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Stasiak AC, Gogler K, Borisova M, Fink P, Mayer C, Stehle T, Zocher G. N-acetylmuramic acid recognition by MurK kinase from the MurNAc auxotrophic oral pathogen Tannerella forsythia. J Biol Chem 2023; 299:105076. [PMID: 37481208 PMCID: PMC10465942 DOI: 10.1016/j.jbc.2023.105076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023] Open
Abstract
The bacterial cell wall consists of a three-dimensional peptidoglycan layer, composed of peptides linked to the sugars N-acetylmuramic acid (MurNAc) and GlcNAc. Unlike other bacteria, the pathogenic Tannerella forsythia, a member of the red complex group of bacteria associated with the late stages of periodontitis, lacks biosynthetic pathways for MurNAc production and therefore obtains MurNAc from the environment. Sugar kinases play a crucial role in the MurNAc recycling process, activating the sugar molecules by phosphorylation. In this study, we present the first crystal structures of a MurNAc kinase, called murein sugar kinase (MurK), in its unbound state as well as in complexes with the ATP analog β-γ-methylene adenosine triphosphate (AMP-PCP) and with MurNAc. We also determined the crystal structures of K1058, a paralogous MurNAc kinase of T. forsythia, in its unbound state and in complex with MurNAc. We identified the active site and residues crucial for MurNAc specificity as the less bulky side chains of S133, P134, and L135, which enlarge the binding cavity for the lactyl ether group, unlike the glutamate or histidine residues present in structural homologs. In establishing the apparent kinetic parameters for both enzymes, we showed a comparable affinity for MurNAc (Km 180 μM and 30 μM for MurK and K1058, respectively), with MurK being over two hundred times faster than K1058 (Vmax 80 and 0.34 μmol min-1 mg-1, respectively). These data might support a structure-guided approach to development of inhibitory MurNAc analogs for pathogen MurK enzymes.
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Affiliation(s)
| | - Karolin Gogler
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, University of Tuebingen, Tuebingen, Germany
| | - Phillipp Fink
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, University of Tuebingen, Tuebingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Georg Zocher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany.
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2
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Rodionova IA, Hosseinnia A, Kim S, Goodacre N, Zhang L, Zhang Z, Palsson B, Uetz P, Babu M, Saier MH. E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding. Sci Rep 2023; 13:7345. [PMID: 37147430 PMCID: PMC10163214 DOI: 10.1038/s41598-023-31812-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/17/2023] [Indexed: 05/07/2023] Open
Abstract
Allantoin is a good source of ammonium for many organisms, and in Escherichia coli it is utilized under anaerobic conditions. We provide evidence that allantoinase (AllB) is allosterically activated by direct binding of the allantoin catabolic enzyme, glycerate 2-kinase (GlxK) in the presence of glyoxylate. Glyoxylate is known to be an effector of the AllR repressor which regulates the allantoin utilization operons in E. coli. AllB has low affinity for allantoin, but its activation by GlxK leads to increased affinity for its substrate. We also show that the predicted allantoin transporter YbbW (re-named AllW) has allantoin specificity and the protein-protein interaction with AllB. Our results show that the AllB-dependent allantoin degradative pathway is subject to previously unrecognized regulatory mechanisms involving direct protein-protein interactions.
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Affiliation(s)
- Irina A Rodionova
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA.
- Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA, 92093-0116, USA.
| | - Ali Hosseinnia
- Department of Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Sunyoung Kim
- Department of Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Norman Goodacre
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Li Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
- College of Food Science and Engineering, Ocean University of China, Yushan Road, Shinan District, Qingdao, 266003, China
| | - Zhongge Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Bernhard Palsson
- Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA, 92093-0116, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA.
