. plantarum actually synthesizes D-lactate-ending peptidoglycan precursors. We also report the construction of a strain which is deficient for both D- and L-lactate dehydrogenase activities and which produces only trace amounts of D- and L-lactate. As a consequence, the peptidoglycan synthesis pathway is drastically affected. The wild-type precursor is still present, but a new type of D-alanine-ending precursor is also synthesized in large quantities, which results in a highly enhanced sensitivity to vancomycin.
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Affiliation(s)
- T Ferain
- Laboratoire de Génétique Moléculaire, Université Catholique de Louvain, Belgium
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35
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Stoll VS, Kimber MS, Pai EF. Insights into substrate binding by D-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus D-lactate dehydrogenase. Structure 1996; 4:437-47. [PMID: 8740366 DOI: 10.1016/s0969-2126(96)00049-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND D-Lactate dehydrogenases (D-LDHs) and L-lactate dehydrogenases (L-LDHs) catalyze a reaction differing only in the chirality of the product. Both enzymes utilize the same kind of amino acid side chains in substrate binding and catalysis. Models based on D-LDH-related enzymes propose that these side chains assume identical roles in both enzymes with their active sites related by a simple geometrical relationship such as a mirror plane. RESULTS The crystal structure of the homodimeric D-LDH from Lactobacillus pentosus has been determined to 2.6 A resolution by multiple isomorphous replacement methods and the resulting molecular model refined to an R-factor of 19.1%. Topologically, the enzyme is closely related to other D-2-ketoacid dehydrogenase enzymes. Each subunit comprises two domains enclosing a deep cleft containing the active site. Substrate binding and domain closure have been modelled. CONCLUSIONS Comparison of the D-LDH structure with other members of the protein family and with the L-specific enzyme has confirmed that no overall structural relationship exists between the L-LDH and D-LDH enzymes - they belong to distinct protein classes. The small size of the ketoacid substrate and the very restricted number of functionally appropriate side chains will constrain the choice of amino acids and their placement in the active site. Our models imply that although the same kinds of amino acids are involved in substrate binding their exact chemical role might differ in the two dehydrogenases.
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Affiliation(s)
- V S Stoll
- Department of Biochemistry, University of Toronto, Ontario, Canada
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36
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Milewski WM, Boyle-Vavra S, Moreira B, Ebert CC, Daum RS. Overproduction of a 37-kilodalton cytoplasmic protein homologous to NAD+-linked D-lactate dehydrogenase associated with vancomycin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 1996; 40:166-72. [PMID: 8787900 PMCID: PMC163077 DOI: 10.1128/aac.40.1.166] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We previously reported the isolation of a laboratory-derived Staphylococcus aureus mutant, 523k, that has constitutive low-level resistance to vancomycin (MIC = 5 micrograms/ml) and teicoplanin (MIC = 5 micrograms/ml) and elaborates a ca. 39-kDa cytoplasmic protein that was not detected in the parent strain 523 (MIC = 1 micrograms/ml). We have now detected the protein in strain 523 by immunoblotting with antiserum raised against the protein. Consistent with our initial observations, densitometric analysis of the immunoblots revealed an increased production of the protein in 523k compared with that of the susceptible parent 523. The 5' region of the gene encoding the protein of interest was identified by nucleotide sequencing a PCR product amplified from the genome of 523k with degenerate primers designed to encode the amino acid sequence of proteolytic peptides obtained from the protein. The remainder of the gene was identified by library screening, PCR, and nucleotide sequencing. The gene encodes a 36.7-kDa protein with homology to a family of bacterial NAD+-dependent, D-specific 2-hydroxyacid dehydrogenases which includes both D-lactate dehydrogenase and the enterococcal vancomycin resistance protein VanH and is therefore designated ddh. Increased production of the product of ddh, Ddh, was associated with increased D-lactate dehydrogenase activity in 523k, a finding which suggested that Ddh is likely to be the D-lactate dehydrogenase previously identified in S. aureus. The increased D-lactate dehydrogenase activity in strain 523k and the structural similarities among Ddh, D-lactate dehydrogenase, and VanH suggest that overproduction of Ddh might play a role in vancomycin resistance in this strain.
