1
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Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [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: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
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Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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2
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Coricello A, Nardone AJ, Lupia A, Gratteri C, Vos M, Chaptal V, Alcaro S, Zhu W, Takagi Y, Richards NGJ. Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.16.541009. [PMID: 37292727 PMCID: PMC10245805 DOI: 10.1101/2023.05.16.541009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
How motions in enzymes might be linked to catalytic function is of considerable general interest. Recent advances in X-ray crystallography and cryogenic electron microscopy offer the promise of elucidating functionally relevant motions in proteins that are not easily amenable to study by other biophysical methods. Here we use 3D variability analysis (3DVA) on cryo-EM maps for wild type (WT) human asparagine synthetase (ASNS) and the R142I ASNS variant to identify conformational changes in the Arg-142 side chain, which mediates the formation of a catalytically relevant intramolecular tunnel. Our 3DVA results for WT ASNS are consistent with independent molecular dynamics (MD) simulations on a model generated from the X-ray structure of human ASNS. Moreover, MD simulations of computational models for the ASNS/β-aspartyl-AMP/MgPPi and R142I/β-aspartyl-AMP/MgPPi ternary complexes, suggest that the structural integrity of the tunnel is impaired in the R142I variant when β-aspartyl-AMP is present in the synthetase active site. The kinetic properties of the R142I ASNS variant support the proposed function of Arg-142. These studies illustrate the power of cryo-EM to identify localized motions and dissect the conformational landscape of large proteins. When combined with MD simulations, 3DVA is a powerful approach to understanding how conformational dynamics might regulate function in multi-domain enzymes possessing multiple active sites.
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Affiliation(s)
- Adriana Coricello
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - Alanya J Nardone
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Antonio Lupia
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, 09042 Cagliari, Italy
| | - Carmen Gratteri
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Matthijn Vos
- NanoImaging Core Facility, Centre de Resources et Recherches Technologiques, Institut Pasteur, 75015 Paris, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, 69367 Lyon, France
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Wen Zhu
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Yuichiro Takagi
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
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3
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Li JY, Si DH, Mi FQ, Xu WL, Zhang T, Cao R. A Bioinspired Copper-Pair Catalyst in Metal-Organic Frameworks for Molecular Dioxygen Activation and Aerobic Oxidative C-N Coupling. J Am Chem Soc 2024; 146:12444-12453. [PMID: 38680118 DOI: 10.1021/jacs.3c14794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Open Cu sites were loaded to the UiO-67 metal-organic framework (MOF) skeleton by introduction of flexible Cu-binding pyridylmethylamine (pyma) side chains to the biphenyldicarboxylate linkers. Distance between Cu centers in the MOF pores was tuned by controlling the density of metal-binding side chains. "Interacted" Cu-pair or "isolated" monomeric Cu sites were achieved with high and low (pyma)Cu side chain loading, respectively. Spectroscopic and theoretical studies indicate that "interacted" Cu pairs can effectively bind and activate molecular dioxygen to form Cu2O2 clusters, which showed high catalytic activity for aerobic oxidative C-N coupling. On the contrary, MOF catalyst bearing isolated monomeric Cu sites only showed modest catalytic activity. Enhancement in catalytic performance for the Cu-pair catalyst is attributed to the remote synergistic effect of the paired Cu site, which binds molecular dioxygen and cleaves the O═O bond in a collaborative manner. This work demonstrates that noncovalently interacted metal-pair sites can effectively activate inert small molecules and promote heterogeneous catalytic processes.
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Affiliation(s)
- Jun-Yu Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Duan-Hui Si
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian Science and Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, China
| | - Fu-Qi Mi
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang-Lan Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian College, University of the Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, China
| | - Teng Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Fujian College, University of the Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Rong Cao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Fujian Science and Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, China
- Fujian College, University of the Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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4
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Fang T, Szklarczyk D, Hachilif R, von Mering C. Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration. Sci Rep 2024; 14:6009. [PMID: 38472223 PMCID: PMC10933411 DOI: 10.1038/s41598-024-55655-9] [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: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made: how to ensure the reliable identification of orthologs, and how to optimally balance the need for large alignments versus sufficient alignment quality. Here, we propose a divide-and-conquer strategy for MSA generation: instead of building a single, large alignment for each protein, multiple distinct alignments are constructed under distinct clades in the tree of life. Coevolutionary signals are searched separately within these clades, and are only subsequently integrated using machine learning techniques. We find that this strategy markedly improves overall prediction performance, concomitant with better alignment quality. Using the popular DCA algorithm to systematically search pairs of such alignments, a genome-wide all-against-all interaction scan in a bacterial genome is demonstrated. Given the recent successes of AlphaFold in predicting direct PPIs at atomic detail, a discover-and-refine approach is proposed: our method could provide a fast and accurate strategy for pre-screening the entire genome, submitting to AlphaFold only promising interaction candidates-thus reducing false positives as well as computation time.
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Affiliation(s)
- Tao Fang
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Damian Szklarczyk
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Radja Hachilif
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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5
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Rai R, Samanta D, Goh KM, Chadha BS, Sani RK. Biochemical unravelling of the endoxylanase activity in a bifunctional GH39 enzyme cloned and expressed from thermophilic Geobacillus sp. WSUCF1. Int J Biol Macromol 2024; 257:128679. [PMID: 38072346 DOI: 10.1016/j.ijbiomac.2023.128679] [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: 06/13/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024]
Abstract
The glycoside hydrolase family 39 (GH39) proteins are renowned for their extremophilic and multifunctional enzymatic properties, yet the molecular mechanisms underpinning these unique characteristics continue to be an active subject of research. In this study, we introduce WsuXyn, a GH39 protein with a molecular weight of 58 kDa, originating from the thermophilic Geobacillus sp. WSUCF1. Previously reported for its exceptional thermostable β-xylosidase activity, WsuXyn has recently demonstrated a significant endoxylanase activity (3752 U·mg-1) against beechwood xylan, indicating towards its bifunctional nature. Physicochemical characterization revealed that WsuXyn exhibits optimal endoxylanase activity at 70 °C and pH 7.0. Thermal stability assessments revealed that the enzyme is resilient to elevated temperatures, with a half-life of 168 h. Key kinetic parameters highlight the exceptional catalytic efficiency and strong affinity of the protein for xylan substrate. Moreover, WsuXyn-mediated hydrolysis of beechwood xylan has achieved 77 % xylan conversion, with xylose as the primary product. Structural analysis, amalgamated with docking simulations, has revealed strong binding forces between xylotetraose and the protein, with key amino acid residues, including Glu278, Tyr230, Glu160, Gly202, Cys201, Glu324, and Tyr283, playing pivotal roles in these interactions. Therefore, WsuXyn holds a strong promise for biodegradation and value-added product generation through lignocellulosic biomass conversion.
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Affiliation(s)
- Rohit Rai
- Faculty of Applied Medical Sciences, Lovely Professional University, Phagwara 144411, India.
| | - Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia
| | | | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; BuG ReMeDEE consortium and Composite and Nanocomposite Advanced Manufacturing Centre/Biomaterials (CNAM/Bio), Rapid City, SD 57701, USA.
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6
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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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7
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Diaz-Bárcena A, Fernandez-Pacios L, Giraldo P. Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L. Biomolecules 2023; 14:2. [PMID: 38275743 PMCID: PMC10813097 DOI: 10.3390/biom14010002] [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: 11/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
REPI is a pivotal point enzyme in plant benzylisoquinoline alkaloid metabolism as it promotes the evolution of the biosynthetic branch of morphinan alkaloids. Experimental studies of its activity led to the identification of two modules (DRS and DRR) that catalyze two sequential steps of the epimerization of (S)- to (R)-reticuline. Recently, special attention has been paid to its genetic characterization and evolutionary history, but no structural analyses of the REPI protein have been conducted to date. We present here a computational structural characterization of REPI with heme and NADP cofactors in the apo state and in three complexes with substrate (S)-reticuline in DRS and intermediate 1,2-dehydroreticuline in DRS and in DRR. Since no experimental structure exists for REPI, we used its AlphaFold model as a scaffold to build up these four systems, which were submitted to all-atom molecular dynamics (MD) simulations. A comparison of MD results for the four systems revealed key dynamic changes associated with cofactor and ligand binding and provided a dynamic picture of the evolution of their structures and interactions. We also explored the possible dynamic occurrence of tunnels and electrostatic highways potentially involved in alternative mechanisms for channeling the intermediate from DRS to DRR.