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3
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Winkler KF, Panse L, Maiwald C, Hayeß J, Fischer P, Fehlau M, Neubauer P, Kurreck A. Screening the Thermotoga maritima genome for new wide-spectrum nucleoside and nucleotide kinases. J Biol Chem 2023:104746. [PMID: 37094698 DOI: 10.1016/j.jbc.2023.104746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/12/2023] [Accepted: 04/16/2023] [Indexed: 04/26/2023] Open
Abstract
Enzymes from thermophilic organisms are interesting biocatalysts for a wide variety of applications in organic synthesis, biotechnology and molecular biology. Next to an increased stability at elevated temperatures, they were described to show a wider substrate spectrum than their mesophilic counterparts. To identify thermostable biocatalysts for the synthesis of nucleotide analogs, we performed a database search on the carbohydrate and nucleotide metabolism of T. maritima. After expression and purification of 13 enzyme candidates involved in nucleotide synthesis, these enzymes were screened for their substrate scope. We found that the synthesis of 2'-deoxynucleoside 5'-monophosphates (dNMPs) and uridine 5'-monophosphate from nucleosides was catalyzed by the already known wide-spectrum thymidine kinase (TK) and the ribokinase. In contrast, no NMP-forming activity was detected for adenosine-specific kinase, uridine kinase or nucleotidase. The NMP kinases (NMPKs) and the pyruvate-phosphate-dikinase of T. maritima exhibited a rather specific substrate spectrum for the phosphorylation of NMPs, while pyruvate kinase, acetate kinase and three of the NMPKs showed a broad substrate scope with (2'-deoxy)nucleoside 5'-diphosphates as substrates. Based on these promising results, TmNMPKs were applied in enzymatic cascade reactions for nucleoside 5'-triphosphate synthesis using four modified pyrimidine nucleosides and four purine NMPs as substrates, and we determined that base- and sugar-modified substrates were accepted. In summary, besides the already reported TmTK, NMPKs of T. maritima were identified to be interesting enzyme candidates for the enzymatic production of modified nucleotides.
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Affiliation(s)
- Katja F Winkler
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Lena Panse
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | | | - Josefine Hayeß
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Pascal Fischer
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Maryke Fehlau
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany; BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany
| | - Peter Neubauer
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Anke Kurreck
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany; BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
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4
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Rodionov DA, Rodionova IA, Rodionov VA, Arzamasov AA, Zhang K, Rubinstein GM, Tanwee TNN, Bing RG, Crosby JR, Nookaew I, Basen M, Brown SD, Wilson CM, Klingeman DM, Poole FL, Zhang Y, Kelly RM, Adams MWW. Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii. mSystems 2021; 6:e0134520. [PMID: 34060910 PMCID: PMC8579813 DOI: 10.1128/msystems.01345-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022] Open
Abstract
Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono- and oligosaccharides. Through metabolic engineering, ethanol and other industrially important end products can be produced. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species Caldicellulosiruptor saccharolyticus and Caldicellulosiruptor bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to 14 Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site experimental data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose. IMPORTANCE To develop functional metabolic engineering platforms for nonmodel microorganisms, a comprehensive understanding of the physiological and metabolic characteristics is critical. Caldicellulosiruptor bescii and other species in this genus have untapped potential for conversion of unpretreated plant biomass into industrial fuels and chemicals. The highly interactive and complex machinery used by C. bescii to acquire and process complex carbohydrates contained in lignocellulose was elucidated here to complement related efforts to develop a metabolic engineering platform with this bacterium. Guided by the findings here, a clearer picture of how C. bescii natively drives carbohydrate utilization is provided and strategies to engineer this bacterium for optimal conversion of lignocellulose to commercial products emerge.
