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King SM, Sakato-Antoku M, Patel-King RS, Balsbaugh JL. The methylome of motile cilia. Mol Biol Cell 2024; 35:ar89. [PMID: 38696262 DOI: 10.1091/mbc.e24-03-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024] Open
Abstract
Cilia are highly complex motile, sensory, and secretory organelles that contain perhaps 1000 or more distinct protein components, many of which are subject to various posttranslational modifications such as phosphorylation, N-terminal acetylation, and proteolytic processing. Another common modification is the addition of one or more methyl groups to the side chains of arginine and lysine residues. These tunable additions delocalize the side-chain charge, decrease hydrogen bond capacity, and increase both bulk and hydrophobicity. Methylation is usually mediated by S-adenosylmethionine (SAM)-dependent methyltransferases and reversed by demethylases. Previous studies have identified several ciliary proteins that are subject to methylation including axonemal dynein heavy chains that are modified by a cytosolic methyltransferase. Here, we have performed an extensive proteomic analysis of multiple independently derived cilia samples to assess the potential for SAM metabolism and the extent of methylation in these organelles. We find that cilia contain all the enzymes needed for generation of the SAM methyl donor and recycling of the S-adenosylhomocysteine and tetrahydrofolate byproducts. In addition, we find that at least 155 distinct ciliary proteins are methylated, in some cases at multiple sites. These data provide a comprehensive resource for studying the consequences of methyl marks on ciliary biology.
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Affiliation(s)
- Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Ramila S Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Jeremy L Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT 06269
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2
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Kelly SD, Williams DM, Zhu S, Kim T, Jana M, Nothof J, Thota VN, Lowary TL, Whitfield C. Klebsiella pneumoniae O-polysaccharide biosynthesis highlights the diverse organization of catalytic modules in ABC transporter-dependent glycan assembly. J Biol Chem 2024; 300:107420. [PMID: 38815868 DOI: 10.1016/j.jbc.2024.107420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/19/2024] [Indexed: 06/01/2024] Open
Abstract
Klebsiella pneumoniae provides influential prototypes for lipopolysaccharide O antigen (OPS) biosynthesis in Gram-negative bacteria. Sequences of OPS-biosynthesis gene clusters in serotypes O4 and O7 suggest fundamental differences in the organization of required enzyme modules compared to other serotypes. Furthermore, some required activities were not assigned by homology shared with characterized enzymes. The goal of this study was therefore to resolve the serotype O4 and O7 pathways to expand our broader understanding of glycan polymerization and chain termination processes. The O4 and O7 antigens were produced from cloned genetic loci in recombinant Escherichia coli. Systematic in vivo and in vitro approaches were then applied to assign each enzyme in each of the pathways, defining the necessary components for polymerization and chain termination. OPS assembly is accomplished by multiprotein complexes formed by interactions between polymerase components variably distributed in single and multimodule proteins. In each complex, a terminator function is present in a protein containing a characteristic coiled-coil molecular ruler, which determines glycan chain length. In serotype O4, we discovered a CMP-α-3-deoxy-ᴅ-manno-octulosonic acid-dependent chain-terminating glycosyltransferase that is the founding member of a new glycosyltransferase family (GT137) and potentially identifies a new glycosyltransferase fold. The O7 OPS is terminated by a methylphosphate moiety, like the K. pneumoniae O3 antigen, but the methyltransferase-kinase enzyme pairs responsible for termination in these serotypes differ in sequence and predicted structures. Together, the characterization of O4 and O7 has established unique enzyme activities and provided new insight into glycan-assembly strategies that are widely distributed in bacteria.
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Affiliation(s)
- Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Danielle M Williams
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Shawna Zhu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Taeok Kim
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Manas Jana
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jeremy Nothof
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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3
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Hudspeth J, Rogge K, Dörner S, Müll M, Hoffmeister D, Rupp B, Werten S. Methyl transfer in psilocybin biosynthesis. Nat Commun 2024; 15:2709. [PMID: 38548735 PMCID: PMC10978996 DOI: 10.1038/s41467-024-46997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Psilocybin, the natural hallucinogen produced by Psilocybe ("magic") mushrooms, holds great promise for the treatment of depression and several other mental health conditions. The final step in the psilocybin biosynthetic pathway, dimethylation of the tryptophan-derived intermediate norbaeocystin, is catalysed by PsiM. Here we present atomic resolution (0.9 Å) crystal structures of PsiM trapped at various stages of its reaction cycle, providing detailed insight into the SAM-dependent methylation mechanism. Structural and phylogenetic analyses suggest that PsiM derives from epitranscriptomic N6-methyladenosine writers of the METTL16 family, which is further supported by the observation that bound substrates physicochemically mimic RNA. Inherent limitations of the ancestral monomethyltransferase scaffold hamper the efficiency of psilocybin assembly and leave PsiM incapable of catalysing trimethylation to aeruginascin. The results of our study will support bioengineering efforts aiming to create novel variants of psilocybin with improved therapeutic properties.
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Affiliation(s)
- Jesse Hudspeth
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA
| | - Kai Rogge
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Sebastian Dörner
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Maximilian Müll
- Research Group Biosynthetic Design of Natural Products, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Bernhard Rupp
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- k.-k. Hofkristallamt, San Diego, California, USA
| | - Sebastiaan Werten
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.
