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Söderholm A, Newton MS, Patrick WM, Selmer M. Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa: Decarboxylation is not essential for indole formation. J Biol Chem 2020; 295:15948-15956. [PMID: 32928960 PMCID: PMC7681013 DOI: 10.1074/jbc.ra120.014936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/11/2020] [Indexed: 11/27/2022] Open
Abstract
In tryptophan biosynthesis, the reaction catalyzed by the enzyme indole-3-glycerol phosphate synthase (IGPS) starts with a condensation step in which the substrate's carboxylated phenyl group makes a nucleophilic attack to form the pyrrole ring of the indole, followed by a decarboxylation that restores the aromaticity of the phenyl. IGPS from Pseudomonas aeruginosa has the highest turnover number of all characterized IGPS enzymes, providing an excellent model system to test the necessity of the decarboxylation step. Since the 1960s, this step has been considered to be mechanistically essential based on studies of the IGPS–phosphoribosylanthranilate isomerase fusion protein from Escherichia coli. Here, we present the crystal structure of P. aeruginosa IGPS in complex with reduced CdRP, a nonreactive substrate analog, and using a sensitive discontinuous assay, we demonstrate weak promiscuous activity on the decarboxylated substrate 1-(phenylamino)-1-deoxyribulose-5-phosphate, with an ∼1000× lower rate of IGP formation than from the native substrate. We also show that E. coli IGPS, at an even lower rate, can produce IGP from decarboxylated substrate. Our structure of P. aeruginosa IGPS has eight molecules in the asymmetric unit, of which seven contain ligand and one displays a previously unobserved conformation closer to the reactive state. One of the few nonconserved active-site residues, Phe201 in P. aeruginosa IGPS, is by mutagenesis demonstrated to be important for the higher turnover of this enzyme on both substrates. Our results demonstrate that despite IGPS's classification as a carboxy-lyase (i.e. decarboxylase), decarboxylation is not a completely essential step in its catalysis.
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Affiliation(s)
- Annika Söderholm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Matilda S Newton
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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Rohweder B, Lehmann G, Eichner N, Polen T, Rajendran C, Ruperti F, Linde M, Treiber T, Jung O, Dettmer K, Meister G, Bott M, Gronwald W, Sterner R. Library Selection with a Randomized Repertoire of (βα) 8-Barrel Enzymes Results in Unexpected Induction of Gene Expression. Biochemistry 2019; 58:4207-4217. [PMID: 31557000 DOI: 10.1021/acs.biochem.9b00579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential of the frequently encountered (βα)8-barrel fold to acquire new functions was tested by an approach combining random mutagenesis and selection in vivo. For this purpose, the genes encoding 52 different phosphate-binding (βα)8-barrel proteins were subjected to error-prone PCR and cloned into an expression plasmid. The resulting mixed repertoire was used to transform different auxotrophic Escherichia coli strains, each lacking an enzyme with a phosphate-containing substrate. After plating of the different transformants on minimal medium, growth was observed only for two strains, lacking either the gene for the serine phosphatase SerB or the phosphoserine aminotransferase SerC. The same mutants of the E. coli genes nanE (encoding a putative N-acetylmannosamine-6-phosphate 2-epimerase) and pdxJ (encoding the pyridoxine 5'-phosphate synthase) were responsible for rescuing both ΔserB and ΔserC. Unexpectedly, the complementing NanE and PdxJ variants did not catalyze the SerB or SerC reactions in vitro. Instead, RT-qPCR, RNAseq, and transcriptome analysis showed that they rescue the deletions by enlisting the help of endogenous E. coli enzymes HisB and HisC through exclusive up-regulation of histidine operon transcription. While the promiscuous SerB activity of HisB is well-established, our data indicate that HisC is promiscuous for the SerC reaction, as well. The successful rescue of ΔserB and ΔserC through point mutations and recruitment of additional amino acids in NanE and PdxJ provides another example for the adaptability of the (βα)8-barrel fold.