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Affiliation(s)
- Dmitry A. Rodionov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Irina A. Rodionova
- Department of Bioengineering, University of California—San Diego, La Jolla, California, USA
| | - Vladimir A. Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr A. Arzamasov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Ke Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Gabriel M. Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Tania N. N. Tanwee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mirko Basen
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Biowissenschaften, Mikrobiologie, Universität Rostock, Rostock, Germany
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Charlotte M. Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- University of Otago, Dunedin, New Zealand
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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5
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James P, Isupov MN, De Rose SA, Sayer C, Cole IS, Littlechild JA. A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans: Structure and Biochemical Characterization. Front Microbiol 2020; 11:592353. [PMID: 33193259 PMCID: PMC7661550 DOI: 10.3389/fmicb.2020.592353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
A novel transketolase has been reconstituted from two separate polypeptide chains encoded by a ‘split-gene’ identified in the genome of the hyperthermophilic bacterium, Carboxydothermus hydrogenoformans. The reconstituted active α2β2 tetrameric enzyme has been biochemically characterized and its activity has been determined using a range of aldehydes including glycolaldehyde, phenylacetaldehyde and cyclohexanecarboxaldehyde as the ketol acceptor and hydroxypyruvate as the donor. This reaction proceeds to near 100% completion due to the release of the product carbon dioxide and can be used for the synthesis of a range of sugars of interest to the pharmaceutical industry. This novel reconstituted transketolase is thermally stable with no loss of activity after incubation for 1 h at 70°C and is stable after 1 h incubation with 50% of the organic solvents methanol, ethanol, isopropanol, DMSO, acetonitrile and acetone. The X-ray structure of the holo reconstituted α2β2 tetrameric transketolase has been determined to 1.4 Å resolution. In addition, the structure of an inactive tetrameric β4 protein has been determined to 1.9 Å resolution. The structure of the active reconstituted α2β2 enzyme has been compared to the structures of related enzymes; the E1 component of the pyruvate dehydrogenase complex and D-xylulose-5-phosphate synthase, in an attempt to rationalize differences in structure and substrate specificity between these enzymes. This is the first example of a reconstituted ‘split-gene’ transketolase to be biochemically and structurally characterized allowing its potential for industrial biocatalysis to be evaluated.
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Affiliation(s)
- Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Isobel S Cole
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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6
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High Conversion of D-Fructose into D-Allulose by Enzymes Coupling with an ATP Regeneration System. Mol Biotechnol 2019; 61:432-441. [PMID: 30963480 DOI: 10.1007/s12033-019-00174-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
D-Allulose is a rare monosaccharide that exists in extremely small quantities in nature, and it is also hard to prepare at a large scale via chemical or enzyme synthetic route due to low conversion and downstream separation complexity. Using D-psicose epimerase and L-rhamnulose kinase, a method enabling high conversion of D-allulose from D-fructose without the need for a tedious isomer separation step was established recently. However, this method requires expensive ATP to facilitate the reaction. In the present study, an ATP regenerate system was developed coupling with polyphosphate kinase. In our optimized reaction with purified enzymes, the conversion rate of 99% D-fructose was achieved at the concentrations of 2 mM ATP, 5 mM polyphosphate, 20 mM D-fructose, and 20 mM Mg2+ when incubated at 50 °C and at pH 7.5. ATP usage can be reduced to 10% of the theoretical amount compared to that without the ATP regeneration system. A fed-batch mode was also studied to minimize the inhibitory effect of polyphosphate. The biosynthetic system reported here offers a potential and promising platform for the conversion of D-fructose into D-allulose at reduced ATP cost.