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Affiliation(s)
- Alba Diaz-Bárcena
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (L.F.-P.); (P.G.)
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8
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Heinks T, Koopmeiners S, Montua N, Sewald N, Höhne M, Bornscheuer UT, Fischer von Mollard G. Co-Immobilization of a Multi-Enzyme Cascade: (S)-Selective Amine Transaminases, l-Amino Acid Oxidase and Catalase. Chembiochem 2023; 24:e202300425. [PMID: 37368451 DOI: 10.1002/cbic.202300425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 06/28/2023]
Abstract
An enzyme cascade was established previously consisting of a recycling system with an l-amino acid oxidase (hcLAAO4) and a catalase (hCAT) for different α-keto acid co-substrates of (S)-selective amine transaminases (ATAs) in kinetic resolutions of racemic amines. Only 1 mol % of the co-substrate was required and l-amino acids instead of α-keto acids could be applied. However, soluble enzymes cannot be reused easily. Immobilization of hcLAAO4, hCAT and the (S)-selective ATA from Vibrio fluvialis (ATA-Vfl) was addressed here. Immobilization of the enzymes together rather than on separate beads showed higher reaction rates most likely due to fast co-substrate channeling between ATA-Vfl and hcLAAO4 due to their close proximity. Co-immobilization allowed further reduction of the co-substrate amount to 0.1 mol % most likely due to a more efficient H2 O2 -removal caused by the stabilized hCAT and its proximity to hcLAAO4. Finally, the co-immobilized enzyme cascade was reused in 3 cycles of preparative kinetic resolutions to produce (R)-1-PEA with high enantiomeric purity (97.3 %ee). Further recycling was inefficient due to the instability of ATA-Vfl, while hcLAAO4 and hCAT revealed high stability. An engineered ATA-Vfl-8M was used in the co-immobilized enzyme cascade to produce (R)-1-(3-ethoxy-4-methoxyphenyl)-2-(methylsulfonyl)ethanamine, an apremilast-intermediate, with a 1,000 fold lower input of the co-substrate.
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Affiliation(s)
- Tobias Heinks
- Faculty of Chemistry, Biochemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Simon Koopmeiners
- Faculty of Chemistry, Biochemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Nicolai Montua
- Faculty of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Norbert Sewald
- Faculty of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Matthias Höhne
- Department of Chemistry/Biocatalysis, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix Hausdorff-Str. 4, 17487, Greifswald, Germany
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9
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Khusnutdinova AN, Batyrova KA, Brown G, Fedorchuk T, Chai YS, Skarina T, Flick R, Petit AP, Savchenko A, Stogios P, Yakunin AF. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J 2023; 290:4966-4983. [PMID: 37437000 DOI: 10.1111/febs.16903] [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: 05/18/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
Fluorine forms the strongest single bond to carbon with the highest bond dissociation energy among natural products. However, fluoroacetate dehalogenases (FADs) have been shown to hydrolyze this bond in fluoroacetate under mild reaction conditions. Furthermore, two recent studies demonstrated that the FAD RPA1163 from Rhodopseudomonas palustris can also accept bulkier substrates. In this study, we explored the substrate promiscuity of microbial FADs and their ability to defluorinate polyfluorinated organic acids. Enzymatic screening of eight purified dehalogenases with reported fluoroacetate defluorination activity revealed significant hydrolytic activity against difluoroacetate in three proteins. Product analysis using liquid chromatography-mass spectrometry identified glyoxylic acid as the final product of enzymatic DFA defluorination. The crystal structures of DAR3835 from Dechloromonas aromatica and NOS0089 from Nostoc sp. were determined in the apo-state along with the DAR3835 H274N glycolyl intermediate. Structure-based site-directed mutagenesis of DAR3835 demonstrated a key role for the catalytic triad and other active site residues in the defluorination of both fluoroacetate and difluoroacetate. Computational analysis of the dimer structures of DAR3835, NOS0089, and RPA1163 indicated the presence of one substrate access tunnel in each protomer. Moreover, protein-ligand docking simulations suggested similar catalytic mechanisms for the defluorination of both fluoroacetate and difluoroacetate, with difluoroacetate being defluorinated via two consecutive defluorination reactions producing glyoxylate as the final product. Thus, our findings provide molecular insights into substrate promiscuity and catalytic mechanism of FADs, which are promising biocatalysts for applications in synthetic chemistry and bioremediation of fluorochemicals.
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Affiliation(s)
- Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Khorcheska A Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Fedorchuk
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Yao Sheng Chai
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Health Research Innovation Centre, University of Calgary, AB, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, UK
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10
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Kumar S, Sega S, Lynn-Barbe JK, Harris DL, Koehn JT, Crans DC, Crick DC. Proline Dehydrogenase and Pyrroline 5 Carboxylate Dehydrogenase from Mycobacterium tuberculosis: Evidence for Substrate Channeling. Pathogens 2023; 12:1171. [PMID: 37764979 PMCID: PMC10537722 DOI: 10.3390/pathogens12091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
In Mycobacterium tuberculosis, proline dehydrogenase (PruB) and ∆1-pyrroline-5-carboxylate (P5C) dehydrogenase (PruA) are monofunctional enzymes that catalyze proline oxidation to glutamate via the intermediates P5C and L-glutamate-γ-semialdehyde. Both enzymes are essential for the replication of pathogenic M. tuberculosis. Highly active enzymes were expressed and purified using a Mycobacterium smegmatis expression system. The purified enzymes were characterized using natural substrates and chemically synthesized analogs. The structural requirements of the quinone electron acceptor were examined. PruB displayed activity with all tested lipoquinone analogs (naphthoquinone or benzoquinone). In PruB assays utilizing analogs of the native naphthoquinone [MK-9 (II-H2)] specificity constants Kcat/Km were an order of magnitude greater for the menaquinone analogs than the benzoquinone analogs. In addition, mycobacterial PruA was enzymatically characterized for the first time using exogenous chemically synthesized P5C. A Km value of 120 ± 0.015 µM was determined for P5C, while the Km value for NAD+ was shown to be 33 ± 4.3 µM. Furthermore, proline competitively inhibited PruA activity and coupled enzyme assays, suggesting that the recombinant purified monofunctional PruB and PruA enzymes of M. tuberculosis channel substrate likely increase metabolic flux and protect the bacterium from methylglyoxal toxicity.
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Affiliation(s)
- Santosh Kumar
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Steven Sega
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Jamie K. Lynn-Barbe
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Dannika L. Harris
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
| | - Jordan T. Koehn
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA;
| | - Debbie C. Crans
- Chemistry Department, Colorado State University, Fort Collins, CO 80523-1682, USA;
| | - Dean C. Crick
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA; (S.K.)
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11
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Suremann NF, McCarthy BD, Gschwind W, Kumar A, Johnson BA, Hammarström L, Ott S. Molecular Catalysis of Energy Relevance in Metal-Organic Frameworks: From Higher Coordination Sphere to System Effects. Chem Rev 2023; 123:6545-6611. [PMID: 37184577 DOI: 10.1021/acs.chemrev.2c00587] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The modularity and synthetic flexibility of metal-organic frameworks (MOFs) have provoked analogies with enzymes, and even the term MOFzymes has been coined. In this review, we focus on molecular catalysis of energy relevance in MOFs, more specifically water oxidation, oxygen and carbon dioxide reduction, as well as hydrogen evolution in context of the MOF-enzyme analogy. Similar to enzymes, catalyst encapsulation in MOFs leads to structural stabilization under turnover conditions, while catalyst motifs that are synthetically out of reach in a homogeneous solution phase may be attainable as secondary building units in MOFs. Exploring the unique synthetic possibilities in MOFs, specific groups in the second and third coordination sphere around the catalytic active site have been incorporated to facilitate catalysis. A key difference between enzymes and MOFs is the fact that active site concentrations in the latter are often considerably higher, leading to charge and mass transport limitations in MOFs that are more severe than those in enzymes. High catalyst concentrations also put a limit on the distance between catalysts, and thus the available space for higher coordination sphere engineering. As transport is important for MOF-borne catalysis, a system perspective is chosen to highlight concepts that address the issue. A detailed section on transport and light-driven reactivity sets the stage for a concise review of the currently available literature on utilizing principles from Nature and system design for the preparation of catalytic MOF-based materials.