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4
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Sakato-Antoku M, Patel-King RS, Balsbaugh JL, King SM. Methylation of ciliary dynein motors involves the essential cytosolic assembly factor DNAAF3/PF22. Proc Natl Acad Sci U S A 2024; 121:e2318522121. [PMID: 38261620 PMCID: PMC10835030 DOI: 10.1073/pnas.2318522121] [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: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Axonemal dynein motors drive ciliary motility and can consist of up to twenty distinct components with a combined mass of ~2 MDa. In mammals, failure of dyneins to assemble within the axonemal superstructure leads to primary ciliary dyskinesia. Syndromic phenotypes include infertility, rhinitis, severe bronchial conditions, and situs inversus. Nineteen specific cytosolic factors (Dynein Axonemal Assembly Factors; DNAAFs) are necessary for axonemal dynein assembly, although the detailed mechanisms involved remain very unclear. Here, we identify the essential assembly factor DNAAF3 as a structural ortholog of S-adenosylmethionine-dependent methyltransferases. We demonstrate that dynein heavy chains, especially those forming the ciliary outer arms, are methylated on key residues within various nucleotide-binding sites and on microtubule-binding domain helices directly involved in the transition to low binding affinity. These variable modifications, which are generally missing in a Chlamydomonas null mutant for the DNAAF3 ortholog PF22 (DAB1), likely impact on motor mechanochemistry fine-tuning the activities of individual dynein complexes.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
| | - Ramila S Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
| | - Jeremy L Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT 06269
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
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5
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Haase M, David B, Paschold B, Classen T, Schneider P, Pozhydaieva N, Gohlke H, Pietruszka J. Application of the C3-Methyltransferase StspM1 for the Synthesis of the Natural Pyrroloindole Motif. ACS Catal 2024; 14:227-236. [PMID: 38205025 PMCID: PMC10775177 DOI: 10.1021/acscatal.3c04952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
Even though pyrroloindoles are widely present in natural products with different kinds of biological activities, their selective synthesis remains challenging with existing tools in organic chemistry, and there is furthermore a demand for stereoselective and mild methods to access this structural motif. Nature uses C3-methyltransferases to form the pyrroloindole framework, starting from the amino acid tryptophan. In the present study, the SAM-dependent methyltransferase StspM1 from Streptomyces sp. HPH0547 is used to build the pyrroloindole structural motif in tryptophan-based diketopiperazines (DKP). The substrate scope of the enzyme regarding different Trp-Trp-DKP isomers was investigated on an experimental and computational level. After further characterization and optimization of the methylation reaction with a design of experiment approach, a preparative scale reaction with the immobilized enzyme including a SAM regeneration system was performed to show the synthetic use of this biocatalytic tool to access the pyrroloindole structural motif.
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Affiliation(s)
- Mona Haase
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Benoit David
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics) Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Beatrix Paschold
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Thomas Classen
- Institute
of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy
Science Center (BioSC), Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Pascal Schneider
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Nadiia Pozhydaieva
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Holger Gohlke
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics) Forschungszentrum
Jülich, 52426 Jülich, Germany
- Institute
for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science
Center (BioSC), Heinrich Heine University
Düsseldorf, 40225 Düsseldorf, Germany
| | - Jörg Pietruszka
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
- Institute
of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy
Science Center (BioSC), Forschungszentrum
Jülich, 52426 Jülich, Germany
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6
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Loo CE, Hix MA, Wang T, Cisneros GA, Kohli RM. Revealing Drivers for Carboxy- S-adenosyl-l-methionine Use by Neomorphic Variants of a DNA Methyltransferase. ACS Chem Biol 2023; 18:2224-2232. [PMID: 37379458 PMCID: PMC10592258 DOI: 10.1021/acschembio.3c00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Methylation of DNA plays a key role in diverse biological processes spanning from bacteria to mammals. DNA methyltransferases (MTases) typically employ S-adenosyl-l-methionine (SAM) as a critical cosubstrate and the relevant methyl donor for modification of the C5 position of cytosine. Recently, work on the CpG-specific bacterial MTase, M.MpeI, has shown that a single N374K point mutation can confer the enzyme with the neomorphic ability to use the sparse, naturally occurring metabolite carboxy-S-adenosyl-l-methionine (CxSAM) in order to generate the unnatural DNA modification, 5-carboxymethylcytosine (5cxmC). Here, we aimed to investigate the mechanistic basis for this DNA carboxymethyltransferase (CxMTase) activity by employing a combination of computational modeling and in vitro characterization. Modeling of substrate interactions with the enzyme variant allowed us to identify a favorable salt bridge between CxSAM and N374K that helps to rationalize selectivity of the CxMTase. Unexpectedly, we also discovered a potential role for a key active site E45 residue that makes a bidentate interaction with the ribosyl sugar of CxSAM, located on the opposite face of the CxMTase active site. Prompted by these modeling results, we further explored the space-opening E45D mutation and found that the E45D/N374K double mutant in fact inverts selectivity, preferring CxSAM over SAM in biochemical assays. These findings provide new insight into CxMTase active site architecture and may offer broader utility given the numerous opportunities offered by using SAM analogs for selective molecular labeling in concert with nucleic acid or even protein-modifying MTases.
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Affiliation(s)
- Christian E. Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mark A. Hix
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Tong Wang
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - G. Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75801, United States; Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75801, United States
| | - Rahul M. Kohli
- Department of Medicine and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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7
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Muñoz-Vargas MA, González-Gordo S, Taboada J, Palma JM, Corpas FJ. In Silico RNAseq and Biochemical Analyses of Glucose-6-Phosphate Dehydrogenase (G6PDH) from Sweet Pepper Fruits: Involvement of Nitric Oxide (NO) in Ripening and Modulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:3408. [PMID: 37836149 PMCID: PMC10574341 DOI: 10.3390/plants12193408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023]
Abstract
Pepper (Capsicum annuum L.) fruit is a horticultural product consumed worldwide which has great nutritional and economic relevance. Besides the phenotypical changes that pepper fruit undergo during ripening, there are many associated modifications at transcriptomic, proteomic, biochemical, and metabolic levels. Nitric oxide (NO) is a recognized signal molecule that can exert regulatory functions in diverse plant processes including fruit ripening, but the relevance of NADPH as a fingerprinting of the crop physiology including ripening has also been proposed. Glucose-6-phosphate dehydrogenase (G6PDH) is the first and rate-limiting enzyme of the oxidative phase of the pentose phosphate pathway (oxiPPP) with the capacity to generate NADPH. Thus far, the available information on G6PDH and other NADPH-generating enzymatic systems in pepper plants, and their expression during the ripening of sweet pepper fruit, is very scarce. Therefore, an analysis at the transcriptomic, molecular and functional levels of the G6PDH system has been accomplished in this work for the first time. Based on a data-mining approach to the pepper genome and fruit transcriptome (RNA-seq), four G6PDH genes were identified in pepper plants and designated CaG6PDH1 to CaG6PDH4, with all of them also being expressed in fruits. While CaG6PDH1 encodes a cytosolic isozyme, the other genes code for plastid isozymes. The time-course expression analysis of these CaG6PDH genes during different fruit ripening stages, including green immature (G), breaking point (BP), and red ripe (R), showed that they were differentially modulated. Thus, while CaG6PDH2 and CaG6PDH4 were upregulated at ripening, CaG6PDH1 was downregulated, and CaG6PDH3 was slightly affected. Exogenous treatment of fruits with NO gas triggered the downregulation of CaG6PDH2, whereas the other genes were positively regulated. In-gel analysis using non-denaturing PAGE of a 50-75% ammonium-sulfate-enriched protein fraction from pepper fruits allowed for identifying two isozymes designated CaG6PDH I and CaG6PDH II, according to their electrophoretic mobility. In order to test the potential modulation of such pepper G6PDH isozymes, in vitro analyses of green pepper fruit samples in the presence of different compounds including NO donors (S-nitrosoglutathione and nitrosocysteine), peroxynitrite (ONOO-), a hydrogen sulfide (H2S) donor (NaHS, sodium hydrosulfide), and reducing agents such as reduced glutathione (GSH) and L-cysteine (L-Cys) were assayed. While peroxynitrite and the reducing compounds provoked a partial inhibition of one or both isoenzymes, NaHS exerted 100% inhibition of the two CaG6PDHs. Taken together these data provide the first data on the modulation of CaG6PDHs at gene and activity levels which occur in pepper fruit during ripening and after NO post-harvest treatment. As a consequence, this phenomenon may influence the NADPH availability for the redox homeostasis of the fruit and balance its active nitro-oxidative metabolism throughout the ripening process.