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7
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Grimaud F, Pizzut-Serin S, Tarquis L, Ladevèze S, Morel S, Putaux JL, Potocki-Veronese G. In Vitro Synthesis and Crystallization of β-1,4-Mannan. Biomacromolecules 2018; 20:846-853. [DOI: 10.1021/acs.biomac.8b01457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florent Grimaud
- LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France
| | | | - Laurence Tarquis
- LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France
| | - Simon Ladevèze
- LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France
| | - Sandrine Morel
- LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France
| | - Jean-Luc Putaux
- Univ. Grenoble Alpes, CNRS, CERMAV, F-38000 Grenoble, France
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8
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Rodionova IA, Goodacre N, Do J, Hosseinnia A, Babu M, Uetz P, Saier MH. The uridylyltransferase GlnD and tRNA modification GTPase MnmE allosterically control Escherichia coli folylpoly-γ-glutamate synthase FolC. J Biol Chem 2018; 293:15725-15732. [PMID: 30089654 DOI: 10.1074/jbc.ra118.004425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/31/2018] [Indexed: 01/20/2023] Open
Abstract
Folate derivatives are important cofactors for enzymes in several metabolic processes. Folate-related inhibition and resistance mechanisms in bacteria are potential targets for antimicrobial therapies and therefore a significant focus of current research. Here, we report that the activity of Escherichia coli poly-γ-glutamyl tetrahydrofolate/dihydrofolate synthase (FolC) is regulated by glutamate/glutamine-sensing uridylyltransferase (GlnD), THF-dependent tRNA modification enzyme (MnmE), and UDP-glucose dehydrogenase (Ugd) as shown by direct in vitro protein-protein interactions. Using kinetics analyses, we observed that GlnD, Ugd, and MnmE activate FolC many-fold by decreasing the K half of FolC for its substrate l-glutamate. Moreover, FolC inhibited the GTPase activity of MnmE at low GTP concentrations. The growth phenotypes associated with these proteins are discussed. These results, obtained using direct in vitro enzyme assays, reveal unanticipated networks of allosteric regulatory interactions in the folate pathway in E. coli and indicate regulation of polyglutamylated tetrahydrofolate biosynthesis by the availability of nitrogen sources, signaled by the glutamine-sensing GlnD protein.
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Affiliation(s)
- Irina A Rodionova
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,
| | - Norman Goodacre
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284, and
| | - Jimmy Do
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Ali Hosseinnia
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284, and
| | - Milton H Saier
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,
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9
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Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants. Nat Commun 2018; 9:1765. [PMID: 29720581 PMCID: PMC5931981 DOI: 10.1038/s41467-018-04201-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/12/2018] [Indexed: 11/09/2022] Open
Abstract
Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes. While most kinases are ATP-dependent some utilize pyrophosphate (PPi) instead. Here the authors structurally characterize a PPi-dependent kinase, identify its key recognition residues and find further PPi-dependent ribokinase family members with this signature pattern.
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10
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Kaznadzey A, Shelyakin P, Belousova E, Eremina A, Shvyreva U, Bykova D, Emelianenko V, Korosteleva A, Tutukina M, Gelfand MS. The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation. Sci Rep 2018; 8:3177. [PMID: 29453395 PMCID: PMC5816610 DOI: 10.1038/s41598-018-21534-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/06/2018] [Indexed: 12/29/2022] Open
Abstract
Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, transporter, and transcription factor. The Escherichia coli sulphoglycolysis cassette was thus predicted to be associated with lactose degradation. This prediction was confirmed experimentally: expression of genes coding for aldolase (yihT), isomerase (yihS), and kinase (yihV) was dramatically increased during growth on lactose. These genes were previously shown to be activated during growth on sulphoquinovose, so our observation may indicate multi-functional capabilities of the respective proteins. Transcription starts for yihT, yihV and yihW were mapped in silico, in vitro and in vivo. Out of three promoters for yihT, one was active only during growth on lactose. We further showed that switches in yihT transcription are controlled by YihW, a DeoR-family transcription factor in the Escherichia coli cassette. YihW acted as a carbon source-dependent dual regulator involved in sustaining the baseline growth in the absence of lac-operon, with function either complementary, or opposite to a global regulator of carbohydrate metabolism, cAMP-CRP.
