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Fuchs A, Romeis D, Hupfeld E, Sieber V. Biocatalytic Conversion of Carrageenans for the Production of 3,6-Anhydro-D-galactose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5816-5827. [PMID: 38442258 PMCID: PMC10958521 DOI: 10.1021/acs.jafc.3c08613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Marine biomass stands out as a sustainable resource for generating value-added chemicals. In particular, anhydrosugars derived from carrageenans exhibit a variety of biological functions, rendering them highly promising for utilization and cascading in food, cosmetic, and biotechnological applications. However, the limitation of available sulfatases to break down the complex sulfation patterns of carrageenans poses a significant limitation for the sustainable production of valuable bioproducts from red algae. In this study, we screened several carrageenolytic polysaccharide utilization loci for novel sulfatase activities to assist the efficient conversion of a variety of sulfated galactans into the target product 3,6-anhydro-D-galactose. Inspired by the carrageenolytic pathways in marine heterotrophic bacteria, we systematically combined these novel sulfatases with other carrageenolytic enzymes, facilitating the development of the first enzymatic one-pot biotransformation of ι- and κ-carrageenan to 3,6-anhdyro-D-galactose. We further showed the applicability of this enzymatic bioconversion to a broad series of hybrid carrageenans, rendering this process a promising and sustainable approach for the production of value-added biomolecules from red-algal feedstocks.
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Affiliation(s)
- Alexander Fuchs
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Dennis Romeis
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Enrico Hupfeld
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
- SynBioFoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Catalytic
Research Center, Ernst-Otto-Fischer-Straße1, 85748 Garching, Germany
- School
of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia 4072, Australia
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2
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Kinateder T, Mayer C, Nazet J, Sterner R. Improving enzyme functional annotation by integrating in vitro and in silico approaches: The example of histidinol phosphate phosphatases. Protein Sci 2024; 33:e4899. [PMID: 38284491 PMCID: PMC10804674 DOI: 10.1002/pro.4899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/13/2023] [Accepted: 01/01/2024] [Indexed: 01/30/2024]
Abstract
Advances in sequencing technologies have led to a rapid growth of public protein sequence databases, whereby the fraction of proteins with experimentally verified function continuously decreases. This problem is currently addressed by automated functional annotations with computational tools, which however lack the accuracy of experimental approaches and are susceptible to error propagation. Here, we present an approach that combines the efficiency of functional annotation by in silico methods with the rigor of enzyme characterization in vitro. First, a thorough experimental analysis of a representative enzyme of a group of homologues is performed which includes a focused alanine scan of the active site to determine a fingerprint of function-determining residues. In a second step, this fingerprint is used in combination with a sequence similarity network to identify putative isofunctional enzymes among the homologues. Using this approach in a proof-of-principle study, homologues of the histidinol phosphate phosphatase (HolPase) from Pseudomonas aeruginosa, many of which were annotated as phosphoserine phosphatases, were predicted to be HolPases. This functional annotation of the homologues was verified by in vitro testing of several representatives and an analysis of the occurrence of annotated HolPases in the corresponding phylogenetic groups. Moreover, the application of the same approach to the homologues of the HolPase from the archaeon Nitrosopumilus maritimus, which is not related to the HolPase from P. aeruginosa and was newly discovered in the course of this work, led to the annotation of the putative HolPase from various archaeal species.