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Affiliation(s)
| | | | | | - José M. Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Stress, Development and Signaling in Plants, Estación Experimental del Zaidín (Spanish National Research Council, CSIC), C/Profesor Albareda, 1, 18008 Granada, Spain; (M.A.M.-V.); (S.G.-G.); (J.T.)
| | - Francisco J. Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Stress, Development and Signaling in Plants, Estación Experimental del Zaidín (Spanish National Research Council, CSIC), C/Profesor Albareda, 1, 18008 Granada, Spain; (M.A.M.-V.); (S.G.-G.); (J.T.)
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8
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Yoo J, Lee J, Kim J. Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification. Nucleic Acids Res 2023; 51:9432-9441. [PMID: 37587716 PMCID: PMC10516636 DOI: 10.1093/nar/gkad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/26/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
Posttranscriptional modifications of tRNA are widely conserved in all domains of life. Especially, those occurring within the anticodon often modulate translational efficiency. Derivatives of 5-hydroxyuridine are specifically found in bacterial tRNA, where 5-methoxyuridine and 5-carboxymethoxyuridine are the major species in Gram-positive and Gram-negative bacteria, respectively. In certain tRNA species, 5-carboxymethoxyuridine can be further methylated by CmoM to form the methyl ester. In this report, we present the X-ray crystal structure of Escherichia coli CmoM complexed with tRNASer1, which contains 5-carboxymethoxyuridine at the 5'-end of anticodon (the 34th position of tRNA). The 2.22 Å resolution structure of the enzyme-tRNA complex reveals that both the protein and tRNA undergo local conformational changes around the binding interface. Especially, the hypomodified uracil base is flipped out from the canonical stacked conformation enabling the specific molecular interactions with the enzyme. Moreover, the structure illustrates that the enzyme senses exclusively the anticodon arm region of the substrate tRNA and examines the presence of key determinants, 5-carboxymethoxyuridine at position 34 and guanosine at position 35, offering molecular basis for the discriminatory mechanism against non-cognate tRNAs.
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Affiliation(s)
- Jaehun Yoo
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jangmin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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9
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Shanbhag AP. Stairway to Stereoisomers: Engineering Short- and Medium-Chain Ketoreductases To Produce Chiral Alcohols. Chembiochem 2023; 24:e202200687. [PMID: 36640298 DOI: 10.1002/cbic.202200687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/15/2023]
Abstract
The short- and medium-chain dehydrogenase/reductase superfamilies are responsible for most chiral alcohol production in laboratories and industries. In nature, they participate in diverse roles such as detoxification, housekeeping, secondary metabolite production, and catalysis of several chemicals with commercial and environmental significance. As a result, they are used in industries to create biopolymers, active pharmaceutical intermediates (APIs), and are also used as components of modular enzymes like polyketide synthases for fabricating bioactive molecules. Consequently, random, semi-rational and rational engineering have helped transform these enzymes into product-oriented efficient catalysts. The rise of newer synthetic chemicals and their enantiopure counterparts has proved challenging, and engineering them has been the subject of numerous studies. However, they are frequently limited to the synthesis of a single chiral alcohol. The study attempts to defragment and describe hotspots of engineering short- and medium-chain dehydrogenases/reductases for the production of chiral synthons.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS-TIFR), Bellary Road, Bangalore, 560003, India
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10
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Lashley A, Miller R, Provenzano S, Jarecki SA, Erba P, Salim V. Functional Diversification and Structural Origins of Plant Natural Product Methyltransferases. Molecules 2022; 28:molecules28010043. [PMID: 36615239 PMCID: PMC9822479 DOI: 10.3390/molecules28010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
In plants, methylation is a common step in specialized metabolic pathways, leading to a vast diversity of natural products. The methylation of these small molecules is catalyzed by S-adenosyl-l-methionine (SAM)-dependent methyltransferases, which are categorized based on the methyl-accepting atom (O, N, C, S, or Se). These methyltransferases are responsible for the transformation of metabolites involved in plant defense response, pigments, and cell signaling. Plant natural product methyltransferases are part of the Class I methyltransferase-superfamily containing the canonical Rossmann fold. Recent advances in genomics have accelerated the functional characterization of plant natural product methyltransferases, allowing for the determination of substrate specificities and regioselectivity and further realizing the potential for enzyme engineering. This review compiles known biochemically characterized plant natural product methyltransferases that have contributed to our knowledge in the diversification of small molecules mediated by methylation steps.
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Affiliation(s)
- Audrey Lashley
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
| | - Ryan Miller
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA 70112, USA
| | - Stephanie Provenzano
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- School of Medicine, Louisiana State University Health Shreveport, Shreveport, LA 71103, USA
| | - Sara-Alexis Jarecki
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
| | - Paul Erba
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA 70112, USA
| | - Vonny Salim
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- Correspondence:
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11
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Majumdar S, Gupta U, Chinnasamy HV, Laxmipathy S, Matheshwaran S. Zn 2+-Induced Conformational Change Affects the SAM Binding in a Mycobacterial SAM-Dependent Methyltransferase. ACS OMEGA 2022; 7:35901-35910. [PMID: 36249403 PMCID: PMC9558604 DOI: 10.1021/acsomega.2c04555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Zinc is a cofactor for enzymes involved in DNA replication, peptidoglycan hydrolysis, and pH maintenance, in addition to the transfer of the methyl group to thiols. Here, we discovered a new role of Zn2+ as an inhibitor for S-adenosyl methionine (SAM) binding in a mycobacterial methyltransferase. Rv1377c is annotated as a putative methyltransferase that is upregulated upon the mitomycin C treatment of Mycobacterium tuberculosis. Sequence analysis and experimental validation allowed the identification of distinct motifs responsible for SAM binding. A detailed analysis of the AlphaFold-predicted structure of Rv1377c revealed four cysteine residues capable of coordinating a Zn2+ ion located in proximity to the SAM-binding site. Further, experimental studies showed distinct conformational changes upon Zn2+ binding to the protein, which compromised its ability to bind SAM. This is the first report wherein Zn2+-driven conformational changes in a methyltransferase undermines its ability to bind SAM.