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Affiliation(s)
- Bettina Rohweder
- Institute of Biophysics and Physical Biochemistry , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Gerhard Lehmann
- Institute of Biochemistry, Genetics and Microbiology , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Norbert Eichner
- Institute of Biochemistry, Genetics and Microbiology , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Tino Polen
- IBG-1: Biotechnology , Institute of Bio- and Geosciences , Forschungszentrum Jülich GmbH , D-52425 Jülich , Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Fabian Ruperti
- Institute of Biophysics and Physical Biochemistry , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Thomas Treiber
- Institute of Biochemistry, Genetics and Microbiology , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Oona Jung
- Institute of Functional Genomics , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Katja Dettmer
- Institute of Functional Genomics , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Michael Bott
- IBG-1: Biotechnology , Institute of Bio- and Geosciences , Forschungszentrum Jülich GmbH , D-52425 Jülich , Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry , University of Regensburg , Universitätsstrasse 31 , D-93053 Regensburg , Germany
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3
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop. Biochem J 2016; 473:1141-52. [PMID: 26929404 DOI: 10.1042/bj20151271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022]
Abstract
We investigate the evolution of co-occurring analogous enzymes involved in L-tryptophan and L-histidine biosynthesis in Actinobacteria Phylogenetic analysis of trpF homologues, a missing gene in certain clades of this lineage whose absence is complemented by a dual-substrate HisA homologue, termed PriA, found that they fall into three categories: (i) trpF-1, an L-tryptophan biosynthetic gene horizontally acquired by certain Corynebacterium species; (ii) trpF-2, a paralogue known to be involved in synthesizing a pyrrolopyrrole moiety and (iii) trpF-3, a variable non-conserved orthologue of trpF-1 We previously investigated the effect of trpF-1 upon the evolution of PriA substrate specificity, but nothing is known about the relationship between trpF-3 and priA After in vitro steady-state enzyme kinetics we found that trpF-3 encodes a phosphoribosyl anthranilate isomerase. However, mutation of this gene in Streptomyces sviceus did not lead to auxothrophy, as expected from the biosynthetic role of trpF-1 Biochemical characterization of a dozen co-occurring TrpF-2 or TrpF-3, with PriA homologues, explained the prototrophic phenotype, and unveiled an enzyme activity trade-off between TrpF and PriA. X-ray structural analysis suggests that the function of these PriA homologues is mediated by non-conserved mutations in the flexible L5 loop, which may be responsible for different substrate affinities. Thus, the PriA homologues that co-occur with TrpF-3 represent a novel enzyme family, termed PriB, which evolved in response to PRA isomerase activity. The characterization of co-occurring enzymes provides insights into the influence of functional redundancy on the evolution of enzyme function, which could be useful for enzyme functional annotation.
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Bhargav SP, Vahokoski J, Kallio JP, Torda AE, Kursula P, Kursula I. Two independently folding units of Plasmodium profilin suggest evolution via gene fusion. Cell Mol Life Sci 2015; 72:4193-203. [PMID: 26012696 PMCID: PMC11113795 DOI: 10.1007/s00018-015-1932-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/13/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
Gene fusion is a common mechanism of protein evolution that has mainly been discussed in the context of multidomain or symmetric proteins. Less is known about fusion of ancestral genes to produce small single-domain proteins. Here, we show with a domain-swapped mutant Plasmodium profilin that this small, globular, apparently single-domain protein consists of two foldons. The separation of binding sites for different protein ligands in the two halves suggests evolution via an ancient gene fusion event, analogous to the formation of multidomain proteins. Finally, the two fragments can be assembled together after expression as two separate gene products. The possibility to engineer both domain-swapped dimers and half-profilins that can be assembled back to a full profilin provides perspectives for engineering of novel protein folds, e.g., with different scaffolding functions.
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Affiliation(s)
| | - Juha Vahokoski
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, 90014, Oulu, Finland
| | - Juha Pekka Kallio
- Helmholtz Centre for Infection Research, Notkestrasse 85, 22607, Hamburg, Germany
- German Electron Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Andrew E Torda
- Centre for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg, Germany
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Inari Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, 90014, Oulu, Finland.
- Helmholtz Centre for Infection Research, Notkestrasse 85, 22607, Hamburg, Germany.
- German Electron Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany.
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway.