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Affiliation(s)
- Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
| | - Carina Mayer
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
| | - Julian Nazet
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for BiochemistryUniversity of RegensburgRegensburgGermany
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3
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Busch MR, Drexler L, Mahato DR, Hiefinger C, Osuna S, Sterner R. Retracing the Rapid Evolution of an Herbicide-Degrading Enzyme by Protein Engineering. ACS Catal 2023; 13:15558-15571. [PMID: 38567019 PMCID: PMC7615792 DOI: 10.1021/acscatal.3c04010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The mechanisms underlying the rapid evolution of novel enzymatic activities from promiscuous side activities are poorly understood. Recently emerged enzymes catalyzing the catabolic degradation of xenobiotic substances that have been spread out into the environment during the last decades provide an exquisite opportunity to study these mechanisms. A prominent example is the herbicide atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine), which is degraded through a number of enzymatic reactions constituting the Atz pathway. Here, we analyzed the evolution of the hydroxyatrazine ethylaminohydrolase AtzB, a Zn(II)-dependent metalloenzyme that adopts the amidohydrolase fold and catalyzes the second step of the Atz pathway. We searched for promiscuous side activities of AtzB, which might point to the identity of its progenitor. These investigations revealed that AtzB has low promiscuous guanine deaminase activity. Furthermore, we found that the two closest AtzB homologues, which have not been functionally annotated up to now, are guanine deaminases with modest promiscuous hydroxyatrazine hydrolase activity. Based on sequence comparisons with the closest AtzB homologues, the guanine deaminase activity of AtzB could be increased by three orders of magnitude through the introduction of only four active site mutations. Interestingly, introducing the inverse four mutations into the AtzB homologues significantly enhanced their hydroxyatrazine hydrolase activity, and in one case is even equivalent to that of wild-type AtzB. Molecular dynamics simulations elucidated the structural and molecular basis for the mutation-induced activity changes. The example of AtzB highlights how novel enzymes with high catalytic proficiency can evolve from low promiscuous side activities by only few mutational events within a short period of time.
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Affiliation(s)
- Markus R. Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Lukas Drexler
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Dhani Ram Mahato
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Caroline Hiefinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
- ICREA, Barcelona 08010, Spain
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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4
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Miller J, Urvoas A, Gigant B, Ouldali M, Arteni A, Mesneau A, Valerio-Lepiniec M, Artzner F, Dujardin E, Minard P. Engineering of brick and staple components for ordered assembly of synthetic repeat proteins. J Struct Biol 2023; 215:108012. [PMID: 37567372 DOI: 10.1016/j.jsb.2023.108012] [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: 04/26/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Synthetic ɑRep repeat proteins are engineered as Brick and Staple protein pairs that together self-assemble into helical filaments. In most cases, the filaments spontaneously form supercrystals. Here, we describe an expanded series of ɑRep Bricks designed to stabilize the interaction between consecutive Bricks, to control the length of the assembled multimers, or to alter the spatial distribution of the Staple on the filaments. The effects of these Brick modifications on the assembly, on the final filament structure and on the crystal symmetry are analyzed by biochemical methods, electron microscopy and small angle X-ray scattering. We further extend the concept of Brick/Staple protein origami by designing a new type of "Janus"-like Brick protein that is equally assembled by orthogonal staples binding its inner or outer surfaces and thus ending inside or outside the filaments. The relative roles of longitudinal and lateral associations in the assembly process are discussed. This set of results demonstrates important proofs-of-principle for engineering these remarkably versatile proteins toward nanometer-to-micron scale constructions.
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Affiliation(s)
- Jessalyn Miller
- Emory University Department of Chemistry, 1515 Dickey Drive, Atlanta, GA 30322, USA(1); Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Benoit Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Ana Arteni
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agnes Mesneau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Franck Artzner
- Institut de Physique de Rennes (IPR), CNRS, UMR 6251, Université de Rennes 1, F-35042 Rennes, France
| | - Erik Dujardin
- Laboratoire Interdisciplinaire Carnot de Bourgogne, CNRS UMR 6303, Université de Bourgogne Franche-Comté, 21000 Dijon, France.
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France.