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Affiliation(s)
- Soneya Majumdar
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh India
| | - Umang Gupta
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh India
| | - Hariharan V. Chinnasamy
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh India
| | - Sathishkumar Laxmipathy
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh India
| | - Saravanan Matheshwaran
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh India
- Center
for Environmental Science and Engineering, Indian Institute of Technology, Kanpur 208016, Uttar
Pradesh India
- Mehta
Family Centre for Engineering in Medicine, Indian Institute of Technology, Kanpur 208016, Uttar
Pradesh India
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12
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Qiu K, Ben‐Tal N, Kolodny R. Similar protein segments shared between domains of different evolutionary lineages. Protein Sci 2022; 31:e4407. [PMID: 36040261 PMCID: PMC9387206 DOI: 10.1002/pro.4407] [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: 04/25/2022] [Revised: 07/01/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022]
Abstract
The emergence of novel proteins, beyond these that can be readily made by duplication and recombination of preexisting domains, is elusive. De novo emergence from random sequences is unlikely because the vast majority of random chains would not even fold, let alone function. An alternative explanation is that novel proteins emerge by duplication and fusion of pre‐existing polypeptide segments. In this case, traces of such ancient events may remain within contemporary proteins in the form of reused segments. Together with the late Dan Tawfik, we detected such similar segments, far shorter than intact protein domains, which are found in different environments. The detection of these, “bridging themes,” was based on a unique search strategy, where in addition to searching for similarity of shared fragments, so‐called “themes,” we also explicitly searched for cases in which the sequence segments before and after the theme are dissimilar (both in sequence and structure). Here, using a similar strategy, we further expanded the search and discovered almost 500 additional “bridging themes,” linking domains that are often from ancient folds. The themes, of 20 residues or more (average 53), do not retain their structure despite sharing 37% sequence identity on average. Indeed, conformation flexibility may confer an evolutionary advantage, in that it fits in multiple environments. We elaborate on two interesting themes, shared between Rossmann/Trefoil‐Plexin‐like domains and a β‐propeller‐like domain.
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Affiliation(s)
- Kaiyu Qiu
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv Israel
| | - Nir Ben‐Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv Israel
| | - Rachel Kolodny
- Department of Computer Science University of Haifa Haifa Israel
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13
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Kumar V, Turnbull WB, Kumar A. Review on Recent Developments in Biocatalysts for Friedel–Crafts Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
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14
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Ogando NS, El Kazzi P, Zevenhoven-Dobbe JC, Bontes BW, Decombe A, Posthuma CC, Thiel V, Canard B, Ferron F, Decroly E, Snijder EJ. Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Proc Natl Acad Sci U S A 2021; 118:e2108709118. [PMID: 34845015 PMCID: PMC8670481 DOI: 10.1073/pnas.2108709118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2021] [Indexed: 11/18/2022] Open
Abstract
As coronaviruses (CoVs) replicate in the host cell cytoplasm, they rely on their own capping machinery to ensure the efficient translation of their messenger RNAs (mRNAs), protect them from degradation by cellular 5' exoribonucleases (ExoNs), and escape innate immune sensing. The CoV nonstructural protein 14 (nsp14) is a bifunctional replicase subunit harboring an N-terminal 3'-to-5' ExoN domain and a C-terminal (N7-guanine)-methyltransferase (N7-MTase) domain that is presumably involved in viral mRNA capping. Here, we aimed to integrate structural, biochemical, and virological data to assess the importance of conserved N7-MTase residues for nsp14's enzymatic activities and virus viability. We revisited the crystal structure of severe acute respiratory syndrome (SARS)-CoV nsp14 to perform an in silico comparative analysis between betacoronaviruses. We identified several residues likely involved in the formation of the N7-MTase catalytic pocket, which presents a fold distinct from the Rossmann fold observed in most known MTases. Next, for SARS-CoV and Middle East respiratory syndrome CoV, site-directed mutagenesis of selected residues was used to assess their importance for in vitro enzymatic activity. Most of the engineered mutations abolished N7-MTase activity, while not affecting nsp14-ExoN activity. Upon reverse engineering of these mutations into different betacoronavirus genomes, we identified two substitutions (R310A and F426A in SARS-CoV nsp14) abrogating virus viability and one mutation (H424A) yielding a crippled phenotype across all viruses tested. Our results identify the N7-MTase as a critical enzyme for betacoronavirus replication and define key residues of its catalytic pocket that can be targeted to design inhibitors with a potential pan-coronaviral activity spectrum.
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Affiliation(s)
- Natacha S Ogando
- Department of Medical Microbiology, Leiden University Medical Center 2333 ZA Leiden, The Netherlands
| | - Priscila El Kazzi
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université 13288 Marseille, France
| | | | - Brenda W Bontes
- Department of Medical Microbiology, Leiden University Medical Center 2333 ZA Leiden, The Netherlands
| | - Alice Decombe
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université 13288 Marseille, France
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center 2333 ZA Leiden, The Netherlands
| | - Volker Thiel
- Institute of Virology and Immunology (IVI) 3350 Bern, Switzerland
- De partment of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern 3012 Bern, Switzerland
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université 13288 Marseille, France
- European Virus Bioinformatics Center (EVBC), Jena 07743, Germany
| | - François Ferron
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université 13288 Marseille, France
- European Virus Bioinformatics Center (EVBC), Jena 07743, Germany
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université 13288 Marseille, France;
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center 2333 ZA Leiden, The Netherlands;
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15
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Kamiński K, Ludwiczak J, Jasiński M, Bukala A, Madaj R, Szczepaniak K, Dunin-Horkawicz S. Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. Brief Bioinform 2021; 23:6375059. [PMID: 34571541 PMCID: PMC8769691 DOI: 10.1093/bib/bbab371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/04/2021] [Accepted: 08/22/2021] [Indexed: 11/15/2022] Open
Abstract
The Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved βαβ motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-adenosylmethionine, the oxidoreductases, depending on the family, bind nicotinamide (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) or flavin-based (flavin adenine dinucleotide) cofactors. In this study, we showed that despite its short length, the βαβ motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the βαβ motif. A benchmark on two independent test sets, one containing βαβ motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver at https://lbs.cent.uw.edu.pl/rossmann-toolbox and are available as a Python package at https://github.com/labstructbioinf/rossmann-toolbox.