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6
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Noda-García L, Juárez-Vázquez AL, Ávila-Arcos MC, Verduzco-Castro EA, Montero-Morán G, Gaytán P, Carrillo-Tripp M, Barona-Gómez F. Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome. BMC Evol Biol 2015; 15:107. [PMID: 26058375 PMCID: PMC4462073 DOI: 10.1186/s12862-015-0378-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/11/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Current sequence-based approaches to identify enzyme functional shifts, such as enzyme promiscuity, have proven to be highly dependent on a priori functional knowledge, hampering our ability to reconstruct evolutionary history behind these mechanisms. Hidden Markov Model (HMM) profiles, broadly used to classify enzyme families, can be useful to distinguish between closely related enzyme families with different specificities. The (βα)8-isomerase HisA/PriA enzyme family, involved in L-histidine (HisA, mono-substrate) biosynthesis in most bacteria and plants, but also in L-tryptophan (HisA/TrpF or PriA, dual-substrate) biosynthesis in most Actinobacteria, has been used as model system to explore evolutionary hypotheses and therefore has a considerable amount of evolutionary, functional and structural knowledge available. We searched for functional evolutionary intermediates between the HisA and PriA enzyme families in order to understand the functional divergence between these families. RESULTS We constructed a HMM profile that correctly classifies sequences of unknown function into the HisA and PriA enzyme sub-families. Using this HMM profile, we mined a large metagenome to identify plausible evolutionary intermediate sequences between HisA and PriA. These sequences were used to perform phylogenetic reconstructions and to identify functionally conserved amino acids. Biochemical characterization of one selected enzyme (CAM1) with a mutation within the functionally essential N-terminus phosphate-binding site, namely, an alanine instead of a glycine in HisA or a serine in PriA, showed that this evolutionary intermediate has dual-substrate specificity. Moreover, site-directed mutagenesis of this alanine residue, either backwards into a glycine or forward into a serine, revealed the robustness of this enzyme. None of these mutations, presumably upon functionally essential amino acids, significantly abolished its enzyme activities. A truncated version of this enzyme (CAM2) predicted to adopt a (βα)6-fold, and thus entirely lacking a C-terminus phosphate-binding site, was identified and shown to have HisA activity. CONCLUSION As expected, reconstruction of the evolution of PriA from HisA with HMM profiles suggest that functional shifts involve mutations in evolutionarily intermediate enzymes of otherwise functionally essential residues or motifs. These results are in agreement with a link between promiscuous enzymes and intragenic epistasis. HMM provides a convenient approach for gaining insights into these evolutionary processes.
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Affiliation(s)
- Lianet Noda-García
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México. .,Current Addresses: Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
| | - Ana L Juárez-Vázquez
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
| | - María C Ávila-Arcos
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México. .,Current Addresses: Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Ernesto A Verduzco-Castro
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
| | - Gabriela Montero-Morán
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México. .,Current Addresses: División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, México.
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, CP 62250, Cuernavaca, México.
| | - Mauricio Carrillo-Tripp
- Biomolecular Diversity Laboratories, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.
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7
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Nagao C, Nagano N, Mizuguchi K. Prediction of detailed enzyme functions and identification of specificity determining residues by random forests. PLoS One 2014; 9:e84623. [PMID: 24416252 PMCID: PMC3885575 DOI: 10.1371/journal.pone.0084623] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/15/2013] [Indexed: 12/03/2022] Open
Abstract
Determining enzyme functions is essential for a thorough understanding of cellular processes. Although many prediction methods have been developed, it remains a significant challenge to predict enzyme functions at the fourth-digit level of the Enzyme Commission numbers. Functional specificity of enzymes often changes drastically by mutations of a small number of residues and therefore, information about these critical residues can potentially help discriminate detailed functions. However, because these residues must be identified by mutagenesis experiments, the available information is limited, and the lack of experimentally verified specificity determining residues (SDRs) has hindered the development of detailed function prediction methods and computational identification of SDRs. Here we present a novel method for predicting enzyme functions by random forests, EFPrf, along with a set of putative SDRs, the random forests derived SDRs (rf-SDRs). EFPrf consists of a set of binary predictors for enzymes in each CATH superfamily and the rf-SDRs are the residue positions corresponding to the most highly contributing attributes obtained from each predictor. EFPrf showed a precision of 0.98 and a recall of 0.89 in a cross-validated benchmark assessment. The rf-SDRs included many residues, whose importance for specificity had been validated experimentally. The analysis of the rf-SDRs revealed both a general tendency that functionally diverged superfamilies tend to include more active site residues in their rf-SDRs than in less diverged superfamilies, and superfamily-specific conservation patterns of each functional residue. EFPrf and the rf-SDRs will be an effective tool for annotating enzyme functions and for understanding how enzyme functions have diverged within each superfamily.
