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Peng J, Hughes GR, Müller MM, Seebeck FP. Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation. Angew Chem Int Ed Engl 2024; 63:e202312104. [PMID: 37955592 PMCID: PMC10952888 DOI: 10.1002/anie.202312104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.
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Affiliation(s)
- Jiaming Peng
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
| | - Gregory R. Hughes
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Manuel M. Müller
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Florian P. Seebeck
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
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Peng J, Hughes GR, Müller MM, Seebeck FP. Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation. Angew Chem Weinheim Bergstr Ger 2024; 136:e202312104. [PMID: 38516647 PMCID: PMC10952241 DOI: 10.1002/ange.202312104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Indexed: 03/23/2024]
Abstract
S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.
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Affiliation(s)
- Jiaming Peng
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
| | - Gregory R. Hughes
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Manuel M. Müller
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Florian P. Seebeck
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
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Banreti A, Bhattacharya S, Wien F, Matsuo K, Réfrégiers M, Meinert C, Meierhenrich U, Hudry B, Thompson D, Noselli S. Biological effects of the loss of homochirality in a multicellular organism. Nat Commun 2022; 13:7059. [PMID: 36400783 PMCID: PMC9674851 DOI: 10.1038/s41467-022-34516-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
Homochirality is a fundamental feature of all known forms of life, maintaining biomolecules (amino-acids, proteins, sugars, nucleic acids) in one specific chiral form. While this condition is central to biology, the mechanisms by which the adverse accumulation of non-L-α-amino-acids in proteins lead to pathophysiological consequences remain poorly understood. To address how heterochirality build-up impacts organism's health, we use chiral-selective in vivo assays to detect protein-bound non-L-α-amino acids (focusing on aspartate) and assess their functional significance in Drosophila. We find that altering the in vivo chiral balance creates a 'heterochirality syndrome' with impaired caspase activity, increased tumour formation, and premature death. Our work shows that preservation of homochirality is a key component of protein function that is essential to maintain homeostasis across the cell, tissue and organ level.
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Affiliation(s)
- Agnes Banreti
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
| | - Shayon Bhattacharya
- grid.10049.3c0000 0004 1936 9692Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Frank Wien
- grid.426328.9DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Koichi Matsuo
- grid.257022.00000 0000 8711 3200HiSOR Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| | - Matthieu Réfrégiers
- grid.417870.d0000 0004 0614 8532Centre de Biophysique Moléculaire, CNRS; UPR4301, 45071 Orléans, France
| | - Cornelia Meinert
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, Institut de Chimie de Nice, CNRS; UMR 7272, 06108 Nice, France
| | - Uwe Meierhenrich
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, Institut de Chimie de Nice, CNRS; UMR 7272, 06108 Nice, France
| | - Bruno Hudry
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
| | - Damien Thompson
- grid.10049.3c0000 0004 1936 9692Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Stéphane Noselli
- grid.461605.0Université Côte d’Azur, CNRS, Inserm, Institut de Biologie Valrose, 06108 Nice, France
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Abstract
Since Jacques Monod's foundational work in the 1940s, investigators studying bacterial physiology have largely (but not exclusively) focused on the exponential phase of bacterial cultures, which is characterized by rapid growth and high biosynthesis activity in the presence of excess nutrients. However, this is not the predominant state of bacterial life. In nature, most bacteria experience nutrient limitation most of the time. In fact, investigators even prior to Monod had identified other aspects of bacterial growth, including what is now known as the stationary phase, when nutrients become limiting. This review will discuss how bacteria transition to growth arrest in response to nutrient limitation through changes in transcription, translation, and metabolism. We will then examine how these changes facilitate survival during potentially extended periods of nutrient limitation, with particular attention to the metabolic strategies that underpin bacterial longevity in this state.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA;
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington, USA;
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Song S, Chen A, Zhu J, Yan Z, An Q, Zhou J, Liao H, Yu Y. Structure basis of the caffeic acid O-methyltransferase from Ligusiticum chuanxiong to understand its selective mechanism. Int J Biol Macromol 2022; 194:317-330. [PMID: 34838855 DOI: 10.1016/j.ijbiomac.2021.11.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/20/2021] [Indexed: 02/08/2023]
Abstract
Caffeic acid O-methyltransferase from Ligusticum chuanxiong (LcCOMT) showed strict regiospecificity despite a relative degree of preference. Compared with caffeic acid, methyl caffeate was the preferential substrate by its low Km and high Kcat. In this study, we obtained the SAM binary (1.80 Å) and SAH binary (1.95 Å) complex LcCOMT crystal structures, and established the ternary complex structure with methyl caffeate by molecular docking. The active site of LcCOMT included phenolic substrate pocket, SAM/SAH ligand pocket and conserved catalytic residues as well. The regiospecificity of LcCOMT that permitted only 3-hydroxyl group to be methylated arise from the interactions between the active site and the phenyl ring. However, the propanoid tail governed the relative preference of LcCOMT. The ester group in methyl caffeate stabilized the anionic intermediate caused by His268-Asp269 pair, whereas caffeic acid was unable to stabilize the anionic intermediate due to the adjacent carboxylate anion in the propanoid tail. Ser183 residue formed an additional hydrogen bond with SAH and its role was identified by S183A mutation. Ile318 residue might be a potential site for determination of substrate preference, and its mutation led to the change of tertiary conformation. The results supported the selective mechanism of LcCOMT.
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Affiliation(s)
- Simin Song
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Anqi Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Jianquan Zhu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Zicheng Yan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Qiuju An
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China.
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China.
| | - Yamei Yu
- Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.
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Kamble NU, Majee M. PROTEIN l-ISOASPARTYL METHYLTRANSFERASE (PIMT) in plants: regulations and functions. Biochem J 2020; 477:4453-71. [PMID: 33245750 DOI: 10.1042/BCJ20200794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Proteins are essential molecules that carry out key functions in a cell. However, as a result of aging or stressful environments, the protein undergoes a range of spontaneous covalent modifications, including the formation of abnormal l-isoaspartyl residues from aspartyl or asparaginyl residues, which can disrupt the protein's inherent structure and function. PROTEIN l-ISOASPARTYL METHYLTRANSFERASE (PIMT: EC 2.1.1.77), an evolutionarily conserved ancient protein repairing enzyme (PRE), converts such abnormal l-isoaspartyl residues to normal l-aspartyl residues and re-establishes the protein's native structure and function. Although originally discovered in animals as a PRE, PIMT emerged as a key PRE in plants, particularly in seeds, in which PIMT plays a predominant role in preserving seed vigor and viability for prolonged periods of time. Interestingly, higher plants encode a second PIMT (PIMT2) protein which possesses a unique N-terminal extension, and exhibits several distinct features and far more complexity than non-plant PIMTs. Recent studies indicate that the role of PIMT is not restricted to preserving seed vigor and longevity but is also implicated in enhancing the growth and survivability of plants under stressful environments. Furthermore, expression studies indicate the tantalizing possibility that PIMT is involved in various physiological processes apart from its role in seed vigor, longevity and plant's survivability under abiotic stress. This review article particularly describes new insights and emerging interest in all facets of this enzyme in plants along with a concise comparative overview on isoAsp formation, and the role and regulation of PIMTs across evolutionary diverse species. Additionally, recent methods and their challenges in identifying isoaspartyl containing proteins (PIMT substrates) are highlighted.
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