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Affiliation(s)
- Kamil Kamiński
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.,Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Pasteura 3, 02-093 Warsaw, Poland
| | - Maciej Jasiński
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Adriana Bukala
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Rafal Madaj
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Krzysztof Szczepaniak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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16
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Sartor P, Denkhaus L, Gerhardt S, Einsle O, Fetzner S. Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis. J Struct Biol 2021; 213:107794. [PMID: 34506908 DOI: 10.1016/j.jsb.2021.107794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
The S-adenosyl-L-methionine-dependent methyltransferase Rv0560c of Mycobacterium tuberculosis belongs to an orthologous group of heterocyclic toxin methyltransferases (Htm) which likely contribute to resistance of mycobacteria towards antimicrobial natural compounds as well as drugs. HtmM.t. catalyzes the methylation of the Pseudomonas aeruginosa toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one (also known as 2-heptyl-4-hydroxyquinoline N-oxide), a potent inhibitor of respiratory electron transfer, its 1-hydroxyquinolin-4(1H)-one core (QNO), structurally related (iso)quinolones, and some mycobactericidal compounds. In this study, crystal structures of HtmM.t. in complex with S-adenosyl-L-homocysteine (SAH) and the methyl-accepting substrates QNO or 4-hydroxyisoquinoline-1(2H)-one, or the methylated product 1-methoxyquinolin-4(1H)-one, were determined at < 1.9 Å resolution. The monomeric protein exhibits the typical Rossmann fold topology and conserved residues of class I methyltransferases. Its SAH binding pocket is connected via a short tunnel to a large solvent-accessible cavity, which accommodates the methyl-accepting substrate. Residues W44, F168, and F208 in connection with F212 form a hydrophobic clamp around the heteroaromatic ring of the methyl-accepting substrate and likely play a major role in substrate positioning. Structural and biochemical data suggest that H139 and T136 are key active site residues, with H139 acting as general base that activates the methyl-accepting hydroxy group. Our structural data may contribute to the design of Htm inhibitors or of antimycobacterial drugs unamenable for methylation.
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Affiliation(s)
- Pascal Sartor
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
| | - Lukas Denkhaus
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Stefan Gerhardt
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Oliver Einsle
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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17
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Targeted knockout of the gene OsHOL1 removes methyl iodide emissions from rice plants. Sci Rep 2021; 11:17010. [PMID: 34426588 PMCID: PMC8382704 DOI: 10.1038/s41598-021-95198-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Iodine deficiency represents a public health problem worldwide. To increase the amount of iodine in the diet, biofortification strategies of plants have been tried. They rely on the exogenous administration of iodine to increase its absorption and accumulation. However, iodine is not stable in plants and can be volatilized as methyl iodide through the action of specific methyltransferases encoded by the HARMLESS TO OZONE LAYER (HOL) genes. The release of methyl iodide in the atmosphere represents a threat for the environment due to its ozone depletion potential. Rice paddies are among the strongest producers of methyl iodide. Thus, the agronomic approach of iodine biofortification is not appropriate for this crop, leading to further increases of iodine emissions. In this work, we used the genome editing CRISPR/Cas9 technology to knockout the rice HOL genes and investigate their function. OsHOL1 resulted a major player in methyl iodide production, since its knockout abolished the process. Moreover, its overexpression reinforced it. Conversely, knockout of OsHOL2 did not produce effects. Our experiments helped elucidating the function of the rice HOL genes, providing tools to develop new rice varieties with reduced iodine emissions and thus more suitable for biofortification programs without further impacting on the environment.
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18
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Zhou J, Horton JR, Blumenthal RM, Zhang X, Cheng X. Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nat Commun 2021; 12:3436. [PMID: 34103525 PMCID: PMC8187626 DOI: 10.1038/s41467-021-23693-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile infections are an urgent medical problem. The newly discovered C. difficile adenine methyltransferase A (CamA) is specified by all C. difficile genomes sequenced to date (>300), but is rare among other bacteria. CamA is an orphan methyltransferase, unassociated with a restriction endonuclease. CamA-mediated methylation at CAAAAA is required for normal sporulation, biofilm formation, and intestinal colonization by C. difficile. We characterized CamA kinetic parameters, and determined its structure bound to DNA containing the recognition sequence. CamA contains an N-terminal domain for catalyzing methyl transfer, and a C-terminal DNA recognition domain. Major and minor groove DNA contacts in the recognition site involve base-specific hydrogen bonds, van der Waals contacts and the Watson-Crick pairing of a rearranged A:T base pair. These provide sufficient sequence discrimination to ensure high specificity. Finally, the surprisingly weak binding of the methyl donor S-adenosyl-L-methionine (SAM) might provide avenues for inhibiting CamA activity using SAM analogs.
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Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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19
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Piechulla B, Zhang C, Eisenschmidt-Bönn D, Chen F, Magnus N. Non-canonical substrates for terpene synthases in bacteria are synthesized by a new family of methyltransferases. FEMS Microbiol Rev 2021; 45:6232159. [PMID: 33864462 DOI: 10.1093/femsre/fuab024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/15/2021] [Indexed: 01/01/2023] Open
Abstract
The 'biogenetic isoprene rule', formulated in the mid 20th century, predicted that terpenoids are biosynthesized via polymerization of C5 isoprene units. The polymerizing enzymes have been identified to be isoprenyl diphosphate synthases, products of which are catalyzed by terpene synthases (TPSs) to achieve vast structural diversity of terpene skeletons. Irregular terpenes (e.g, C11, C12, C16, C17) are also frequently observed, and they have presumed to be synthesized by the modification of terpene skeletons. This review highlights the exciting discovery of an additional route to the biosynthesis of irregular terpenes which involves the action of a newly discovered enzyme family of isoprenyl diphosphate methyltransferases (IDMTs). These enzymes methylate, and sometimes cyclize, the classical isoprenyl diphosphate substrates to produce modified, non-canonical substrates for specifically evolved TPSs. So far, this new pathway has been found only in bacteria. Structure and sequence comparisons of the IDMTs strongly indicate a conservation of their active pockets and overall topologies. Some bacterial IDMTs and TPSs appear in small gene clusters, which may facilitate future mining of bacterial genomes for identification of irregular terpene-producing enzymes. The IDMT-TPS route for terpenoid biosynthesis presents another example of nature's ingenuity in creating chemical diversity, particularly terpenoids, for organismal fitness. IDMT isoprenyl diphosphate methyltransferases IDPMT isopentenyl diphosphate methyltransferase GDPMT geranyl diphosphate methyltransferase FDPMT farnesyl diphosphate methyltransferases BGC biosynthetic gene cluster TPS terpene synthase MIBS 2-methylisoborneol synthase MBS 2-methylenebornane synthase DMADP Dimethylallyl diphosphate SAM S-adenosyl-L-methionine.