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5
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Klein T, Funke F, Rossbach O, Lehmann G, Vockenhuber M, Medenbach J, Suess B, Meister G, Babinger P. Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli. Int J Mol Sci 2023; 24:11536. [PMID: 37511294 PMCID: PMC10380284 DOI: 10.3390/ijms241411536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
An open research field in cellular regulation is the assumed crosstalk between RNAs, metabolic enzymes, and metabolites, also known as the REM hypothesis. High-throughput assays have produced extensive interactome data with metabolic enzymes frequently found as hits, but only a few examples have been biochemically validated, with deficits especially in prokaryotes. Therefore, we rationally selected nineteen Escherichia coli enzymes from such datasets and examined their ability to bind RNAs using two complementary methods, iCLIP and SELEX. Found interactions were validated by EMSA and other methods. For most of the candidates, we observed no RNA binding (12/19) or a rather unspecific binding (5/19). Two of the candidates, namely glutamate-5-kinase (ProB) and quinone oxidoreductase (QorA), displayed specific and previously unknown binding to distinct RNAs. We concentrated on the interaction of QorA to the mRNA of yffO, a grounded prophage gene, which could be validated by EMSA and MST. Because the physiological function of both partners is not known, the biological relevance of this interaction remains elusive. Furthermore, we found novel RNA targets for the MS2 phage coat protein that served us as control. Our results indicate that RNA binding of metabolic enzymes in procaryotes is less frequent than suggested by the results of high-throughput studies, but does occur.
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Affiliation(s)
- Thomas Klein
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Franziska Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Michael Vockenhuber
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Jan Medenbach
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Beatrix Suess
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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6
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Busch MR, Rajendran C, Sterner R. Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli. Biochemistry 2023; 62:863-872. [PMID: 36599150 DOI: 10.1021/acs.biochem.2c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli, which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 Å and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number (kcat) and/or the Michaelis constant (KM). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.
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Affiliation(s)
- Markus R Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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7
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Kinateder T, Drexler L, Straub K, Merkl R, Sterner R. Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis. Protein Sci 2023; 32:e4536. [PMID: 36502290 PMCID: PMC9798254 DOI: 10.1002/pro.4536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from γ-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d-glycero-d-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d-glycero-d-manno-heptose-1,7-bisphosphate (αHBP or βHBP) with a strong preference for one anomer (αGmhB or βGmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for βHBP but not αHBP, while βGmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of αGmhBs, βGmhBs, and HisB-N sequences revealed that HisB-Ns form a compact subcluster derived from βGmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous βGmhB from δ- to γ-Proteobacteria where it evolved to the modern HisB-N.
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Affiliation(s)
- Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Lukas Drexler
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of RegensburgRegensburgGermany
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8
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Kropp C, Straub K, Linde M, Babinger P. Hexamerization and thermostability emerged very early during geranylgeranylglyceryl phosphate synthase evolution. Protein Sci 2020; 30:583-596. [PMID: 33342010 PMCID: PMC7888582 DOI: 10.1002/pro.4016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
A large number of archaea live in hyperthermophilic environments. In consequence, their proteins need to adopt to these harsh conditions, including the enzymes that catalyze the synthesis of their membrane ether lipids. The enzyme that catalyzes the formation of the first ether bond in these lipids, geranylgeranylglyceryl phosphate synthase (GGGPS), exists as a hexamer in many hyperthermophilic archaea, and a recent study suggested that hexamerization serves for a fine‐tuning of the flexibility – stability trade‐off under hyperthermophilic conditions. We have recently reconstructed the sequences of ancestral group II GGGPS enzymes and now present a detailed biochemical characterization of nine of these predecessors, which allowed us to trace back the evolution of hexameric GGGPS and to draw conclusions about the properties of extant GGGPS branches that were not accessible to experiments up to now. Almost all ancestral GGGPS proteins formed hexamers, which demonstrates that hexamerization is even more widespread among the GGGPS family than previously assumed. Furthermore, all experimentally studied ancestral proteins showed high thermostability. Our results indicate that the hexameric oligomerization state and thermostability were present very early during the evolution of group II GGGPS, while the fine tuning of the flexibility – stability trade‐off developed very late, independent of the emergence of hexamerization.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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9
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Hertle R, Nazet J, Semmelmann F, Schlee S, Funke F, Merkl R, Sterner R. Reprogramming the Specificity of a Protein Interface by Computational and Data-Driven Design. Structure 2020; 29:292-304.e3. [PMID: 33296666 DOI: 10.1016/j.str.2020.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/21/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
The formation of specific protein complexes in a cell is a non-trivial problem given the co-existence of thousands of different polypeptide chains. A particularly difficult case are two glutamine amidotransferase complexes (anthranilate synthase [AS] and aminodeoxychorismate synthase [ADCS]), which are composed of homologous pairs of synthase and glutaminase subunits. We have attempted to identify discriminating interface residues of the glutaminase subunit TrpG from AS, which are responsible for its specific interaction with the synthase subunit TrpEx and prevent binding to the closely related synthase subunit PabB from ADCS. For this purpose, TrpG-specific interface residues were grafted into the glutaminase subunit PabA from ADCS by two different approaches, namely a computational and a data-driven one. Both approaches resulted in PabA variants that bound TrpEx with higher affinity than PabB. Hence, we have accomplished a reprogramming of protein-protein interaction specificity that provides insights into the evolutionary adaptation of protein interfaces.