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Affiliation(s)
- W M Milewski
- Department of Pediatrics, University of Chicago, Illinois 60637, USA
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37
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Agraz A, Paulsen J, Börner B, Hustedt H. Renaturation, purification, and characterization of recombinant d-2-hydroxyisocaproate dehydrogenase from Escherichia coli. Enzyme Microb Technol 1995. [DOI: 10.1016/0141-0229(94)00097-b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Garmyn D, Ferain T, Bernard N, Hols P, Delplace B, Delcour J. Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis. J Bacteriol 1995; 177:3427-37. [PMID: 7539419 PMCID: PMC177045 DOI: 10.1128/jb.177.12.3427-3437.1995] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The gene encoding D-lactate dehydrogenase was isolated on a 2.9-kb insert from a library of Pediococcus acidilactici DNA by complementation for growth under anaerobiosis of an Escherichia coli lactate dehydrogenase and pyruvate-formate lyase double mutant. The nucleotide sequence of ldhD encodes a protein of 331 amino acids (predicted molecular mass of 37,210 Da) which shows similarity to the family of D-2-hydroxyacid dehydrogenases. The enzyme encoded by the cloned fragment is equally active on pyruvate and hydroxypyruvate, indicating that the enzyme has both D-lactate and D-glycerate dehydrogenase activities. Three other open reading frames were found in the 2.9-kb insert, one of which (rpsB) is highly similar to bacterial genes coding for ribosomal protein S2. Northern (RNA) blotting analyses indicated the presence of a 2-kb dicistronic transcript of ldhD (a metabolic gene) and rpsB (a putative ribosomal protein gene) together with a 1-kb monocistronic rpsB mRNA. These transcripts are abundant in the early phase of exponential growth but steadily fade away to disappear in the stationary phase. Primer extension analysis identified two distinct promoters driving either cotranscription of ldhD and rpsB or transcription of rpsB alone.
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Affiliation(s)
- D Garmyn
- Laboratoire de Génétique Moléculaire, Université Catholique, Louvain-la-Neuve, Belgium
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39
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Dartois V, Phalip V, Schmitt P, Diviès C. Purification, properties and DNA sequence of the D-lactate dehydrogenase from Leuconostoc mesenteroides subsp. cremoris. Res Microbiol 1995; 146:291-302. [PMID: 7569323 DOI: 10.1016/0923-2508(96)81052-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The complete sequence of the D-lactate dehydrogenase (D-ldh) gene from Leuconostoc mesenteroides subsp. cremoris, cloned in Escherichia coli, were determined. The deduced amino acid sequence showed homologies with all members of the D-specific-2-hydroxyacid dehydrogenase family. Furthermore, the essential residues detected so far as being involved in catalysis were also conserved. Purification of the enzyme revealed physico-chemical properties corresponding to those predicted from the sequence. The active enzyme was a dimer of 40-kDa subunits. The Km values for pyruvate, lactate, NADH and NAD were 0.3, 19, 0.03 and 0.16 mM, indicating that the enzyme reduced pyruvate in vivo. Besides the D-LDH activity, L. mesenteroides subsp. cremoris also displayed HicDH enzymatic activity, catalysing the reduction of pyruvate analogs. The purified D-LDH displayed low HicDH-type activity; therefore, differences in specificity profiles between the crude extract and the purified enzyme suggested the occurrence of a specific HicDH.