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Affiliation(s)
- Birgit Piechulla
- University of Rostock, Institute for Biological Sciences, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Chi Zhang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniela Eisenschmidt-Bönn
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Nancy Magnus
- University of Rostock, Institute for Biological Sciences, Albert-Einstein-Str. 3, 18059 Rostock, Germany
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20
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Valle C, Martin B, Ferron F, Roig-Zamboni V, Desmyter A, Debart F, Vasseur JJ, Canard B, Coutard B, Decroly E. First insights into the structural features of Ebola virus methyltransferase activities. Nucleic Acids Res 2021; 49:1737-1748. [PMID: 33503246 PMCID: PMC7897494 DOI: 10.1093/nar/gkaa1276] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 11/29/2022] Open
Abstract
The Ebola virus is a deadly human pathogen responsible for several outbreaks in Africa. Its genome encodes the 'large' L protein, an essential enzyme that has polymerase, capping and methyltransferase activities. The methyltransferase activity leads to RNA co-transcriptional modifications at the N7 position of the cap structure and at the 2'-O position of the first transcribed nucleotide. Unlike other Mononegavirales viruses, the Ebola virus methyltransferase also catalyses 2'-O-methylation of adenosines located within the RNA sequences. Herein, we report the crystal structure at 1.8 Å resolution of the Ebola virus methyltransferase domain bound to a fragment of a camelid single-chain antibody. We identified structural determinants and key amino acids specifically involved in the internal adenosine-2'-O-methylation from cap-related methylations. These results provide the first high resolution structure of an ebolavirus L protein domain, and the framework to investigate the effects of epitranscriptomic modifications and to design possible antiviral drugs against the Filoviridae family.
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Affiliation(s)
- Coralie Valle
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Baptiste Martin
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - François Ferron
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Véronique Roig-Zamboni
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Aline Desmyter
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Françoise Debart
- IBMM, UMR 5247 CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | | | - Bruno Canard
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm, 1207-IHU Méditerranée Infection) Marseille, France
| | - Etienne Decroly
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
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21
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Bengel LL, Aberle B, Egler-Kemmerer AN, Kienzle S, Hauer B, Hammer SC. Engineered Enzymes Enable Selective N-Alkylation of Pyrazoles With Simple Haloalkanes. Angew Chem Int Ed Engl 2021; 60:5554-5560. [PMID: 33300646 PMCID: PMC7986378 DOI: 10.1002/anie.202014239] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/01/2020] [Indexed: 01/06/2023]
Abstract
Selective alkylation of pyrazoles could solve a challenge in chemistry and streamline synthesis of important molecules. Here we report catalyst‐controlled pyrazole alkylation by a cyclic two‐enzyme cascade. In this enzymatic system, a promiscuous enzyme uses haloalkanes as precursors to generate non‐natural analogs of the common cosubstrate S‐adenosyl‐l‐methionine. A second engineered enzyme transfers the alkyl group in highly selective C−N bond formations to the pyrazole substrate. The cosubstrate is recycled and only used in catalytic amounts. Key is a computational enzyme‐library design tool that converted a promiscuous methyltransferase into a small enzyme family of pyrazole‐alkylating enzymes in one round of mutagenesis and screening. With this enzymatic system, pyrazole alkylation (methylation, ethylation, propylation) was achieved with unprecedented regioselectivity (>99 %), regiodivergence, and in a first example on preparative scale.
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Affiliation(s)
- Ludwig L Bengel
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Benjamin Aberle
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Alexander-N Egler-Kemmerer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Samuel Kienzle
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Bernhard Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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22
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Bengel LL, Aberle B, Egler‐Kemmerer A, Kienzle S, Hauer B, Hammer SC. Modifizierte Enzyme ermöglichen die selektive
N
‐Alkylierung von Pyrazolen unter Verwendung einfacher Halogenalkane. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ludwig L. Bengel
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Benjamin Aberle
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Alexander‐N. Egler‐Kemmerer
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Samuel Kienzle
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Bernhard Hauer
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
| | - Stephan C. Hammer
- Fakultät Chemie Organische Chemie und Biokatalyse Universität Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
- Abteilung für Technische Biochemie Institut für Biochemie und Technische Biochemie Universität Stuttgart Allmandring 31 70569 Stuttgart Deutschland
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23
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Medvedev KE, Kinch LN, Dustin Schaeffer R, Pei J, Grishin NV. A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit. J Mol Biol 2020; 433:166788. [PMID: 33387532 DOI: 10.1016/j.jmb.2020.166788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/26/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The Rossmann-like fold is the most prevalent and diversified doubly-wound superfold of ancient evolutionary origin. Rossmann-like domains are present in a variety of metabolic enzymes and are capable of binding diverse ligands. Discerning evolutionary relationships among these domains is challenging because of their diverse functions and ancient origin. We defined a minimal Rossmann-like structural motif (RLM), identified RLM-containing domains among known 3D structures (20%) and classified them according to their homologous relationships. New classifications were incorporated into our Evolutionary Classification of protein Domains (ECOD) database. We defined 156 homology groups (H-groups), which were further clustered into 123 possible homology groups (X-groups). Our analysis revealed that RLM-containing proteins constitute approximately 15% of the human proteome. We found that disease-causing mutations are more frequent within RLM domains than within non-RLM domains of these proteins, highlighting the importance of RLM-containing proteins for human health.
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Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States.