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Affiliation(s)
- Nina F Suremann
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Brian D McCarthy
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Wanja Gschwind
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Amol Kumar
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Ben A Johnson
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
- Technical University Munich (TUM), Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315 Straubing, Germany
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Sascha Ott
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
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12
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Multifunctional Enzymes in Microbial Secondary Metabolic Processes. Catalysts 2023. [DOI: 10.3390/catal13030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.
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13
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Mukherjee A, Ashrafi AM, Bytesnikova Z, Svec P, Richtera L, Adam V. An investigation on the multiple roles of CeO2 nanoparticle in electrochemical sensing: biomimetic activity and electron acceptor. J Electroanal Chem (Lausanne) 2023. [DOI: 10.1016/j.jelechem.2023.117301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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14
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Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures. Int J Mol Sci 2022; 23:ijms232315149. [PMID: 36499474 PMCID: PMC9741079 DOI: 10.3390/ijms232315149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.
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15
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Prejanò M, Škerlová J, Stenmark P, Himo F. Reaction Mechanism of Human PAICS Elucidated by Quantum Chemical Calculations. J Am Chem Soc 2022; 144:14258-14268. [PMID: 35914774 PMCID: PMC9376930 DOI: 10.1021/jacs.2c05072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Human PAICS is a bifunctional enzyme that is involved
in the de novo purine biosynthesis, catalyzing the
conversion of
aminoimidazole ribonucleotide (AIR) into N-succinylcarboxamide-5-aminoimidazole
ribonucleotide (SAICAR). It comprises two distinct active sites, AIR
carboxylase (AIRc) where the AIR is initially converted to carboxyaminoimidazole
ribonucleotide (CAIR) by reaction with CO2 and SAICAR synthetase
(SAICARs) in which CAIR then reacts with an aspartate to form SAICAR,
in an ATP-dependent reaction. Human PAICS is a promising target for
the treatment of various types of cancer, and it is therefore of high
interest to develop a detailed understanding of its reaction mechanism.
In the present work, density functional theory calculations are employed
to investigate the PAICS reaction mechanism. Starting from the available
crystal structures, two large models of the AIRc and SAICARs active
sites are built and different mechanistic proposals for the carboxylation
and phosphorylation–condensation mechanisms are examined. For
the carboxylation reaction, it is demonstrated that it takes place
in a two-step mechanism, involving a C–C bond formation followed
by a deprotonation of the formed tetrahedral intermediate (known as
isoCAIR) assisted by an active site histidine residue. For the phosphorylation–condensation
reaction, it is shown that the phosphorylation of CAIR takes place
before the condensation reaction with the aspartate. It is further
demonstrated that the three active site magnesium ions are involved
in binding the substrates and stabilizing the transition states and
intermediates of the reaction. The calculated barriers are in good
agreement with available experimental data.
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Affiliation(s)
- Mario Prejanò
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 160 00 Prague, Czech Republic
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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16
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Ma Y, Zhang N, Vernet G, Kara S. Design of fusion enzymes for biocatalytic applications in aqueous and non-aqueous media. Front Bioeng Biotechnol 2022; 10:944226. [PMID: 35935496 PMCID: PMC9354712 DOI: 10.3389/fbioe.2022.944226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/30/2022] [Indexed: 12/26/2022] Open
Abstract
Biocatalytic cascades play a fundamental role in sustainable chemical synthesis. Fusion enzymes are one of the powerful toolboxes to enable the tailored combination of multiple enzymes for efficient cooperative cascades. Especially, this approach offers a substantial potential for the practical application of cofactor-dependent oxidoreductases by forming cofactor self-sufficient cascades. Adequate cofactor recycling while keeping the oxidized/reduced cofactor in a confined microenvironment benefits from the fusion fashion and makes the use of oxidoreductases in harsh non-aqueous media practical. In this mini-review, we have summarized the application of various fusion enzymes in aqueous and non-aqueous media with a focus on the discussion of linker design within oxidoreductases. The design and properties of the reported linkers have been reviewed in detail. Besides, the substrate loadings in these studies have been listed to showcase one of the key limitations (low solubility of hydrophobic substrates) of aqueous biocatalysis when it comes to efficiency and economic feasibility. Therefore, a straightforward strategy of applying non-aqueous media has been briefly discussed while the potential of using the fusion oxidoreductase of interest in organic media was highlighted.
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Affiliation(s)
- Yu Ma
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Ningning Zhang
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Guillem Vernet
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Selin Kara
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
- *Correspondence: Selin Kara,
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17
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A Nanopore Sensing Assay Resolves Cascade Reactions in a Multienzyme System. Angew Chem Int Ed Engl 2022; 61:e202200866. [DOI: 10.1002/anie.202200866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Indexed: 11/07/2022]
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18
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Petty HR. Enzyme Trafficking and Co-Clustering Precede and Accurately Predict Human Breast Cancer Recurrences: An Interdisciplinary Review. Am J Physiol Cell Physiol 2022; 322:C991-C1010. [PMID: 35385324 DOI: 10.1152/ajpcell.00042.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Although great effort has been expended to understand cancer's origins, less attention has been given to the primary cause of cancer deaths - cancer recurrences and their sequelae. This interdisciplinary review addresses mechanistic features of aggressive cancer by studying metabolic enzyme patterns within ductal carcinoma in situ (DCIS) of the breast lesions. DCIS lesions from patients who did or did not experience a breast cancer recurrence were compared. Several proteins, including phospho-Ser226-glucose transporter type 1, phosphofructokinase type L and phosphofructokinase/fructose 2,6-bisphosphatase type 4 are found in nucleoli of ductal epithelial cells in samples from patients who will not subsequently recur, but traffic to the cell periphery in samples from patients who will experience a cancer recurrence. Large co-clusters of enzymes near plasmalemmata will enhance product formation because enzyme concentrations in clusters are very high while solvent molecules and solutes diffuse through small channels. These structural changes will accelerate aerobic glycolysis. Agglomerations of pentose phosphate pathway and glutathione synthesis enzymes enhance GSH formation. As aggressive cancer lesions are incomplete at early stages, they may be unrecognizable. We have found that machine learning provides superior analyses of tissue images and may be used to identify biomarker patterns associated with recurrent and non-recurrent patients with high accuracy. This suggests a new prognostic test to predict DCIS patients who are likely to recur and those who are at low risk for recurrence. Mechanistic interpretations provide a deeper understanding of anti-cancer drug action and suggest that aggressive metastatic cancer cells are sensitive to reductive chemotherapy.
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Affiliation(s)
- Howard R Petty
- Dept. of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI, United States
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19
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Shon H, Matveeva EA, Jull EC, Hu Y, Coupet TA, Lee YS. Evidence Supporting Substrate Channeling between Domains of Human PAICS: A Time-Course Analysis of 13C-Bicarbonate Incorporation. Biochemistry 2022; 61:575-582. [PMID: 35285625 PMCID: PMC8988938 DOI: 10.1021/acs.biochem.1c00803] [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
Human phosphoribosylaminoimidazole carboxylase phosphoribosylaminoimdiazole succinocarboxamide synthetase (PAICS) is a dual activity enzyme catalyzing two consecutive reactions in de novo purine nucleotide synthesis. Crystallographic structures of recombinant human PAICS suggested the channeling of 4-carboxy-5-aminoimidazole-1-ribose-5'-phosphate (CAIR) between two active sites of PAICS, while a prior work of an avian PAICS suggested otherwise. Here, we present time-course mass spectrometric data supporting the channeling of CAIR between domains of recombinant human PAICS. Time-course mass spectral analysis showed that CAIR added to the bulk solution (CAIRbulk) is decarboxylated and re-carboxylated before the accumulation of succinyl-5-aminoimidazole-4-carboxamide-1-ribose-5'-phosphate (SAICAR). An experiment with 13C-bicarbonate showed that SAICAR production was proportional to re-carboxylated CAIR instead of total CAIR or CAIRbulk. This result indicates that the SAICAR synthase domain selectively uses enzyme-made CAIR over CAIRbulk, which is consistent with the channeling model. This channeling between PAICS domains may be a part of a larger channeling process in de novo purine nucleotide synthesis.