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Affiliation(s)
- Chioko Nagao
- National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
- * E-mail: (CN); (KM)
| | - Nozomi Nagano
- Computational Biology Research Center, AIST, Koto-ku, Tokyo, Japan
| | - Kenji Mizuguchi
- National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
- * E-mail: (CN); (KM)
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8
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Reisinger B, Sperl J, Holinski A, Schmid V, Rajendran C, Carstensen L, Schlee S, Blanquart S, Merkl R, Sterner R. Evidence for the Existence of Elaborate Enzyme Complexes in the Paleoarchean Era. J Am Chem Soc 2013; 136:122-9. [DOI: 10.1021/ja4115677] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bernd Reisinger
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Josef Sperl
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Alexandra Holinski
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Veronika Schmid
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Chitra Rajendran
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Linn Carstensen
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sandra Schlee
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Samuel Blanquart
- Equipe
Bonsai,
Institut National de Recherche en Informatique et en Automatique, INRIA Lille Nord Europe, 40 avenue Halley, 59650 Villeneuve d’Ascq, France
| | - Rainer Merkl
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute
of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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9
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Reisinger B, Kuzmanovic N, Löffler P, Merkl R, König B, Sterner R. Nutzung natürlicher Proteinsymmetrie zum Design lichtschaltbarer Enzyminhibitoren. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307207] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Reisinger B, Kuzmanovic N, Löffler P, Merkl R, König B, Sterner R. Exploiting protein symmetry to design light-controllable enzyme inhibitors. Angew Chem Int Ed Engl 2013; 53:595-8. [PMID: 24520030 DOI: 10.1002/anie.201307207] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Indexed: 11/07/2022]
Abstract
The activity of the metabolic branch-point enzyme PriA from Mycobacterium tuberculosis (mtPriA) can be controlled reversibly by light. Two-pronged inhibitors based on the dithienylethene scaffold were designed utilizing mtPriA's natural rotational symmetry. Switching from the flexible, ring-open to the rigid, ring-closed isomer reduces inhibition activity by one order of magnitude.
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Affiliation(s)
- Bernd Reisinger
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, 93040 Regensburg (Germany)
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11
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Noda-García L, Barona-Gómez F. Enzyme evolution beyond gene duplication: A model for incorporating horizontal gene transfer. Mob Genet Elements 2013; 3:e26439. [PMID: 24251070 DOI: 10.4161/mge.26439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding the evolution of enzyme function after gene duplication has been a major goal of molecular biologists, biochemists and evolutionary biologists alike, for almost half a century. In contrast, the impact that horizontal gene transfer (HGT) has had on the evolution of enzyme specialization and the assembly of metabolic networks has just started to being investigated. Traditionally, evolutionary studies of enzymes have been limited to either the function of enzymes in vitro, or to sequence variability at the population level, where in almost all cases the starting conceptual framework embraces gene duplication as the mechanism responsible for the appearance of genetic redundancy. Very recently, we merged comparative phylogenomics, detection of selection signals, enzyme kinetics, X-ray crystallography and computational molecular dynamics, to characterize the sub-functionalization process of an amino acid biosynthetic enzyme prompted by an episode of HGT in bacteria. Some of the evolutionary implications of these functional studies, including a proposed model of enzyme specialization independent of gene duplication, are developed in this commentary.
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Affiliation(s)
- Lianet Noda-García
- Evolution of Metabolic Diversity Laboratory; Laboratorio Nacional de Genómica para la Biodiversidad (Langebio); Cinvestav-IPN; Irapuato, México
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12
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Establishing catalytic activity on an artificial (βα)8-barrel protein designed from identical half-barrels. FEBS Lett 2013; 587:2798-805. [PMID: 23806364 DOI: 10.1016/j.febslet.2013.06.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/27/2013] [Accepted: 06/16/2013] [Indexed: 01/28/2023]
Abstract
It has been postulated that the ubiquitous (βα)8-barrel enzyme fold has evolved by duplication and fusion of an ancestral (βα)4-half-barrel. We have previously reconstructed this process in the laboratory by fusing two copies of the C-terminal half-barrel HisF-C of imidazole glycerol phosphate synthase (HisF). The resulting construct HisF-CC was stepwise stabilized to Sym1 and Sym2, which are extremely robust but catalytically inert proteins. Here, we report on the generation of a circular permutant of Sym2 and the establishment of a sugar isomerization reaction on its scaffold. Our results demonstrate that duplication and mutagenesis of (βα)4-half-barrels can readily lead to a stable and catalytically active (βα)8-barrel enzyme.