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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24
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Brzezinski K. S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains. Biomolecules 2020; 10:biom10121682. [PMID: 33339190 PMCID: PMC7765604 DOI: 10.3390/biom10121682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/27/2022] Open
Abstract
S-adenosyl-l-homocysteine hydrolase (SAHase) is a major regulator of cellular methylation reactions that occur in eukaryotic and prokaryotic organisms. SAHase activity is also a significant source of l-homocysteine and adenosine, two compounds involved in numerous vital, as well as pathological processes. Therefore, apart from cellular methylation, the enzyme may also influence other processes important for the physiology of particular organisms. Herein, presented is the structural characterization and comparison of SAHases of eukaryotic and prokaryotic origin, with an emphasis on the two principal domains of SAHase subunit based on the Rossmann motif. The first domain is involved in the binding of a substrate, e.g., S-adenosyl-l-homocysteine or adenosine and the second domain binds the NAD+ cofactor. Despite their structural similarity, the molecular interactions between an adenosine-based ligand molecule and macromolecular environment are different in each domain. As a consequence, significant differences in the conformation of d-ribofuranose rings of nucleoside and nucleotide ligands, especially those attached to adenosine moiety, are observed. On the other hand, the chemical nature of adenine ring recognition, as well as an orientation of the adenine ring around the N-glycosidic bond are of high similarity for the ligands bound in the substrate- and cofactor-binding domains.
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Affiliation(s)
- Krzysztof Brzezinski
- Laboratory of Structural Microbiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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25
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Squeglia F, Romano M, Ruggiero A, Maga G, Berisio R. Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins. Front Chem 2020; 8:602162. [PMID: 33381492 PMCID: PMC7769135 DOI: 10.3389/fchem.2020.602162] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
As intracellular parasites, viruses hijack the host cell metabolic machinery for their replication. Among other cellular proteins, the DEAD-box (DDX) RNA helicases have been shown to be hijacked by coronaviruses and to participate in essential DDX-mediated viral replication steps. Human DDX RNA helicases play essential roles in a broad array of biological processes and serve multiple roles at the virus-host interface. The viral proteins responsible for DDX interactions are highly conserved among coronaviruses, suggesting that they might also play conserved functions in the SARS-CoV-2 replication cycle. In this review, we provide an update of the structural and functional data of DDX as possible key factors involved in SARS-CoV-2 hijacking mechanisms. We also attempt to fill the existing gaps in the available structural information through homology modeling. Based on this information, we propose possible paths exploited by the virus to replicate more efficiently by taking advantage of host DDX proteins. As a general rule, sequestration of DDX helicases by SARS-CoV-2 is expected to play a pro-viral role in two ways: by enhancing key steps of the virus life cycle and, at the same time, by suppressing the host innate immune response.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics (IGM-CNR), Pavia, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
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26
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Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites. PLoS Comput Biol 2020; 16:e1007904. [PMID: 32453784 PMCID: PMC7319350 DOI: 10.1371/journal.pcbi.1007904] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 06/26/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB and on all-atom molecular dynamics simulations in water). We identified structural descriptors—angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs compact binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water. The topology of a folded polypeptide chain has great impact on the resulting protein function and its interaction with ligands. Interestingly, topological constraints appear to affect binding of one of the most ubiquitous substrates in the cell, S-adenosylmethionine (SAM), to its target proteins. Here, we demonstrate how binding sites of specific proteins restrict SAM conformational freedom in comparison to its unbound state, with a special interest in proteins with non-trivial topology, including an exciting group of knotted methyltransferases. Using a vast array of computational methods combined with NMR experiments, we identify key structural features of knotted methyltransferases that impose unorthodox SAM conformations. We compare them with the characteristics of standard, unknotted SAM binding proteins. These results are significant for understanding differences between analogous, yet topologically different enzymes, as well as for future rational drug design.
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27
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Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells 2020; 9:E1267. [PMID: 32443810 PMCID: PMC7291026 DOI: 10.3390/cells9051267] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 01/18/2023] Open
Abstract
The current coronavirus disease-2019 (COVID-19) pandemic is due to the novel coronavirus SARS-CoV-2. The scientific community has mounted a strong response by accelerating research and innovation, and has quickly set the foundation for understanding the molecular determinants of the disease for the development of targeted therapeutic interventions. The replication of the viral genome within the infected cells is a key stage of the SARS-CoV-2 life cycle. It is a complex process involving the action of several viral and host proteins in order to perform RNA polymerization, proofreading and final capping. This review provides an update of the structural and functional data on the key actors of the replicatory machinery of SARS-CoV-2, to fill the gaps in the currently available structural data, which is mainly obtained through homology modeling. Moreover, learning from similar viruses, we collect data from the literature to reconstruct the pattern of interactions among the protein actors of the SARS-CoV-2 RNA polymerase machinery. Here, an important role is played by co-factors such as Nsp8 and Nsp10, not only as allosteric activators but also as molecular connectors that hold the entire machinery together to enhance the efficiency of RNA replication.
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Affiliation(s)
- Maria Romano
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Giovanni Maga
- Institute of Molecular Genetics, IGM, CNR, 27100 Pavia, Italy;
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
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28
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Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Wiersum G, Kim Y, Jedrzejczak R, Maltseva NI, Endres M, Jaroszewski L, Godzik A, Joachimiak A, Satchell KJF. The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.17.047498. [PMID: 32511376 PMCID: PMC7263505 DOI: 10.1101/2020.04.17.047498] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 is a member of the coronaviridae family and is the etiological agent of the respiratory Coronavirus Disease 2019. The virus has spread rapidly around the world resulting in over two million cases and nearly 150,000 deaths as of April 17, 2020. Since no treatments or vaccines are available to treat COVID-19 and SARS-CoV-2, respiratory complications derived from the infections have overwhelmed healthcare systems around the world. This virus is related to SARS-CoV-1, the virus that caused the 2002-2004 outbreak of Severe Acute Respiratory Syndrome. In January 2020, the Center for Structural Genomics of Infectious Diseases implemented a structural genomics pipeline to solve the structures of proteins essential for coronavirus replication-transcription. Here we show the first structure of the SARS-CoV-2 nsp10-nsp16 2'-O-methyltransferase complex with S-adenosylmethionine at a resolution of 1.80 Å. This heterodimer complex is essential for capping viral mRNA transcripts for efficient translation and to evade immune surveillance.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Olga Kiryukhina
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Grant Wiersum
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Michael Endres
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Lukasz Jaroszewski
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, CA, USA
| | - Adam Godzik
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, CA, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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29
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Valentic TR, Payne JT, Smolke CD. Structure-Guided Engineering of a Scoulerine 9-O-Methyltransferase Enables the Biosynthesis of Tetrahydropalmatrubine and Tetrahydropalmatine in Yeast. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05417] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy R. Valentic
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, California 94305, United States
| | - James T. Payne
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, California 94305, United States
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, California 94305, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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30
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Ferron F, Debat HJ, Shannon A, Decroly E, Canard B. A N7-guanine RNA cap methyltransferase signature-sequence as a genetic marker of large genome, non-mammalian Tobaniviridae. NAR Genom Bioinform 2019; 2:lqz022. [PMID: 32289120 PMCID: PMC7107822 DOI: 10.1093/nargab/lqz022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/22/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
The order Nidovirales is a diverse group of (+)RNA viruses, classified together based on their common genome organisation and conserved replicative enzymes, despite drastic differences in size and complexity. One such difference pertains to the mechanisms and enzymes responsible for generation of the proposed viral 5′ RNA cap. Within the Coronaviridae family, two separate methytransferases (MTase), nsp14 and nsp16, perform the RNA-cap N7-guanine and 2′-OH methylation respectively for generation of the proposed m7GpppNm type I cap structure. For the majority of other families within the Nidovirales order, the presence, structure and key enzymes involved in 5′ capping are far less clear. These viruses either lack completely an RNA MTase signature sequence, or lack an N7-guanine methyltransferase signature sequence, obscuring our understanding about how RNA-caps are N7-methylated for these families. Here, we report the discovery of a putative Rossmann fold RNA methyltransferase in 10 Tobaniviridae members in Orf1a, an unusual genome locus for this gene. Multiple sequence alignments and structural analyses lead us to propose this novel gene as a typical RNA-cap N7-guanine MTase with substrate specificity and active-site organization similar to the canonical eukaryotic RNA-cap N7-guanine MTase.