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Affiliation(s)
- Hyungjoo Shon
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Elena A Matveeva
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Ella C Jull
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yijia Hu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tiffany A Coupet
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Young-Sam Lee
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
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20
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Sheng Y, Zhou K, Liu L, Wu HC. A Nanopore Sensing Assay Resolves Cascade Reactions in a Multienzyme System. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yingying Sheng
- Institute of Chemistry CAS: Institute of Chemistry Chinese Academy of Sciences Key laboratory of Analytical Chemistry for Living Biosystems 100191 Beijing CHINA
| | - Ke Zhou
- Institute of Chemistry CAS: Institute of Chemistry Chinese Academy of Sciences Key Laboratory of Analytical Chemistry for Living Biosystems 100191 Beijing CHINA
| | - Lei Liu
- Institute of High Energy Physics Chinese Academy of Sciences Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety CHINA
| | - Hai-Chen Wu
- Institute of Chemistry Chinese Academy of Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Zhongguancun North First Street 2 100190 Beijing CHINA
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21
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Abstract
Over the past fifteen years, we have unveiled a new mechanism by which cells achieve greater efficiency in de novo purine biosynthesis. This mechanism relies on the compartmentalization of de novo purine biosynthetic enzymes into a dynamic complex called the purinosome. In this review, we highlight our current understanding of the purinosome with emphasis on its biophysical properties and function and on the cellular mechanisms that regulate its assembly. We propose a model for functional purinosomes in which they consist of at least ten enzymes that localize near mitochondria and carry out de novo purine biosynthesis by metabolic channeling. We conclude by discussing challenges and opportunities associated with studying the purinosome and analogous metabolons. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Anthony M Pedley
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Vidhi Pareek
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA; .,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA;
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22
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Sharma N, Singh S, Tanwar AS, Mondal J, Anand R. Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nandini Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sukhwinder Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ajay S. Tanwar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Jagannath Mondal
- Centre for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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23
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Kondrat S, von Lieres E. Mechanisms and Effects of Substrate Channelling in Enzymatic Cascades. Methods Mol Biol 2022; 2487:27-50. [PMID: 35687228 DOI: 10.1007/978-1-0716-2269-8_3] [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] [Indexed: 06/15/2023]
Abstract
Substrate or metabolite channelling is a transfer of intermediates produced by one enzyme to the sequential enzyme of a reaction cascade or metabolic pathway, without releasing them entirely into bulk. Despite an enormous effort and more than three decades of research, substrate channelling remains the subject of continuing debates and active investigation. Herein, we review the benefits and mechanisms of substrate channelling in vivo and in vitro. We discuss critically the effects that substrate channelling can have on enzymatic cascades, including speeding up or slowing down reaction cascades and protecting intermediates from sequestration and enzymes' surroundings from toxic or otherwise detrimental intermediates. We also discuss how macromolecular crowding affects substrate channelling and point out the galore of open questions.
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Affiliation(s)
- Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany.
- IV. Institut für Theoretische Physik, Universität Stuttgart, Stuttgart, Germany.
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
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24
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Korasick DA, Christgen SL, Qureshi IA, Becker DF, Tanner JJ. Probing the function of a ligand-modulated dynamic tunnel in bifunctional proline utilization A (PutA). Arch Biochem Biophys 2021; 712:109025. [PMID: 34506758 DOI: 10.1016/j.abb.2021.109025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022]
Abstract
In many bacteria, the reactions of proline catabolism are catalyzed by the bifunctional enzyme known as proline utilization A (PutA). PutA catalyzes the two-step oxidation of l-proline to l-glutamate using distinct proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH) active sites, which are separated by over 40 Å and connected by a complex tunnel system. The tunnel system consists of a main tunnel that connects the two active sites and functions in substrate channeling, plus six ancillary tunnels whose functions are unknown. Here we used tunnel-blocking mutagenesis to probe the role of a dynamic ancillary tunnel (tunnel 2a) whose shape is modulated by ligand binding to the PRODH active site. The 1.90 Å resolution crystal structure of Geobacter sulfurreducens PutA variant A206W verified that the side chain of Trp206 cleanly blocks tunnel 2a without perturbing the surrounding structure. Steady-state kinetic measurements indicate the mutation impaired PRODH activity without affecting the GSALDH activity. Single-turnover experiments corroborated a severe impairment of PRODH activity with flavin reduction decreased by nearly 600-fold in A206W relative to wild-type. Substrate channeling is also significantly impacted as A206W exhibited a 3000-fold lower catalytic efficiency in coupled PRODH-GSALDH activity assays, which measure NADH formation as a function of proline. The structure suggests that Trp206 inhibits binding of the substrate l-proline by preventing the formation of a conserved glutamate-arginine ion pair and closure of the PRODH active site. Our data are consistent with tunnel 2a serving as an open space through which the glutamate of the ion pair travels during the opening and closing of the active site in response to binding l-proline. These results confirm the essentiality of the conserved ion pair in binding l-proline and support the hypothesis that the ion pair functions as a gate that controls access to the PRODH active site.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Shelbi L Christgen
- Department Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - Insaf A Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Donald F Becker
- Department Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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25
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Eisele BS, Luka Z, Wu AJ, Yang F, Hale AT, York JD. Sulfation of glycosaminoglycans depends on the catalytic activity of lithium-inhibited phosphatase BPNT2 in vitro. J Biol Chem 2021; 297:101293. [PMID: 34634304 PMCID: PMC8551643 DOI: 10.1016/j.jbc.2021.101293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 01/02/2023] Open
Abstract
Golgi-resident bisphosphate nucleotidase 2 (BPNT2) is a member of a family of magnesium-dependent, lithium-inhibited phosphatases that share a three-dimensional structural motif that directly coordinates metal binding to effect phosphate hydrolysis. BPNT2 catalyzes the breakdown of 3'-phosphoadenosine-5'-phosphate, a by-product of glycosaminoglycan (GAG) sulfation. KO of BPNT2 in mice leads to skeletal abnormalities because of impaired GAG sulfation, especially chondroitin-4-sulfation, which is critical for proper extracellular matrix development. Mutations in BPNT2 have also been found to underlie a chondrodysplastic disorder in humans. The precise mechanism by which the loss of BPNT2 impairs sulfation remains unclear. Here, we used mouse embryonic fibroblasts (MEFs) to test the hypothesis that the catalytic activity of BPNT2 is required for GAG sulfation in vitro. We show that a catalytic-dead Bpnt2 construct (D108A) does not rescue impairments in intracellular or secreted sulfated GAGs, including decreased chondroitin-4-sulfate, present in Bpnt2-KO MEFs. We also demonstrate that missense mutations in Bpnt2 adjacent to the catalytic site, which are known to cause chondrodysplasia in humans, recapitulate defects in overall GAG sulfation and chondroitin-4-sulfation in MEF cultures. We further show that treatment of MEFs with lithium (a common psychotropic medication) inhibits GAG sulfation and that this effect depends on the presence of BPNT2. Taken together, this work demonstrates that the catalytic activity of an enzyme potently inhibited by lithium can modulate GAG sulfation and therefore extracellular matrix composition, revealing new insights into lithium pharmacology.