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Affiliation(s)
- Regina Hertle
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Julian Nazet
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Florian Semmelmann
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Franziska Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany.
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany.
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10
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Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction. Proc Natl Acad Sci U S A 2019; 117:346-354. [PMID: 31871208 DOI: 10.1073/pnas.1912132117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tryptophan synthase (TS) is a heterotetrameric αββα complex. It is characterized by the channeling of the reaction intermediate indole and the mutual activation of the α-subunit TrpA and the β-subunit TrpB via a complex allosteric network. We have analyzed this allosteric network by means of ancestral sequence reconstruction (ASR), which is an in silico method to resurrect extinct ancestors of modern proteins. Previously, the sequences of TrpA and TrpB from the last bacterial common ancestor (LBCA) have been computed by means of ASR and characterized. LBCA-TS is similar to modern TS by forming a αββα complex with indole channeling taking place. However, LBCA-TrpA allosterically decreases the activity of LBCA-TrpB, whereas, for example, the modern ncTrpA from Neptuniibacter caesariensis allosterically increases the activity of ncTrpB. To identify amino acid residues that are responsible for this inversion of the allosteric effect, all 6 evolutionary TrpA and TrpB intermediates that stepwise link LBCA-TS with ncTS were characterized. Remarkably, the switching from TrpB inhibition to TrpB activation by TrpA occurred between 2 successive TS intermediates. Sequence comparison of these 2 intermediates and iterative rounds of site-directed mutagenesis allowed us to identify 4 of 413 residues from TrpB that are crucial for its allosteric activation by TrpA. The effect of our mutational studies was rationalized by a community analysis based on molecular dynamics simulations. Our findings demonstrate that ancestral sequence reconstruction can efficiently identify residues contributing to allosteric signal propagation in multienzyme complexes.
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11
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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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12
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Kneuttinger AC, Zwisele S, Straub K, Bruckmann A, Busch F, Kinateder T, Gaim B, Wysocki VH, Merkl R, Sterner R. Light-Regulation of Tryptophan Synthase by Combining Protein Design and Enzymology. Int J Mol Sci 2019; 20:E5106. [PMID: 31618845 PMCID: PMC6829457 DOI: 10.3390/ijms20205106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 01/24/2023] Open
Abstract
The spatiotemporal control of enzymes by light is of growing importance for industrial biocatalysis. Within this context, the photo-control of allosteric interactions in enzyme complexes, common to practically all metabolic pathways, is particularly relevant. A prominent example of a metabolic complex with a high application potential is tryptophan synthase from Salmonella typhimurium (TS), in which the constituting TrpA and TrpB subunits mutually stimulate each other via a sophisticated allosteric network. To control TS allostery with light, we incorporated the unnatural amino acid o-nitrobenzyl-O-tyrosine (ONBY) at seven strategic positions of TrpA and TrpB. Initial screening experiments showed that ONBY in position 58 of TrpA (aL58ONBY) inhibits TS activity most effectively. Upon UV irradiation, ONBY decages to tyrosine, largely restoring the capacity of TS. Biochemical characterization, extensive steady-state enzyme kinetics, and titration studies uncovered the impact of aL58ONBY on the activities of TrpA and TrpB and identified reaction conditions under which the influence of ONBY decaging on allostery reaches its full potential. By applying those optimal conditions, we succeeded to directly light-activate TS(aL58ONBY) by a factor of ~100. Our findings show that rational protein design with a photo-sensitive unnatural amino acid combined with extensive enzymology is a powerful tool to fine-tune allosteric light-activation of a central metabolic enzyme complex.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Stefanie Zwisele