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Affiliation(s)
- Anna Kaznadzey
- A. A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127051, Russia
| | - Pavel Shelyakin
- A. A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127051, Russia
- N. I. Vavilov Institute of General Genetics, RAS, ul. Gubkina 3, Moscow, 119991, Russia
| | - Evgeniya Belousova
- M. V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia
| | - Aleksandra Eremina
- The University of Edinburgh, Alexander Crum Brown Rd, Edinburgh, Scotland, EH9 3FF, UK
| | - Uliana Shvyreva
- Institute of Cell Biophysics, RAS, Institutskaya 3, Pushchino, 142290, Russia
| | - Darya Bykova
- M. V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia
| | - Vera Emelianenko
- M. V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia
| | | | - Maria Tutukina
- Institute of Cell Biophysics, RAS, Institutskaya 3, Pushchino, 142290, Russia.
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.
| | - Mikhail S Gelfand
- A. A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127051, Russia
- M. V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
- Faculty of Computer Science, Higher School of Economics, Kochnovsky pr. 3, Moscow, 125319, Russia
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11
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Lee BD, Apel WA, DeVeaux LC, Sheridan PP. Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius. J Ind Microbiol Biotechnol 2017; 44:1443-1458. [PMID: 28776272 DOI: 10.1007/s10295-017-1968-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 07/18/2017] [Indexed: 11/24/2022]
Abstract
Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grew while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.
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Affiliation(s)
- Brady D Lee
- Idaho National Laboratory, Biological Systems Department, Idaho Falls, ID, USA. .,Department of Biological Sciences, Idaho State University, Pocatello, ID, USA. .,Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, USA.
| | - William A Apel
- Idaho National Laboratory, Biological Systems Department, Idaho Falls, ID, USA.,Aspenglow Associates, LLC, P. O. Box 12692, Jackson, WY, 83002, USA
| | - Linda C DeVeaux
- Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD, USA
| | - Peter P Sheridan
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
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12
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Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH. The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli. J Biol Chem 2017. [PMID: 28634232 DOI: 10.1074/jbc.m117.795294] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The histidine-phosphorylatable phosphocarrier protein (HPr) is an essential component of the sugar-transporting phosphotransferase system (PTS) in many bacteria. Recent interactome findings suggested that HPr interacts with several carbohydrate-metabolizing enzymes, but whether HPr plays a regulatory role was unclear. Here, we provide evidence that HPr interacts with a large number of proteins in Escherichia coli We demonstrate HPr-dependent allosteric regulation of the activities of pyruvate kinase (PykF, but not PykA), phosphofructokinase (PfkB, but not PfkA), glucosamine-6-phosphate deaminase (NagB), and adenylate kinase (Adk). HPr is either phosphorylated on a histidyl residue (HPr-P) or non-phosphorylated (HPr). PykF is activated only by non-phosphorylated HPr, which decreases the PykF Khalf for phosphoenolpyruvate by 10-fold (from 3.5 to 0.36 mm), thus influencing glycolysis. PfkB activation by HPr, but not by HPr-P, resulted from a decrease in the Khalf for fructose-6-P, which likely influences both gluconeogenesis and glycolysis. Moreover, NagB activation by HPr was important for the utilization of amino sugars, and allosteric inhibition of Adk activity by HPr-P, but not by HPr, allows HPr to regulate the cellular energy charge coordinately with glycolysis. These observations suggest that HPr serves as a directly interacting global regulator of carbon and energy metabolism and probably of other physiological processes in enteric bacteria.
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Affiliation(s)
- Irina A Rodionova
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Zhongge Zhang
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Jitender Mehla
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Norman Goodacre
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Andrew Emili
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Milton H Saier
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,.