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Affiliation(s)
- V Dartois
- ENSBANA, Laboratoire de Microbiologie, Dijon, France
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40
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Henrich B, Binishofer B, Bläsi U. Primary structure and functional analysis of the lysis genes of Lactobacillus gasseri bacteriophage phi adh. J Bacteriol 1995; 177:723-32. [PMID: 7836307 PMCID: PMC176649 DOI: 10.1128/jb.177.3.723-732.1995] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The lysis genes of the Lactobacillus gasseri bacteriophage phi adh were isolated by complementation of a lambda Sam mutation in Escherichia coli. Nucleotide sequencing of a 1,735-bp DNA fragment revealed two adjacent coding regions of 342 bp (hol) and 951 bp (lys) in the same reading frame which appear to belong to a common transcriptional unit. Proteins corresponding to the predicted gene products, holin (12.9 kDa) and lysin (34.7 kDa), were identified by in vitro and in vivo expression of the cloned genes. The phi adh holin is a membrane-bound protein with structural similarity to lysis proteins of other phage, known to be required for the transit of murein hydrolases through the cytoplasmic membrane. The phi adh lysin shows homology with mureinolytic enzymes encoded by the Lactobacillus bulgaricus phage mv4, the Streptococcus pneumoniae phage Cp-1, Cp-7, and Cp-9, and the Lactococcus lactis phage phi LC3. Significant homology with the N termini of known muramidases suggests that phi adh lysin acts by a similar catalytic mechanism. In E. coli, the phi adh lysin seems to be associated with the total membrane fraction, from which it can be extracted with lauryl sarcosinate. Either one of the phi adh lysis proteins provoked lysis of E. coli when expressed along with holins or lysins of phage lambda or Bacillus subtilis phage phi 29. Concomitant expression of the combined holin and lysin functions of phi adh in E. coli, however, did not result in efficient cell lysis.
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Affiliation(s)
- B Henrich
- Abteilung Mikrobiologie, Universität Kaiserslautern, Germany
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41
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Lu Z, Li Y, Zhang Y, Kutish GF, Rock DL, Van Etten JL. Analysis of 45 kb of DNA located at the left end of the chlorella virus PBCV-1 genome. Virology 1995; 206:339-52. [PMID: 7831789 DOI: 10.1016/s0042-6822(95)80049-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Forty-five kilobases of DNA, including the previously sequenced 2.2-kb inverted repeat region, located at the left termini of the 330-kb Chlorella virus PBCV-1 genome were sequenced and analyzed. Eighty-five complete open reading frames (ORFs) larger than 195 nucleotides were identified. Thirty-seven of the 85 ORFs, which are densely packed on both strands of the DNA, were considered major ORFs. Fifteen of the major ORFs have similarity to genes in the databases, including bacterial glycerophosphoryl diester phosphodiesterase, bacteriophage T4 endonuclease V, D-isomer specific 2-hydroxyacid dehydrogenases, and beta-alanine synthetase and bacterial nitrilases. Two major ORFs resemble the virus major capsid protein. Three major ORFs contain three or more ankyrin-like repeat elements and four ORFs encode proline-rich proteins.
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Affiliation(s)
- Z Lu
- Plum Island Animal Disease Center, ARS, USDA, NAA, Greenport, New York 11944-0848
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42
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43
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Bernard N, Johnsen K, Ferain T, Garmyn D, Hols P, Holbrook JJ, Delcour J. NAD(+)-dependent D-2-hydroxyisocaproate dehydrogenase of Lactobacillus delbrueckii subsp. bulgaricus. Gene cloning and enzyme characterization. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 224:439-46. [PMID: 7925358 DOI: 10.1111/j.1432-1033.1994.00439.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A genomic library from Lactobacillus delbrueckii subsp. bulgaricus was used to complement an Escherichia coli mutant strain deficient for both lactate dehydrogenase and pyruvate formate lyase, and thus unable to grow anaerobically. One recombinant clone was found to display a broad specificity NAD(+)-dependent D-2-hydroxyacid dehydrogenase activity. The corresponding gene (named hdhD) was subcloned and sequenced. The deduced amino acid sequence of the encoded enzyme indicates a 333-residue protein closely related to D-2-hydroxyisocaproate (i.e. 2-hydroxy-4-methyl-pentanoate) dehydrogenase (D-HO-HxoDH) of Lactobacillus casei and other NAD(+)-dependent D-lactate dehydrogenases (D-LDH) from several other bacterial species. The hdhD gene was overexpressed under the control of the lambda phage PL promoter and the enzyme was purified with a two-step method. The L. delbrueckii subsp. bulgaricus enzyme, like that of L. casei, was shown to be active on a wide variety of 2-oxoacid substrates except those having a branched beta-carbon.