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Affiliation(s)
- Brynna S Eisele
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Alice J Wu
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Fei Yang
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Andrew T Hale
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - John D York
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
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26
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Ronnebaum TA, Eaton SA, Brackhahn EAE, Christianson DW. Engineering the Prenyltransferase Domain of a Bifunctional Assembly-Line Terpene Synthase. Biochemistry 2021; 60:3162-3172. [PMID: 34609847 DOI: 10.1021/acs.biochem.1c00600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Copalyl diphosphate (CPP) synthase from Penicillium verruculosum (PvCPS) is a bifunctional diterpene synthase with both prenyltransferase and class II cyclase activities. The prenyltransferase α domain catalyzes the condensation of C5 dimethylallyl diphosphate with three successively added C5 isopentenyl diphosphates (IPPs) to form C20 geranylgeranyl diphosphate (GGPP), which then undergoes a class II cyclization reaction at the βγ domain interface to generate CPP. The prenyltransferase α domain mediates oligomerization to form a 648-kD (αβγ)6 hexamer. In the current study, we explore prenyltransferase structure-function relationships in this oligomeric assembly-line platform with the goal of generating alternative linear isoprenoid products. Specifically, we report steady-state enzyme kinetics, product analysis, and crystal structures of various site-specific variants of the prenyltransferase α domain. Crystal structures of the H786A, F760A, S723Y, S723F, and S723T variants have been determined at resolutions of 2.80, 3.10, 3.15, 2.65, and 2.00 Å, respectively. The substitution of S723 with bulky aromatic amino acids in the S723Y and S723F variants constricts the active site, thereby directing the formation of the shorter C15 isoprenoid, farnesyl diphosphate. While the S723T substitution only subtly alters enzyme kinetics and does not compromise GGPP biosynthesis, the crystal structure of this variant reveals a nonproductive binding mode for IPP that likely accounts for substrate inhibition at high concentrations. Finally, mutagenesis of the catalytic general acid in the class II cyclase domain, D313A, significantly compromises prenyltransferase activity. This result suggests molecular communication between the prenyltransferase and cyclase domains despite their distant connection by a flexible polypeptide linker.
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Affiliation(s)
- Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Samuel A Eaton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Emily A E Brackhahn
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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27
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Pareek V, Sha Z, He J, Wingreen NS, Benkovic SJ. Metabolic channeling: predictions, deductions, and evidence. Mol Cell 2021; 81:3775-3785. [PMID: 34547238 PMCID: PMC8485759 DOI: 10.1016/j.molcel.2021.08.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 12/19/2022]
Abstract
With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks operate with maximal catalytic efficiency and minimal interference? A logical answer was the postulate of metabolic channeling, which in its simplest embodiment assumes that the product generated by one enzyme passes directly to a second without diffusion into the surrounding medium. This tight coupling of activities might increase a pathway's metabolic flux and/or serve to sequester unstable/toxic/reactive intermediates as well as prevent their access to other networks. Here, we present evidence for this concept, commencing with enzymes that feature a physical molecular tunnel, to multi-enzyme complexes that retain pathway substrates through electrostatics or enclosures, and finally to metabolons that feature collections of enzymes assembled into clusters with variable stoichiometric composition. Lastly, we discuss the advantages of reversibly assembled metabolons in the context of the purinosome, the purine biosynthesis metabolon.
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Affiliation(s)
- Vidhi Pareek
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhou Sha
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Jingxuan He
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ned S Wingreen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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28
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Omidvar M, Zdarta J, Sigurdardóttir SB, Pinelo M. Mimicking natural strategies to create multi-environment enzymatic reactors: From natural cell compartments to artificial polyelectrolyte reactors. Biotechnol Adv 2021; 54:107798. [PMID: 34265377 DOI: 10.1016/j.biotechadv.2021.107798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/09/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022]
Abstract
Engineering microenvironments for sequential enzymatic reactions has attracted specific interest within different fields of research as an effective strategy to improve the catalytic performance of enzymes. While in industry most enzymatic reactions occur in a single compartment carrier, living cells are however able to conduct multiple reactions simultaneously within confined sub-compartments, or organelles. Engineering multi-compartments with regulated environments and transformation properties enhances enzyme activity and stability and thus increases the overall yield of final products. In this review, we discuss current and potential methods to fabricate artificial cells for sequential enzymatic reactions, which are inspired by mechanisms and metabolic pathways developed by living cells. We aim to advance the understanding of living cell complexity and its compartmentalization and present solutions to mimic these processes in vitro. Particular attention has been given to layer-by-layer assembly of polyelectrolytes for developing multi-compartments. We hope this review paves the way for the next steps toward engineering of smart artificial multi-compartments with adoptive stimuli-responsive properties, mimicking living cells to improve catalytic properties and efficiency of the enzymes and enhance their stability.
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Affiliation(s)
- Maryam Omidvar
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Jakub Zdarta
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark; Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland
| | - Sigyn Björk Sigurdardóttir
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Manuel Pinelo
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark.
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29
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Faylo JL, van Eeuwen T, Kim HJ, Gorbea Colón JJ, Garcia BA, Murakami K, Christianson DW. Structural insight on assembly-line catalysis in terpene biosynthesis. Nat Commun 2021; 12:3487. [PMID: 34108468 PMCID: PMC8190136 DOI: 10.1038/s41467-021-23589-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid synthase that catalyzes the first two steps in the biosynthesis of the diterpene glycoside Fusicoccin A, a mediator of 14-3-3 protein interactions. The prenyltransferase domain of PaFS generates geranylgeranyl diphosphate, which the cyclase domain then utilizes to generate fusicoccadiene, the tricyclic hydrocarbon skeleton of Fusicoccin A. Here, we use cryo-electron microscopy to show that the structure of full-length PaFS consists of a central octameric core of prenyltransferase domains, with the eight cyclase domains radiating outward via flexible linker segments in variable splayed-out positions. Cryo-electron microscopy and chemical crosslinking experiments additionally show that compact conformations can be achieved in which cyclase domains are more closely associated with the prenyltransferase core. This structural analysis provides a framework for understanding substrate channeling, since most of the geranylgeranyl diphosphate generated by the prenyltransferase domains remains on the enzyme for cyclization to form fusicoccadiene.
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Affiliation(s)
- Jacque L Faylo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Trevor van Eeuwen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jose J Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
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30
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Di Venere A, Nicolai E, Minicozzi V, Caccuri AM, Di Paola L, Mei G. The Odd Faces of Oligomers: The Case of TRAF2-C, A Trimeric C-Terminal Domain of TNF Receptor-Associated Factor. Int J Mol Sci 2021; 22:ijms22115871. [PMID: 34070875 PMCID: PMC8198530 DOI: 10.3390/ijms22115871] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/31/2022] Open
Abstract
TNF Receptor Associated Factor 2 (TRAF2) is a trimeric protein that belongs to the TNF receptor associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding and for its interaction with other proteins involved in the TNFR signaling. The monomer-trimer equilibrium of a C- terminal domain truncated form of TRAF2 (TRAF2-C), plays also a relevant role in binding the membrane, causing inward vesiculation. In this study, we have investigated the conformational dynamics of TRAF2-C through circular dichroism, fluorescence, and dynamic light scattering, performing temperature-dependent measurements. The data indicate that the protein retains its oligomeric state and most of its secondary structure, while displaying a significative increase in the heterogeneity of the tyrosines signal, increasing the temperature from ≈15 to ≈35 °C. The peculiar crowding of tyrosine residues (12 out of 18) at the three subunit interfaces and the strong dependence on the trimer concentration indicate that such conformational changes mainly involve the contact areas between each pair of monomers, affecting the oligomeric state. Molecular dynamic simulations in this temperature range suggest that the interfaces heterogeneity is an intrinsic property of the trimer that arises from the continuous, asymmetric approaching and distancing of its subunits. Such dynamics affect the results of molecular docking on the external protein surface using receptor peptides, indicating that the TRAF2-receptor interaction in the solution might not involve three subunits at the same time, as suggested by the static analysis obtainable from the crystal structure. These findings shed new light on the role that the TRAF2 oligomeric state might have in regulating the protein binding activity in vivo.
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Affiliation(s)
- Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
| | - Eleonora Nicolai
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
| | - Velia Minicozzi
- Department of Physics, Tor Vergata University of Rome, Via Della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Anna Maria Caccuri
- Department of Chemistry, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Luisa Di Paola
- Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, University Campus Bio-Medico of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
- Correspondence: (L.D.P.); (G.M.)
| | - Giampiero Mei
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
- Correspondence: (L.D.P.); (G.M.)