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13
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Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, Schlüter A. Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment. J Biotechnol 2016; 232:50-60. [PMID: 27165504 DOI: 10.1016/j.jbiotec.2016.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022]
Abstract
The genome sequence of Defluviitoga tunisiensis L3 originating from a thermophilic biogas-production plant was established and recently published as Genome Announcement by our group. The circular chromosome of D. tunisiensis L3 has a size of 2,053,097bp and a mean GC content of 31.38%. To analyze the D. tunisiensis L3 genome sequence in more detail, a phylogenetic analysis of completely sequenced Thermotogae strains based on shared core genes was performed. It appeared that Petrotoga mobilis DSM 10674(T), originally isolated from a North Sea oil-production well, is the closest relative of D. tunisiensis L3. Comparative genome analyses of P. mobilis DSM 10674(T) and D. tunisiensis L3 showed moderate similarities regarding occurrence of orthologous genes. Both genomes share a common set of 1351 core genes. Reconstruction of metabolic pathways important for the biogas production process revealed that the D. tunisiensis L3 genome encodes a large set of genes predicted to facilitate utilization of a variety of complex polysaccharides including cellulose, chitin and xylan. Ethanol, acetate, hydrogen (H2) and carbon dioxide (CO2) were found as possible end-products of the fermentation process. The latter three metabolites are considered to represent substrates for methanogenic Archaea, the key organisms in the final step of the anaerobic digestion process. To determine the degree of relatedness between D. tunisiensis L3 and dominant biogas community members within the thermophilic biogas-production plant, metagenome sequences obtained from the corresponding microbial community were mapped onto the L3 genome sequence. This fragment recruitment revealed that the D. tunisiensis L3 genome is almost completely covered with metagenome sequences featuring high matching accuracy. This result indicates that strains highly related or even identical to the reference strain D. tunisiensis L3 play a dominant role within the community of the thermophilic biogas-production plant.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Katharina Gabriela Cibis
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Andreas Bremges
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Yvonne Stolze
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | | | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany.
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14
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Shin SM, Choi JM, di Luccio E, Lee YJ, Lee SJ, Lee SJ, Lee SH, Lee DW. The structural basis of substrate promiscuity in UDP-hexose 4-epimerase from the hyperthermophilic Eubacterium Thermotoga maritima. Arch Biochem Biophys 2015; 585:39-51. [PMID: 26344854 DOI: 10.1016/j.abb.2015.08.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/18/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022]
Abstract
UDP-galactose 4-epimerase (GalE) catalyzes the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal), which is a pivotal step in the Leloir pathway for d-galactose metabolism. Although GalE is widely distributed in prokaryotes and eukaryotes, little information is available regarding hyperthermophilic GalE. We overexpressed the TM0509 gene, encoding a putative GalE from Thermotoga maritima (TMGalE), in Escherichia coli and characterized the encoded protein. To further investigate the molecular basis of this enzyme's catalytic function, we determined the crystal structures of TMGalE and TMGalE bound to UDP-Glc at resolutions of 1.9 Å and 2.0 Å, respectively. The enzyme was determined to be a homodimer with a molecular mass of 70 kDa. The enzyme could reversibly catalyze the epimerization of UDP-GalNAc/UDP-GlcNAc as well as UDP-Gal/UDP-Glc at elevated temperatures, with an apparent optimal temperature and pH of 80 °C and 7.0, respectively. Our data showed that TM0509 is a UDP-galactosugar 4-epimerase involved in d-galactose metabolism; consequently, this study provides the first detailed characterization of a hyperthermophilic GalE. Moreover, the promiscuous substrate specificity of TMGalE, which is more similar to human GalE than E. coli GalE, supports the notion that TMGalE might exhibit the earliest form of sugar-epimerizing enzymes in the evolution of galactose metabolism.
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Affiliation(s)
- Sun-Mi Shin
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701, South Korea
| | - Jin Myung Choi
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, South Korea
| | - Eric di Luccio
- School of Food Sciences & Biotechnology, Kyungpook National University, Daegu 702-701, South Korea
| | - Yong-Jik Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701, South Korea
| | - Sang-Jae Lee
- Major in Food Biotechnology, Silla University, Busan 617-736, South Korea
| | - Sang Jun Lee
- Infection & Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, South Korea
| | - Sung Haeng Lee
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, South Korea
| | - Dong-Woo Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701, South Korea.