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Affiliation(s)
- N Bernard
- Unité de Génétique, Université Catholique de Louvain, Belgium
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44
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Yoshida T, Yamaguchi K, Hagishita T, Mitsunaga T, Miyata A, Tanabe T, Toh H, Ohshiro T, Shimao M, Izumi Y. Cloning and expression of the gene for hydroxypyruvate reductase (D-glycerate dehydrogenase from an obligate methylotroph Hyphomicrobium methylovorum GM2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 223:727-32. [PMID: 8055948 DOI: 10.1111/j.1432-1033.1994.tb19046.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The gene encoding hydroxypyruvate reductase, catalyzing the asymmetric reduction of hydroxypyruvate to D-glycerate, and its flanking regions were isolated from a methylotrophic bacterium, Hyphomicrobium methylovorum GM2. Nucleotide sequencing of the recombinant plasmids revealed that the hydroxypyruvate-reductase gene codes for the 322-amino-acid protein with calculated molecular mass 35,726 Da. The sequence was confirmed by sequencing the intact enzyme and peptides obtained by digestion of the enzyme with Achromobacter proteinase I. The amino acid sequence of the enzyme showed similarity to members of the D-isomer-specific 2-hydroxyacid dehydrogenase family. The recombinant plasmid, which was constructed by ligation of the cloned gene and an expression vector pKK223-3, was introduced into Escherichia coli HB101. The recombinant enzyme purified from the transformed E. coli cells was indistinguishable from the enzyme isolated from H. methylovorum GM2 by immunological and enzymological analyses.
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Affiliation(s)
- T Yoshida
- Department of Food and Nutrition, Faculty of Agriculture, Kinki University, Narashi, Japan
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45
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Affiliation(s)
- V O Popov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Moscow
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46
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Cloning, characterization and insertional inactivation of the Lactobacillus helveticus D(?) lactate dehydrogenase gene. Appl Microbiol Biotechnol 1994. [DOI: 10.1007/bf00212254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Bhowmik T, Steele JL. Cloning, characterization and insertional inactivation of the Lactobacillus helveticus D(-) lactate dehydrogenase gene. Appl Microbiol Biotechnol 1994; 41:432-9. [PMID: 7765104 DOI: 10.1007/bf00939032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A plasmid, designated pSUW100, encoding the D(-)lactate dehydrogenase [D(-)-LDH; NAD+ oxidoreductase, EC 1.1.1.28] from Lactobacillus helveticus CNRZ32 was identified from a genomic library by complementation of Escherichia coli FMJ39. The D(-)LDH gene was localized by Tn5 mutagenesis and subcloning to a 1.4-kb region of pSUW100. A 2-kb DraI fragment of pSUW100 encoding D(-)LDH activity was subcloned and its nucleotide sequence determined. Analysis of this sequence identified a putative 1,014-bp D(-)LDH open reading frame that encodes a polypeptide of 337 amino acid residues with a deduced molecular mass of 38 kDa. The distribution of homology to the CNRZ32 D(-)LDH gene in several lactic acid bacteria was determined by Southern hybridization using an internal fragment of the D(-)LDH gene as a probe. Hybridization was detected in leuconostocs and pediococci but not in lactococci or Lactobacillus casei. An integration plasmid was constructed from pSA3 and a 0.60-kb internal fragment of the D(-)LDH gene. This plasmid was used to construct a D(-)LDH-negative derivative of L. helveticus CNRZ 32 by gene disruption; this derivative was determined as producing only L(+)lactic acid. No significant difference in growth or total lactic acid production was observed between CNRZ32 and its D(-)LDH mutant.