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31
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Labourel F, Rajon E. Resource uptake and the evolution of moderately efficient enzymes. Mol Biol Evol 2021; 38:3938-3952. [PMID: 33964160 PMCID: PMC8382906 DOI: 10.1093/molbev/msab132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes speed up reactions that would otherwise be too slow to sustain the metabolism of selfreplicators. Yet, most enzymes seem only moderately efficient, exhibiting kinetic parameters orders of magnitude lower than their expected physically achievable maxima and spanning over surprisingly large ranges of values. Here, we question how these parameters evolve using a mechanistic model where enzyme efficiency is a key component of individual competition for resources. We show that kinetic parameters are under strong directional selection only up to a point, above which enzymes appear to evolve under near-neutrality, thereby confirming the qualitative observation of other modeling approaches. While the existence of a large fitness plateau could potentially explain the extensive variation in enzyme features reported, we show using a population genetics model that such a widespread distribution is an unlikely outcome of evolution on a common landscape, as mutation–selection–drift balance occupy a narrow area even when very moderate biases towards lower efficiency are considered. Instead, differences in the evolutionary context encountered by each enzyme should be involved, such that each evolves on an individual, unique landscape. Our results point to drift and effective population size playing an important role, along with the kinetics of nutrient transporters, the tolerance to high concentrations of intermediate metabolites, and the reversibility of reactions. Enzyme concentration also shapes selection on kinetic parameters, but we show that the joint evolution of concentration and efficiency does not yield extensive variance in evolutionary outcomes when documented costs to protein expression are applied.
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Affiliation(s)
- Florian Labourel
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, F-69622, France
| | - Etienne Rajon
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, F-69622, France
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32
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Liu Z, Zhang R, Zhang W, Xu Y. Ile258Met mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase significantly enhances catalytic efficiency, cofactor affinity, and thermostability. Appl Microbiol Biotechnol 2021; 105:3573-3586. [PMID: 33937927 DOI: 10.1007/s00253-021-11299-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/25/2021] [Accepted: 04/17/2021] [Indexed: 12/20/2022]
Abstract
NAD(H)-dependent 7α-hydroxysteroid dehydrogenase catalyzes the oxidation of chenodeoxycholic acid to 7-oxolithocholic acid. Here, we designed mutations of Ile258 adjacent to the catalytic pocket of Brucella melitensis 7α-hydroxysteroid dehydrogenase. The I258M variant gave a 4.7-fold higher kcat, but 4.5-fold lower KM, compared with the wild type, resulting in a 21.8-fold higher kcat/KM value for chenodeoxycholic acid oxidation. It presented a 2.0-fold lower KM value with NAD+, suggesting stronger binding to the cofactor. I258M produced 7-oxolithocholic acid in the highest yield of 92.3% in 2 h, whereas the wild-type gave 88.4% in 12 h. The I258M mutation increased the half-life from 20.8 to 31.1 h at 30 °C. Molecular dynamics simulations indicated increased interactions and a modified tunnel improved the catalytic efficiency, and enhanced rigidity at three regions around the ligand-binding pocket increased the enzyme thermostability. This is the first report about significantly improved catalytic efficiency, cofactor affinity, and enzyme thermostability through single site-mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase. KEY POINTS: • Sequence and structure analysis guided the site mutation design. • Thermostability, catalytic efficiency and 7-oxo-LCA production were determined. • MD simulation was performed to indicate the improvement by I258M mutation.
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Affiliation(s)
- Zhiyong Liu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China.
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
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33
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Protein complex formation in methionine chain-elongation and leucine biosynthesis. Sci Rep 2021; 11:3524. [PMID: 33568694 PMCID: PMC7876033 DOI: 10.1038/s41598-021-82790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/26/2021] [Indexed: 11/08/2022] Open
Abstract
During the past two decades, glucosinolate (GLS) metabolic pathways have been under extensive studies because of the importance of the specialized metabolites in plant defense against herbivores and pathogens. The studies have led to a nearly complete characterization of biosynthetic genes in the reference plant Arabidopsis thaliana. Before methionine incorporation into the core structure of aliphatic GLS, it undergoes chain-elongation through an iterative three-step process recruited from leucine biosynthesis. Although enzymes catalyzing each step of the reaction have been characterized, the regulatory mode is largely unknown. In this study, using three independent approaches, yeast two-hybrid (Y2H), coimmunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC), we uncovered the presence of protein complexes consisting of isopropylmalate isomerase (IPMI) and isopropylmalate dehydrogenase (IPMDH). In addition, simultaneous decreases in both IPMI and IPMDH activities in a leuc:ipmdh1 double mutants resulted in aggregated changes of GLS profiles compared to either leuc or ipmdh1 single mutants. Although the biological importance of the formation of IPMI and IPMDH protein complexes has not been documented in any organisms, these complexes may represent a new regulatory mechanism of substrate channeling in GLS and/or leucine biosynthesis. Since genes encoding the two enzymes are widely distributed in eukaryotic and prokaryotic genomes, such complexes may have universal significance in the regulation of leucine biosynthesis.
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34
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Tosha T, Yamagiwa R, Sawai H, Shiro Y. NO Dynamics in Microbial Denitrification System. CHEM LETT 2021. [DOI: 10.1246/cl.200629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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35
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Watkins-Dulaney E, Straathof S, Arnold F. Tryptophan Synthase: Biocatalyst Extraordinaire. Chembiochem 2021; 22:5-16. [PMID: 32677310 PMCID: PMC7935429 DOI: 10.1002/cbic.202000379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/15/2020] [Indexed: 12/23/2022]
Abstract
Tryptophan synthase (TrpS) has emerged as a paragon of noncanonical amino acid (ncAA) synthesis and is an ideal biocatalyst for synthetic and biological applications. TrpS catalyzes an irreversible, C-C bond-forming reaction between indole and serine to make l-tryptophan; native TrpS complexes possess fairly broad specificity for indole analogues, but are difficult to engineer to extend substrate scope or to confer other useful properties due to allosteric constraints and their heterodimeric structure. Directed evolution freed the catalytically relevant TrpS β-subunit (TrpB) from allosteric regulation by its TrpA partner and has enabled dramatic expansion of the enzyme's substrate scope. This review examines the long and storied career of TrpS from the perspective of its application in ncAA synthesis and biocatalytic cascades.
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Affiliation(s)
- Ella Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Frances Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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36
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Vanderstraeten J, Briers Y. Synthetic protein scaffolds for the colocalisation of co-acting enzymes. Biotechnol Adv 2020; 44:107627. [DOI: 10.1016/j.biotechadv.2020.107627] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
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37
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Foo JL, Rasouliha BH, Susanto AV, Leong SSJ, Chang MW. Engineering an Alcohol-Forming Fatty Acyl-CoA Reductase for Aldehyde and Hydrocarbon Biosynthesis in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:585935. [PMID: 33123518 PMCID: PMC7573125 DOI: 10.3389/fbioe.2020.585935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
Aldehydes are a class of highly versatile chemicals that can undergo a wide range of chemical reactions and are in high demand as starting materials for chemical manufacturing. Biologically, fatty aldehydes can be produced from fatty acyl-CoA by the action of fatty acyl-CoA reductases. The aldehydes produced can be further converted enzymatically to other valuable derivatives. Thus, metabolic engineering of microorganisms for biosynthesizing aldehydes and their derivatives could provide an economical and sustainable platform for key aldehyde precursor production and subsequent conversion to various value-added chemicals. Saccharomyces cerevisiae is an excellent host for this purpose because it is a robust organism that has been used extensively for industrial biochemical production. However, fatty acyl-CoA-dependent aldehyde-forming enzymes expressed in S. cerevisiae thus far have extremely low activities, hence limiting direct utilization of fatty acyl-CoA as substrate for aldehyde biosynthesis. Toward overcoming this challenge, we successfully engineered an alcohol-forming fatty acyl-CoA reductase for aldehyde production through rational design. We further improved aldehyde production through strain engineering by deleting competing pathways and increasing substrate availability. Subsequently, we demonstrated alkane and alkene production as one of the many possible applications of the aldehyde-producing strain. Overall, by protein engineering of a fatty acyl-CoA reductase to alter its activity and metabolic engineering of S. cerevisiae, we generated strains with the highest reported cytosolic aliphatic aldehyde and alkane/alkene production to date in S. cerevisiae from fatty acyl-CoA.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Bahareh Haji Rasouliha
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Adelia Vicanatalita Susanto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Singapore Institute of Technology, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
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38
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Wei Q, He S, Qu J, Xia J. Synthetic Multienzyme Complexes Assembled on Virus-like Particles for Cascade Biosynthesis In Cellulo. Bioconjug Chem 2020; 31:2413-2420. [DOI: 10.1021/acs.bioconjchem.0c00476] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Qixin Wei
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sicong He
- Department of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jianan Qu
- Department of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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39
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Škerlová J, Unterlass J, Göttmann M, Marttila P, Homan E, Helleday T, Jemth AS, Stenmark P. Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target. J Biol Chem 2020; 295:11656-11668. [PMID: 32571877 DOI: 10.1074/jbc.ra120.013695] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
The bifunctional human enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) catalyzes two essential steps in the de novo purine biosynthesis pathway. PAICS is overexpressed in many cancers and could be a promising target for the development of cancer therapeutics. Here, using gene knockdowns and clonogenic survival and cell viability assays, we demonstrate that PAICS is required for growth and survival of prostate cancer cells. PAICS catalyzes the carboxylation of aminoimidazole ribonucleotide (AIR) and the subsequent conversion of carboxyaminoimidazole ribonucleotide (CAIR) and l-aspartate to N-succinylcarboxamide-5-aminoimidazole ribonucleotide (SAICAR). Of note, we present the first structures of human octameric PAICS in complexes with native ligands. In particular, we report the structure of PAICS with CAIR bound in the active sites of both domains and SAICAR bound in one of the SAICAR synthetase domains. Moreover, we report the PAICS structure with SAICAR and an ATP analog occupying the SAICAR synthetase active site. These structures provide insight into substrate and product binding and the architecture of the active sites, disclosing important structural information for rational design of PAICS inhibitors as potential anticancer drugs.