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Barbara Gaim
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
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13
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Kneuttinger AC, Straub K, Bittner P, Simeth NA, Bruckmann A, Busch F, Rajendran C, Hupfeld E, Wysocki VH, Horinek D, König B, Merkl R, Sterner R. Light Regulation of Enzyme Allostery through Photo-responsive Unnatural Amino Acids. Cell Chem Biol 2019; 26:1501-1514.e9. [PMID: 31495713 DOI: 10.1016/j.chembiol.2019.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/31/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
Abstract
Imidazole glycerol phosphate synthase (ImGPS) is an allosteric bienzyme complex in which substrate binding to the synthase subunit HisF stimulates the glutaminase subunit HisH. To control this stimulation with light, we have incorporated the photo-responsive unnatural amino acids phenylalanine-4'-azobenzene (AzoF), o-nitropiperonyl-O-tyrosine (NPY), and methyl-o-nitropiperonyllysine (mNPK) at strategic positions of HisF. The light-mediated isomerization of AzoF at position 55 (fS55AzoFE ↔ fS55AzoFZ) resulted in a reversible 10-fold regulation of HisH activity. The light-mediated decaging of NPY at position 39 (fY39NPY → fY39) and of mNPK at position 99 (fK99mNPK → fK99) led to a 4- to 6-fold increase of HisH activity. Molecular dynamics simulations explained how the unnatural amino acids interfere with the allosteric machinery of ImGPS and revealed additional aspects of HisH stimulation in wild-type ImGPS. Our findings show that unnatural amino acids can be used as a powerful tool for the spatiotemporal control of a central metabolic enzyme complex by light.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Philipp Bittner
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Nadja A Simeth
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany; Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Enrico Hupfeld
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dominik Horinek
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Burkhard König
- Institute of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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14
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Semmelmann F, Kabeya N, Malcicka M, Bruckmann A, Broschwitz B, Straub K, Merkl R, Monroig O, Sterner R, Ruther J, Ellers J. Functional characterisation of two Δ12-desaturases demonstrates targeted production of linoleic acid as pheromone precursor in Nasonia. ACTA ACUST UNITED AC 2019; 222:jeb.201038. [PMID: 31019064 DOI: 10.1242/jeb.201038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/18/2019] [Indexed: 01/08/2023]
Abstract
Insect pheromones are often derived from fatty acid metabolism. Fatty acid desaturases, enzymes introducing double bonds into fatty acids, are crucial for the biosynthesis of these chemical signals. Δ12-desaturases catalyse the biosynthesis of linoleic acid by introducing a second double bond into oleic acid, but have been identified in only a few animal species. Here, we report the functional characterisation of two Δ12-desaturases, Nvit_D12a and Nvit_D12b, from the parasitic wasp Nasonia vitripennis. We demonstrate that Nvit_D12a is expressed in the rectal vesicle of males where they produce a linoleic acid-derived sex pheromone to attract virgin females. 13C-labelling experiments with Urolepis rufipes, a closely related species belonging to the 'Nasonia group', revealed that females, but not males, are able to synthesise linoleic acid. U. rufipes males produce an isoprenoid sex pheromone in the same gland and do not depend on linoleic acid for pheromone production. This suggests that Δ12-desaturases are common in the 'Nasonia group', but acquired a specialised function in chemical communication of those species that use linoleic acid as a pheromone precursor. Phylogenetic analysis suggests that insect Δ12-desaturases have evolved repeatedly from Δ9-desaturases in different insect taxa. Hence, insects have developed a way to produce linoleic acid independent of the omega desaturase subfamily which harbours all of the eukaryotic Δ12-desaturases known so far.