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Affiliation(s)
- T Bhowmik
- Department of Food Science, University of Wisconsin-Madison 53706
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48
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Chistoserdova LV, Lidstrom ME. Genetics of the serine cycle in Methylobacterium extorquens AM1: identification of sgaA and mtdA and sequences of sgaA, hprA, and mtdA. J Bacteriol 1994; 176:1957-68. [PMID: 8144463 PMCID: PMC205300 DOI: 10.1128/jb.176.7.1957-1968.1994] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In a previous paper, we reported identification of the 5' part of hprA of Methylobacterium extorquens AM1, which encodes the serine cycle enzyme hydroxypyruvate reductase (L. V. Chistoserdova and M. E. Lidstrom, J. Bacteriol. 174:71-77, 1992). Here we present the complete sequence of hprA and partial sequence of genes adjacent to hprA. Upstream of hprA, the 3' part of an open reading frame was discovered, separated from hprA by 263 bp. This open reading frame was identified as the gene encoding another serine cycle enzyme, serine glyoxylate aminotransferase (sgaA). Cells containing an insertion mutation into sgaA were unable to grow on C1 compounds, demonstrating that the gene is required for C1 metabolism. Sequencing downstream of hprA has revealed the presence of another open reading frame (mtdA), which is probably cotranscribed with hprA. This open reading frame was identified as the gene required for the synthesis of 5,10-methylenetetrahydrofolate dehydrogenase. Our data suggest that this enzyme plays an integral role in methylotrophic metabolism in M. extorquens AM1, either in formaldehyde oxidation or as part of the serine cycle.
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Affiliation(s)
- L V Chistoserdova
- W. M. Keck Laboratories 138-78, California Institute of Technology, Pasadena 91125
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49
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Goldberg JD, Yoshida T, Brick P. Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution. J Mol Biol 1994; 236:1123-40. [PMID: 8120891 DOI: 10.1016/0022-2836(94)90016-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
D-Glycerate dehydrogenase (GDH) catalyzes the NADH-linked reduction of hydroxypyruvate to D-glycerate. GDH is a member of a family of NAD-dependent dehydrogenases that is characterized by a specificity for the D-isomer of the hydroxyacid substrate. The crystal structure of the apoenzyme form of GDH from Hyphomicrobium methylovorum has been determined by the method of isomorphous replacement and refined at 2.4 A resolution using a restrained least-squares method. The crystallographic R-factor is 19.4% for all 24,553 measured reflections between 10.0 and 2.4 A resolution. The GDH molecule is a symmetrical dimer composed of subunits of molecular mass 38,000, and shares significant structural homology with another NAD-dependent enzyme, formate dehydrogenase. The GDH subunit consists of two structurally similar domains that are approximately related to each other by 2-fold symmetry. The domains are separated by a deep cleft that forms the putative NAD and substrate binding sites. One of the domains has been identified as the NAD-binding domain based on its close structural similarity to the NAD-binding domains of other NAD-dependent dehydrogenases. The topology of the second domain is different from that found in the various catalytic domains of other dehydrogenases. A model of a ternary complex of GDH has been built in which putative catalytic residues are identified based on sequence homology between the D-isomer specific dehydrogenases. A structural comparison between GDH and L-lactate dehydrogenase indicates a convergence of active site residues and geometries for these two enzymes. The reactions catalyzed are chemically equivalent but of opposing stereospecificity. A hypothesis is presented to explain how the two enzymes may exploit the same coenzyme stereochemistry and a similar spatial arrangement of catalytic residues to carry out reactions that proceed to opposite enantiomers.
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Affiliation(s)
- J D Goldberg
- Blackett Laboratory, Imperial College, London, England
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50
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Dequin S, Barre P. Mixed lactic acid-alcoholic fermentation by Saccharomyces cerevisiae expressing the Lactobacillus casei L(+)-LDH. BIO/TECHNOLOGY (NATURE PUBLISHING COMPANY) 1994; 12:173-7. [PMID: 7764431 DOI: 10.1038/nbt0294-173] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We describe the construction of a Saccharomyces cerevisiae strain expressing the gene encoding the L(+)-lactate dehydrogenase [L(+)-LDH)] from Lactobacillus casei. The recombinant strain is able to perform a mixed lactic acid-alcoholic fermentation. Yeast cells expressing the L(+)-LDH gene from the yeast alcohol dehydrogenase (ADH1) promoter on a multicopy plasmid simultaneously convert glucose to both ethanol and lactate, with up to 20% of the glucose transformed into L(+)-lactate. Such strains may be used in every field where both biological acidification and alcoholic fermentation are required.
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Affiliation(s)
- S Dequin
- Laboratoire de Microbiologie et Technologie des Fermentations, Institut des Produits de la Vigne, INRA, Montpellier, France
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