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Affiliation(s)
- Jana Škerlová
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Judith Unterlass
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Mona Göttmann
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden .,Department of Experimental Medical Science, Lund University, Lund, Sweden
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40
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Calvo E, Cogliati S, Hernansanz-Agustín P, Loureiro-López M, Guarás A, Casuso RA, García-Marqués F, Acín-Pérez R, Martí-Mateos Y, Silla-Castro JC, Carro-Alvarellos M, Huertas JR, Vázquez J, Enríquez JA. Functional role of respiratory supercomplexes in mice: SCAF1 relevance and segmentation of the Q pool. SCIENCE ADVANCES 2020; 6:eaba7509. [PMID: 32637615 PMCID: PMC7314541 DOI: 10.1126/sciadv.aba7509] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/08/2020] [Indexed: 05/16/2023]
Abstract
Mitochondrial respiratory complexes assemble into supercomplexes (SC). Q-respirasome (III2 + IV) requires the supercomplex assembly factor (SCAF1) protein. The role of this factor in the N-respirasome (I + III2 + IV) and the physiological role of SCs are controversial. Here, we study C57BL/6J mice harboring nonfunctional SCAF1, the full knockout for SCAF1, or the wild-type version of the protein and found that exercise performance is SCAF1 dependent. By combining quantitative data-independent proteomics, 2D Blue native gel electrophoresis, and functional analysis of enriched respirasome fractions, we show that SCAF1 confers structural attachment between III2 and IV within the N-respirasome, increases NADH-dependent respiration, and reduces reactive oxygen species (ROS). Furthermore, the expression of AOX in cells and mice confirms that CI-CIII superassembly segments the CoQ in two pools and modulates CI-NADH oxidative capacity.
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Affiliation(s)
- Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
| | - Sara Cogliati
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
- Institute of Nutrition and Food Technology, Biomedical Research Centre, Department of Physiology, University of Granada
| | | | - Marta Loureiro-López
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
| | - Adela Guarás
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
| | - Rafael A. Casuso
- Institute of Nutrition and Food Technology, Biomedical Research Centre, Department of Physiology, University of Granada
| | | | - Rebeca Acín-Pérez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
| | - Yolanda Martí-Mateos
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
| | - JC. Silla-Castro
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
| | | | - Jesús R. Huertas
- Institute of Nutrition and Food Technology, Biomedical Research Centre, Department of Physiology, University of Granada
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
- CIBERCV, Madrid, Spain
| | - J. A. Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III. Madrid 28029, Spain
- CIBERFES, Madrid, Spain
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41
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Lv X, Wu Y, Tian R, Gu Y, Liu Y, Li J, Du G, Ledesma-Amaro R, Liu L. Synthetic metabolic channel by functional membrane microdomains for compartmentalized flux control. Metab Eng 2020; 59:106-118. [DOI: 10.1016/j.ymben.2020.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 10/24/2022]
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42
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Acurin A, a novel hybrid compound, biosynthesized by individually translated PKS- and NRPS-encoding genes in Aspergillus aculeatus. Fungal Genet Biol 2020; 139:103378. [PMID: 32234543 DOI: 10.1016/j.fgb.2020.103378] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 11/21/2022]
Abstract
This work presents the identification and proposed biosynthetic pathway for a compound of mixed polyketide-nonribosomal peptide origin that we named acurin A. The compound was isolated from an extract of the filamentous fungus Aspergillus aculeatus, and its core structure resemble that of the mycotoxin fusarin C produced by several Fusarium species. Based on bioinformatics in combination with RT-qPCR experiments and gene-deletion analysis, we identified a biosynthetic gene cluster (BGC) in A. aculeatus responsible for the biosynthesis of acurin A. Moreover, we were able to show that a polyketide synthase (PKS) and a nonribosomal peptide synthetase (NRPS) enzyme separately encoded by this BGC are responsible for the synthesis of the PK-NRP compound, acurin A, core structure. In comparison, the production of fusarin C is reported to be facilitated by a linked PKS-NRPS hybrid enzyme. Phylogenetic analyses suggest the PKS and NRPS in A. aculeatus resulted from a recent fission of an ancestral hybrid enzyme followed by gene duplication. In addition to the PKS- and NRPS-encoding genes of acurin A, we show that six other genes are influencing the biosynthesis including a regulatory transcription factor. Altogether, we have demonstrated the involvement of eight genes in the biosynthesis of acurin A, including an in-cluster transcription factor. This study highlights the biosynthetic capacity of A. aculeatus and serves as an example of how the CRISPR/Cas9 system can be exploited for the construction of fungal strains that can be readily engineered.
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43
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Oreb M. Construction of artificial membrane transport metabolons – an emerging strategy in metabolic engineering. FEMS Microbiol Lett 2020; 367:5735437. [DOI: 10.1093/femsle/fnaa027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/11/2020] [Indexed: 12/18/2022] Open
Abstract
ABSTRACT
The term ‘membrane transport metabolon’ refers to the physical association of membrane transporters with enzymes that metabolize the transported substrates. In naturally evolved systems, physiological relevance of coupling transport with sequential enzymatic reactions resides, for instance, in faster turnover rates, protection of substrates from competing pathways or shielding the cellular environment from toxic compounds. Such underlying principles offer attractive possibilities for metabolic engineering approaches and concepts for constructing artificial transporter-enzyme complexes are recently being developed. In this minireview, the modes of substrate channeling across biological membranes and design principles for artificial transport metabolons are discussed.
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Affiliation(s)
- Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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44
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Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites. Proc Natl Acad Sci U S A 2019; 116:25583-25590. [PMID: 31776258 PMCID: PMC6926001 DOI: 10.1073/pnas.1911595116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Methylotrophs play a crucial role in the global carbon cycle as they oxidize reduced one-carbon compounds such as methanol or methane to CO2. The step-wise conversion of these substrates generally takes place while the one-carbon units are bound to diffusible carrier molecules. However, our crystal structure of the formyltransferase/hydrolase complex from Methylorubrum extorquens demonstrates that the one-carbon carrier methylofuran tightly binds to the enzyme via its extended and branched polyglutamate chain. A swinging motion of the coenzyme then shuttles one-carbon units between the two active sites of the enzyme complex over a distance of 50 Å. The structure further highlights how the bacterial formate generation system relates to the archaeal CO2 fixation system. Methylotrophy, the ability of microorganisms to grow on reduced one-carbon substrates such as methane or methanol, is a feature of various bacterial species. The prevailing oxidation pathway depends on tetrahydromethanopterin (H4MPT) and methylofuran (MYFR), an analog of methanofuran from methanogenic archaea. Formyltransferase/hydrolase complex (Fhc) generates formate from formyl-H4MPT in two consecutive reactions where MYFR acts as a carrier of one-carbon units. Recently, we chemically characterized MYFR from the model methylotroph Methylorubrum extorquens and identified an unusually long polyglutamate side chain of up to 24 glutamates. Here, we report on the crystal structure of Fhc to investigate the function of the polyglutamate side chain in MYFR and the relatedness of the enzyme complex with the orthologous enzymes in archaea. We identified MYFR as a prosthetic group that is tightly, but noncovalently, bound to Fhc. Surprisingly, the structure of Fhc together with MYFR revealed that the polyglutamate side chain of MYFR is branched and contains glutamates with amide bonds at both their α- and γ-carboxyl groups. This negatively charged and branched polyglutamate side chain interacts with a cluster of conserved positively charged residues of Fhc, allowing for strong interactions. The MYFR binding site is located equidistantly from the active site of the formyltransferase (FhcD) and metallo-hydrolase (FhcA). The polyglutamate serves therefore an additional function as a swinging linker to shuttle the one-carbon carrying amine between the two active sites, thereby likely increasing overall catalysis while decreasing the need for high intracellular MYFR concentrations.