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Affiliation(s)
- François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Humberto J Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, X5119 Córdoba, Argentina
| | - Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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31
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Fricke J, Sherwood A, Kargbo R, Orry A, Blei F, Naschberger A, Rupp B, Hoffmeister D. Enzymatic Route toward 6‐Methylated Baeocystin and Psilocybin. Chembiochem 2019; 20:2824-2829. [DOI: 10.1002/cbic.201900358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Janis Fricke
- Department Pharmaceutical Microbiology at the Hans Knöll InstituteFriedrich-Schiller-Universität Beutenbergstrasse 11a 07745 Jena Germany
| | | | - Robert Kargbo
- The Usona Institute 2800 Woods Hollow Road Madison WI 53711 USA
| | - Andrew Orry
- Molsoft L.L.C. 11199 Sorrento Valley Road San Diego CA 92121 USA
| | - Felix Blei
- Department Pharmaceutical Microbiology at the Hans Knöll InstituteFriedrich-Schiller-Universität Beutenbergstrasse 11a 07745 Jena Germany
| | - Andreas Naschberger
- Department of Genetic EpidemiologyMedizinische Universität Innsbruck Schöpfstrasse 41 6020 Innsbruck Austria
| | - Bernhard Rupp
- Department of Genetic EpidemiologyMedizinische Universität Innsbruck Schöpfstrasse 41 6020 Innsbruck Austria
- Hofkristallamt 991 Audrey Place Vista CA 92084 USA
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans Knöll InstituteFriedrich-Schiller-Universität Beutenbergstrasse 11a 07745 Jena Germany
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32
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Ogando NS, Ferron F, Decroly E, Canard B, Posthuma CC, Snijder EJ. The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity. Front Microbiol 2019; 10:1813. [PMID: 31440227 PMCID: PMC6693484 DOI: 10.3389/fmicb.2019.01813] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/23/2019] [Indexed: 12/20/2022] Open
Abstract
Among RNA viruses, the order Nidovirales stands out for including viruses with the largest RNA genomes currently known. Nidoviruses employ a complex RNA-synthesizing machinery comprising a variety of non-structural proteins (nsps). One of the postulated drivers of the expansion of nidovirus genomes is the presence of a proofreading 3′-to-5′ exoribonuclease (ExoN) belonging to the DEDDh family. ExoN may enhance the fidelity of RNA synthesis by correcting nucleotide incorporation errors made by the RNA-dependent RNA polymerase. Here, we review our current understanding of ExoN evolution, structure, and function. Most experimental data are derived from studies of the ExoN domain of coronaviruses (CoVs), which were triggered by the bioinformatics-based identification of ExoN in the genome of severe acute respiratory syndrome coronavirus (SARS-CoV) and its relatives in 2003. Although convincing data supporting the proofreading hypothesis have been obtained, from biochemical assays and studies with CoV mutants lacking ExoN functionality, the features of ExoN from most other nidovirus families remain to be characterized. Remarkably, viable ExoN knockout mutants were obtained only for two CoVs, mouse hepatitis virus (MHV) and SARS-CoV, whose RNA synthesis and replication kinetics were mildly affected by the lack of ExoN function. In several other CoV species, ExoN inactivation was not tolerated, and knockout mutants could not be rescued when launched using a reverse genetics system. This suggests that ExoN is also critical for primary viral RNA synthesis, a property that poorly matches the profile of an enzyme that would merely boost long-term replication fidelity. In CoVs, ExoN resides in a bifunctional replicase subunit (nsp14) whose C-terminal part has (N7-guanine)-methyltransferase activity. The crystal structure of SARS-CoV nsp14 has shed light on the interplay between these two domains, and on nsp14’s interactions with nsp10, a co-factor that strongly enhances ExoN activity in vitro assays. Further elucidation of the structure-function relationships of ExoN and its interactions with other (viral and/or host) members of the CoV replication machinery will be key to understanding the enzyme’s role in viral RNA synthesis and pathogenesis, and may contribute to the design of new approaches to combat emerging nidoviruses.
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Affiliation(s)
- Natacha S Ogando
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Francois Ferron
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France.,European Virus Bioinformatics Center, Jena, Germany
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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33
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Dilworth D, Barsyte-Lovejoy D. Targeting protein methylation: from chemical tools to precision medicines. Cell Mol Life Sci 2019; 76:2967-2985. [PMID: 31104094 PMCID: PMC11105543 DOI: 10.1007/s00018-019-03147-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/15/2022]
Abstract
The methylation of proteins is integral to the execution of many important biological functions, including cell signalling and transcriptional regulation. Protein methyltransferases (PMTs) are a large class of enzymes that carry out the addition of methyl marks to a broad range of substrates. PMTs are critical for normal cellular physiology and their dysregulation is frequently observed in human disease. As such, PMTs have emerged as promising therapeutic targets with several inhibitors now in clinical trials for oncology indications. The discovery of chemical inhibitors and antagonists of protein methylation signalling has also profoundly impacted our general understanding of PMT biology and pharmacology. In this review, we present general principles for drugging protein methyltransferases or their downstream effectors containing methyl-binding modules, as well as best-in-class examples of the compounds discovered and their impact both at the bench and in the clinic.
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Affiliation(s)
- David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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