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15
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Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet 2014; 15:107-20. [PMID: 24430943 DOI: 10.1038/nrg3643] [Citation(s) in RCA: 525] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The prediction of cellular function from a genotype is a fundamental goal in biology. For metabolism, constraint-based modelling methods systematize biochemical, genetic and genomic knowledge into a mathematical framework that enables a mechanistic description of metabolic physiology. The use of constraint-based approaches has evolved over ~30 years, and an increasing number of studies have recently combined models with high-throughput data sets for prospective experimentation. These studies have led to validation of increasingly important and relevant biological predictions. As reviewed here, these recent successes have tangible implications in the fields of microbial evolution, interaction networks, genetic engineering and drug discovery.
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Affiliation(s)
- Aarash Bordbar
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093-0412, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093-0412, USA
| | - Zachary A King
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093-0412, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093-0412, USA
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16
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Rodionova IA, Li X, Thiel V, Stolyar S, Stanton K, Fredrickson JK, Bryant DA, Osterman AL, Best AA, Rodionov DA. Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria. Front Microbiol 2013; 4:407. [PMID: 24391637 PMCID: PMC3870299 DOI: 10.3389/fmicb.2013.00407] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/09/2013] [Indexed: 12/29/2022] Open
Abstract
L-rhamnose (L-Rha) is a deoxy-hexose sugar commonly found in nature. L-Rha catabolic pathways were previously characterized in various bacteria including Escherichia coli. Nevertheless, homology searches failed to recognize all the genes for the complete L-Rha utilization pathways in diverse microbial species involved in biomass decomposition. Moreover, the regulatory mechanisms of L-Rha catabolism have remained unclear in most species. A comparative genomics approach was used to reconstruct the L-Rha catabolic pathways and transcriptional regulons in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Thermotogae. The reconstructed pathways include multiple novel enzymes and transporters involved in the utilization of L-Rha and L-Rha-containing polymers. Large-scale regulon inference using bioinformatics revealed remarkable variations in transcriptional regulators for L-Rha utilization genes among bacteria. A novel bifunctional enzyme, L-rhamnulose-phosphate aldolase (RhaE) fused to L-lactaldehyde dehydrogenase (RhaW), which is not homologous to previously characterized L-Rha catabolic enzymes, was identified in diverse bacteria including Chloroflexi, Bacilli, and Alphaproteobacteria. By using in vitro biochemical assays we validated both enzymatic activities of the purified recombinant RhaEW proteins from Chloroflexus aurantiacus and Bacillus subtilis. Another novel enzyme of the L-Rha catabolism, L-lactaldehyde reductase (RhaZ), was identified in Gammaproteobacteria and experimentally validated by in vitro enzymatic assays using the recombinant protein from Salmonella typhimurium. C. aurantiacus induced transcription of the predicted L-Rha utilization genes when L-Rha was present in the growth medium and consumed L-Rha from the medium. This study provided comprehensive insights to L-Rha catabolism and its regulation in diverse Bacteria.
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Affiliation(s)
| | - Xiaoqing Li
- Sanford-Burnham Medical Research Institute La Jolla, CA, USA
| | - Vera Thiel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park PA, USA
| | - Sergey Stolyar
- Pacific Northwest National Laboratory, Biological Sciences Division Richland, WA, USA
| | | | - James K Fredrickson
- Pacific Northwest National Laboratory, Biological Sciences Division Richland, WA, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park PA, USA ; Department of Chemistry and Biochemistry, Montana State University Bozeman, MT, USA
| | | | - Aaron A Best
- Department of Biology, Hope College Holland, MI, USA
| | - Dmitry A Rodionov
- Sanford-Burnham Medical Research Institute La Jolla, CA, USA ; A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
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17
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Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL. Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. Front Microbiol 2013; 4:244. [PMID: 23986752 PMCID: PMC3750489 DOI: 10.3389/fmicb.2013.00244] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/31/2013] [Indexed: 01/01/2023] Open
Abstract
Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.