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Reisinger B, Bocola M, List F, Claren J, Rajendran C, Sterner R. A sugar isomerization reaction established on various (βα)₈-barrel scaffolds is based on substrate-assisted catalysis. Protein Eng Des Sel 2012; 25:751-60. [PMID: 23109729 DOI: 10.1093/protein/gzs080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the course of tryptophan biosynthesis, the isomerization of phosphoribosylanthranilate (PRA) is catalyzed by the (βα)₈-barrel enzyme TrpF. The reaction occurs via a general acid-base mechanism with an aspartate and a cysteine residue acting as acid and base, respectively. PRA isomerase activity could be established on two (βα)₈-barrel enzymes involved in histidine biosynthesis, namely HisA and HisF, and on a HisAF chimera, by introducing two aspartate-to-valine substitutions. We have analyzed the reaction mechanism underlying this engineered activity by measuring its pH dependence, solving the crystal structure of a HisF variant with bound product analogue, and applying molecular dynamics simulations and mixed quantum and molecular mechanics calculations. The results suggest that PRA is anchored by the C-terminal phosphate-binding sites of HisA, HisF and HisAF. As a consequence, a conserved aspartate residue, which is equivalent to Cys7 from TrpF, is properly positioned to act as catalytic base. However, no obvious catalytic acid corresponding to Asp126 from TrpF could be identified in the three proteins. Instead, this role appears to be carried out by the carboxylate group of the anthranilate moiety of PRA. Thus, the engineered PRA isomerization activity is based on a reaction mechanism including substrate-assisted catalysis and thus differs substantially from the naturally evolved reaction mechanism used by TrpF.
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Affiliation(s)
- Bernd Reisinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
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Kubelka T, Slavětínská L, Hocek M. Synthesis of Substituted Benzyl Homo-C-Ribonucleosides and -Nucleotides as Carba Analogues of Phosphoribosylanthranilate. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Carstensen L, Sperl JM, Bocola M, List F, Schmid FX, Sterner R. Conservation of the Folding Mechanism between Designed Primordial (βα)8-Barrel Proteins and Their Modern Descendant. J Am Chem Soc 2012; 134:12786-91. [DOI: 10.1021/ja304951v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linn Carstensen
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Josef M. Sperl
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Marco Bocola
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Felix List
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Franz X. Schmid
- Laboratorium für Biochemie
und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Reinhard Sterner
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
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Carstensen L, Zoldák G, Schmid FX, Sterner R. Folding mechanism of an extremely thermostable (βα)(8)-barrel enzyme: a high kinetic barrier protects the protein from denaturation. Biochemistry 2012; 51:3420-32. [PMID: 22455619 DOI: 10.1021/bi300189f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
HisF, the cyclase subunit of imidazole glycerol phosphate synthase (ImGPS) from Thermotoga maritima, is an extremely thermostable (βα)(8)-barrel protein. We elucidated the unfolding and refolding mechanism of HisF. Its unfolding transition is reversible and adequately described by the two-state model, but 6 weeks is necessary to reach equilibrium (at 25 °C). During refolding, initially a burst-phase off-pathway intermediate is formed. The subsequent productive folding occurs in two kinetic phases with time constants of ~3 and ~20 s. They reflect a sequential process via an on-pathway intermediate, as revealed by stopped-flow double-mixing experiments. The final step leads to native HisF, which associates with the glutaminase subunit HisH to form the functional ImGPS complex. The conversion of the on-pathway intermediate to the native protein results in a 10(6)-fold increase of the time constant for unfolding from 89 ms to 35 h (at 4.0 M GdmCl) and thus establishes a high energy barrier to denaturation. We conclude that the extra stability of HisF is used for kinetic protection against unfolding. In its refolding mechanism, HisF resembles other (βα)(8)-barrel proteins.
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Affiliation(s)
- Linn Carstensen
- Universität Regensburg, Institut für Biophysik und physikalische Biochemie, Universitätsstrasse 31, D-93053 Regensburg, Germany
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17
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Evran S, Telefoncu A, Sterner R. Directed evolution of ( )8-barrel enzymes: establishing phosphoribosylanthranilate isomerisation activity on the scaffold of the tryptophan synthase -subunit. Protein Eng Des Sel 2012; 25:285-93. [DOI: 10.1093/protein/gzs015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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