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45
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Zhang D, Lazim R. Exploring indole channeling in tryptophan synthase using steered molecular dynamics simulation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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46
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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47
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Chang M, Shimba K, Hayashi Y, Arai M. Electrostatic interactions at the interface of two enzymes are essential for two-step alkane biosynthesis in cyanobacteria. Biosci Biotechnol Biochem 2019; 84:228-237. [PMID: 31601165 DOI: 10.1080/09168451.2019.1677142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cyanobacterial alkane biosynthesis is catalyzed by acyl-(acyl carrier protein (ACP)) reductase (AAR) and aldehyde-deformylating oxygenase (ADO) in a two-step reaction. AAR reduces acyl-ACPs to fatty aldehydes, which are then converted by ADO to alkanes, the main components of diesel fuel. Interaction between AAR and ADO allows AAR to efficiently deliver the aldehyde to ADO. However, this interaction is poorly understood. Here, using analytical size-exclusion chromatography (SEC), we show that electrostatic interactions play an important role in the binding of the two enzymes. Alanine-scanning mutagenesis at charged residues around the substrate entry site of ADO revealed that E201A mutation greatly reduced hydrocarbon production. SEC measurement of the mutant demonstrated that E201 of ADO is essential for the AAR-ADO interaction. Our results suggest that AAR binds to the substrate entrance gate of ADO and thereby facilitates the insertion of the reactive and relatively insoluble aldehyde into the hydrophobic channel of ADO.Abbreviations: AAR: acyl-ACP reductase; ACP: acyl carrier protein; ADO: aldehyde-deformylating oxygenase; ASA: solvent accessible surface area; BSA: bovine serum albumin; CD: circular dichroism; DMSO: dimethyl sulfoxide; DTT: dithiothreitol; GC-MS: gas chromatography-mass spectrometer; HPLC: high-performance liquid chromatography; IPTG: isopropyl-β-D-thiogalactoside; MRE: mean residue ellipticity; NpAAR: AAR from Nostoc punctiforme PCC 73102; NpADO: ADO from Nostoc punctiforme PCC 73102; PmADO: ADO from Prochlorococcus marinus MIT 9313; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SeAAR: AAR from Synechococcus elongatus PCC 7942; SeADO: ADO from Synechococcus elongatus PCC 7942; SEC: size-exclusion chromatography; TeAAR: AAR from Thermosynechococcus elongatus BP-1; TeADO: ADO from Thermosynechococcus elongatus BP-1; UV: ultraviolet.
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Affiliation(s)
- Mari Chang
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keigo Shimba
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Munehito Arai
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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48
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Close DM, Cooper CJ, Wang X, Chirania P, Gupta M, Ossyra JR, Giannone RJ, Engle N, Tschaplinski TJ, Smith JC, Hedstrom L, Parks JM, Michener JK. Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Mol Microbiol 2019; 112:1784-1797. [PMID: 31532038 DOI: 10.1111/mmi.14393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 11/28/2022]
Abstract
A microbe's ecological niche and biotechnological utility are determined by its specific set of co-evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. Here we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is resistant to inhibition by the relevant intermediate, suggesting that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single-residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results demonstrate how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.
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Affiliation(s)
- Dan M Close
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Xingyou Wang
- Graduate Program in Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Payal Chirania
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Madhulika Gupta
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John R Ossyra
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Nancy Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jeremy C Smith
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee, 37996, USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02454, USA.,Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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49
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Li J, Zhao J, Xu S, Zhang S, Zhang J, Xiao J, Gao R, Tian M, Zeng Y, Lee K, Tarakanova V, Lan K, Feng H, Feng P. Antiviral activity of a purine synthesis enzyme reveals a key role of deamidation in regulating protein nuclear import. SCIENCE ADVANCES 2019; 5:eaaw7373. [PMID: 31633017 PMCID: PMC6785261 DOI: 10.1126/sciadv.aaw7373] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 09/14/2019] [Indexed: 05/13/2023]
Abstract
Protein nuclear translocation is highly regulated and crucial for diverse biological processes. However, our understanding concerning protein nuclear import is incomplete. Here we report that a cellular purine synthesis enzyme inhibits protein nuclear import via deamidation. Employing human Kaposi's sarcoma-associated herpesvirus (KSHV) to probe the role of protein deamidation, we identified a purine synthesis enzyme, phosphoribosylformylglycinamidine synthetase (PFAS) that inhibits KSHV transcriptional activation. PFAS deamidates the replication transactivator (RTA), a transcription factor crucial for KSHV lytic replication. Mechanistically, deamidation of two asparagines flanking a positively charged nuclear localization signal impaired the binding of RTA to an importin β subunit, thus diminishing RTA nuclear localization and transcriptional activation. Finally, RTA proteins of all gamma herpesviruses appear to be regulated by PFAS-mediated deamidation. These findings uncover an unexpected function of a metabolic enzyme in restricting viral replication and a key role of deamidation in regulating protein nuclear import.
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Affiliation(s)
- Junhua Li
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Jun Zhao
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Simin Xu
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Shu Zhang
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Junjie Zhang
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Jun Xiao
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
- Key Laboratory of Protein Chemistry and Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Ruoyun Gao
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Mao Tian
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Yi Zeng
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
- Department of Pathology and Immunology, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, P.R. China
| | - Katie Lee
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
| | - Vera Tarakanova
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ke Lan
- State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Hao Feng
- Key Laboratory of Protein Chemistry and Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Pinghui Feng
- Section of Infection and Immunity, Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, 925 W. 34th Street, Los Angeles, CA 90089-0641, USA
- State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei 430072, P.R. China
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50
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Qu J, Cao S, Wei Q, Zhang H, Wang R, Kang W, Ma T, Zhang L, Liu T, Wing-Ngor Au S, Sun F, Xia J. Synthetic Multienzyme Complexes, Catalytic Nanomachineries for Cascade Biosynthesis In Vivo. ACS NANO 2019; 13:9895-9906. [PMID: 31356751 DOI: 10.1021/acsnano.9b03631] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Multienzyme complexes, or metabolons, are assemblies or clusters of sequential enzymes that naturally exist in metabolic pathways. These nanomachineries catalyze the conversion of metabolites more effectively than the freely floating enzymes by minimizing the diffusion of intermediates in vivo. Bioengineers have devised synthetic versions of multienzyme complexes in cells to synergize heterologous biosynthesis, to improve intracellular metabolic flux, and to achieve higher titer of valuable chemical products. Here, we utilized orthogonal protein reactions (SpyCatcher/SpyTag and SnoopCatcher/SnoopTag pairs) to covalently assemble three key enzymes in the mevalonate biosynthesis pathway and showed 5-fold increase of lycopene and 2-fold increase of astaxanthin production in Escherichia coli. The multienzyme complexes are ellipsoidal nanostructures with hollow interior space and uniform thickness and shapes. Intracellular covalent enzyme assembly has yielded catalytic nanomachineries that drastically enlarged the flux of carotenoid biosynthesis in vivo. These studies also deepened our understanding on the complexity of hierarchical enzyme assembly in vivo.
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Affiliation(s)
| | | | | | | | - Rui Wang
- Department of Biomedical Sciences , City University of Hong Kong , Kowloon , Hong Kong SAR, China
| | | | - Tian Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China
| | - Liang Zhang
- Department of Biomedical Sciences , City University of Hong Kong , Kowloon , Hong Kong SAR, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China
| | | | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China; University of Chinese Academy of Sciences, Beijing, China;National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
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