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Affiliation(s)
- Dmitry A Rodionov
- Sanford-Burnham Medical Research Institute La Jolla, CA, USA ; A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
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18
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Rodionova IA, Leyn SA, Burkart MD, Boucher N, Noll KM, Osterman AL, Rodionov DA. Novel inositol catabolic pathway inThermotoga maritima. Environ Microbiol 2013; 15:2254-66. [DOI: 10.1111/1462-2920.12096] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/18/2013] [Accepted: 01/20/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - Semen A. Leyn
- A. A. Kharkevich Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow; 127994; Russia
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California San Diego; La Jolla; CA; 92093; USA
| | - Nathalie Boucher
- Department of Molecular and Cell Biology; University of Connecticut; Storrs; CT; 06269; USA
| | - Kenneth M. Noll
- Department of Molecular and Cell Biology; University of Connecticut; Storrs; CT; 06269; USA
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19
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Kazanov MD, Li X, Gelfand MS, Osterman AL, Rodionov DA. Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res 2012. [PMID: 23209028 PMCID: PMC3553997 DOI: 10.1093/nar/gks1184] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Large and functionally heterogeneous families of transcription factors have complex evolutionary histories. What shapes specificities toward effectors and DNA sites in paralogous regulators is a fundamental question in biology. Bacteria from the deep-branching lineage Thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (ROK) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. We applied an integrated genomic approach to study functions and specificities of regulators from this family. A comparative analysis of 11 Thermotogae genomes revealed novel mechanisms of transcriptional regulation of the sugar utilization networks, DNA-binding motifs and specific functions. Reconstructed regulons for seven groups of ROK regulators were validated by DNA-binding assays using purified recombinant proteins from the model bacterium Thermotoga maritima. All tested regulators demonstrated specific binding to their predicted cognate DNA sites, and this binding was inhibited by specific effectors, mono- or disaccharides from their respective sugar catabolic pathways. By comparing ligand-binding domains of regulators with structurally characterized kinases from the ROK family, we elucidated signature amino acid residues determining sugar-ligand regulator specificity. Observed correlations between signature residues and the sugar-ligand specificities provide the framework for structure functional classification of the entire ROK family.
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Affiliation(s)
- Marat D Kazanov
- Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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20
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Rodionova IA, Scott DA, Grishin NV, Osterman AL, Rodionov DA. Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Environ Microbiol 2012; 14:2920-34. [PMID: 22925190 DOI: 10.1111/j.1462-2920.2012.02856.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/22/2012] [Accepted: 07/23/2012] [Indexed: 11/28/2022]
Abstract
Thermotoga maritima is a marine hyperthermophilic microorganism that degrades a wide range of simple and complex carbohydrates including pectin and produces fermentative hydrogen at high yield. Galacturonate and glucuronate, two abundant hexuronic acids in pectin and xylan, respectively, are catabolized via committed metabolic pathways to supply carbon and energy for a variety of microorganisms. By a combination of bioinformatics and experimental techniques we identified a novel enzyme family (named UxaE) catalysing a previously unknown reaction in the hexuronic acid catabolic pathway, epimerization of tagaturonate to fructuronate. The enzymatic activity of the purified recombinant tagaturonate epimerase from T. maritima was directly confirmed and kinetically characterized. Its function was also confirmed by genetic complementation of the growth of the Escherichia coli uxaB knockout mutant strain on galacturonate. An inferred novel galacturonate to mannonate catabolic pathway in T. maritima was reconstituted in vitro using a mixture of recombinant purified enzymes UxaE, UxaC and UxuB. Members of the newly identified UxaE family were identified in ~50 phylogenetically diverse heterotrophic bacteria from aquatic and soil environments. The genomic context of respective genes and reconstruction of associated pathways suggest that UxaE enzymatic and biological function remains conserved in all of these species.
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Affiliation(s)
- Irina A Rodionova
- Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.
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