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Affiliation(s)
- Florian Semmelmann
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Naoki Kabeya
- Department of Aquatic Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Miriama Malcicka
- Department of Ecological Sciences, Vrije Universiteit, Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Bastian Broschwitz
- Institute of Zoology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Oscar Monroig
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), Ribera de Cabanes 12595, Spain
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Joachim Ruther
- Institute of Zoology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Jacintha Ellers
- Department of Ecological Sciences, Vrije Universiteit, Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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15
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Straub K, Linde M, Kropp C, Blanquart S, Babinger P, Merkl R. Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase. Biol Chem 2019; 400:367-381. [PMID: 30763032 DOI: 10.1515/hsz-2018-0344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/07/2018] [Indexed: 11/15/2022]
Abstract
For evolutionary studies, but also for protein engineering, ancestral sequence reconstruction (ASR) has become an indispensable tool. The first step of every ASR protocol is the preparation of a representative sequence set containing at most a few hundred recent homologs whose composition determines decisively the outcome of a reconstruction. A common approach for sequence selection consists of several rounds of manual recompilation that is driven by embedded phylogenetic analyses of the varied sequence sets. For ASR of a geranylgeranylglyceryl phosphate synthase, we additionally utilized FitSS4ASR, which replaces this time-consuming protocol with an efficient and more rational approach. FitSS4ASR applies orthogonal filters to a set of homologs to eliminate outlier sequences and those bearing only a weak phylogenetic signal. To demonstrate the usefulness of FitSS4ASR, we determined experimentally the oligomerization state of eight predecessors, which is a delicate and taxon-specific property. Corresponding ancestors deduced in a manual approach and by means of FitSS4ASR had the same dimeric or hexameric conformation; this concordance testifies to the efficiency of FitSS4ASR for sequence selection. FitSS4ASR-based results of two other ASR experiments were added to the Supporting Information. Program and documentation are available at https://gitlab.bioinf.ur.de/hek61586/FitSS4ASR.
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Affiliation(s)
- Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Samuel Blanquart
- University of Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
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16
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Mapping key amino acid residues for the epimerase efficiency and stereospecificity of the sex pheromone biosynthetic short-chain dehydrogenases/reductases of Nasonia. Sci Rep 2019; 9:330. [PMID: 30674966 PMCID: PMC6344473 DOI: 10.1038/s41598-018-37200-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/05/2018] [Indexed: 11/09/2022] Open
Abstract
Males of the parasitic wasp genus Nasonia use blends of chiral hydroxylactones as sex pheromones to attract conspecific females. Whereas all Nasonia species use a mixture of (4R,5S)-5-hydroxy-4-decanolide (RS) and 4-methylquinazoline (MQ) as sex pheromones, Nasonia vitripennis evolved (4R,5R)-5-hydroxy-4-decanolide (RR) as an extra sex pheromone component. We recently identified and functionally characterized three short-chain dehydrogenases/reductases (SDRs) NV10127, NV10128, and NV10129 that are capable of catalyzing the epimerization of RS to RR via (4R)-5-oxo-4-decanolide (ODL) as intermediate. Despite their very high sequence identities of 88-98%, these proteins differ drastically in their ability to epimerize RS to RR and in their stereoselectivity when reducing ODL to RR/RS. Here, in order to unravel the sequence differences underlying these varying functional properties of NV1027, NV10128 and NV10129, we created chimeras of the three enzymes and monitored their catalytic activities in vitro. The results show that a few amino acid changes at the C-termini and active sites of Nasonia vitripennis SDRs lead to substantially altered RS to RR epimerization and ODL-reduction activities. Thus, our study adds to the understanding of pheromone evolution by showing that subtle mutations in key biosynthetic enzymes can result in drastic effects on the composition of chemical signals.
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