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Cai W, Wan Y, Chen Y, Fan H, Li M, Wu S, Lin P, Zeng T, Luo H, Huang D, Fu G. Transcriptomics to evaluate the influence mechanisms of ethanol on the ester production of Wickerhamomyces anomalus with the induction of lactic acid. Food Microbiol 2024; 122:104556. [PMID: 38839235 DOI: 10.1016/j.fm.2024.104556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/17/2024] [Accepted: 04/27/2024] [Indexed: 06/07/2024]
Abstract
Wickerhamomyces anomalus is one of the most important ester-producing strains in Chinese baijiu brewing. Ethanol and lactic acid are the main metabolites produced during baijiu brewing, but their synergistic influence on the growth and ester production of W. anomalus is unclear. Therefore, in this paper, based on the contents of ethanol and lactic acid during Te-flavor baijiu brewing, the effects of different ethanol concentrations (3, 6, and 9% (v/v)) combined with 1% lactic acid on the growth and ester production of W. anomalus NCUF307.1 were studied and their influence mechanisms were analyzed by transcriptomics. The results showed that the growth of W. anomalus NCUF307.1 under the induction of lactic acid was inhibited by ethanol. Although self-repair mechanism of W. anomalus NCUF307.1 induced by lactic acid was initiated at all concentrations of ethanol, resulting in significant up-regulation of genes related to the Genetic Information Processing pathway, such as cell cycle-yeast, meiosis-yeast, DNA replication and other pathways. However, the accumulation of reactive oxygen species and the inhibition of pathways associated with carbohydrate and amino acid metabolism may be the main reason for the inhibition of growth in W. anomalus NCUF307.1. In addition, 3% and 6% ethanol combined with 1% lactic acid could promote the ester production of W. anomalus NCUF307.1, which may be related to the up-regulation of EAT1, ADH5 and TGL5 genes, while the inhibition in 9% ethanol may be related to down-regulation of ATF2, EAT1, ADH2, ADH5, and TGL3 genes.
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Affiliation(s)
- Wenqin Cai
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Yin Wan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Yanru Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Haowei Fan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Mengxiang Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; Liquor Making Biological Technology and Application Key Laboratory of Sichuan Province, Yibin, 644000, PR, China
| | - Shengwen Wu
- Sitir Liquor Co., Ltd, Zhangshu, 331200, PR, China
| | - Pei Lin
- Sitir Liquor Co., Ltd, Zhangshu, 331200, PR, China
| | | | - Huibo Luo
- Liquor Making Biological Technology and Application Key Laboratory of Sichuan Province, Yibin, 644000, PR, China
| | - Dan Huang
- Liquor Making Biological Technology and Application Key Laboratory of Sichuan Province, Yibin, 644000, PR, China
| | - Guiming Fu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China.
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2
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Mathur Y, Hazra AB. Methylations in vitamin B 12 biosynthesis and catalysis. Curr Opin Struct Biol 2022; 77:102490. [PMID: 36371846 DOI: 10.1016/j.sbi.2022.102490] [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: 05/10/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/12/2022]
Abstract
Vitamin B12 is an essential biomolecule that assists in the catalysis of methyl transfer and radical-based reactions in cellular metabolism. The structure of B12 is characterized by a tetrapyrrolic corrin ring with a central cobalt ion coordinated with an upper ligand, and a lower ligand anchored via a nucleotide loop. Multiple methyl groups decorate B12, and their presence (or absence) have structural and functional consequences. In this minireview, we focus on the methyl groups that distinguish vitamin B12 from other tetrapyrrolic biomolecules and from its own naturally occurring analogues called cobamides. We draw information from recent advances in the field to understand the origins of these methyl groups and the enzymes that incorporate them, and discuss their biological significance.
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Affiliation(s)
- Yamini Mathur
- Department of Biology, Indian Institute of Science Education and Research, Pune, India. https://twitter.com/yaminipmathur
| | - Amrita B Hazra
- Department of Biology, Indian Institute of Science Education and Research, Pune, India; Department of Chemistry, Indian Institute of Science Education and Research, Pune, India.
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3
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Li N, Desiderio DM, Zhan X. The use of mass spectrometry in a proteome-centered multiomics study of human pituitary adenomas. MASS SPECTROMETRY REVIEWS 2022; 41:964-1013. [PMID: 34109661 DOI: 10.1002/mas.21710] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
A pituitary adenoma (PA) is a common intracranial neoplasm, and is a complex, chronic, and whole-body disease with multicausing factors, multiprocesses, and multiconsequences. It is very difficult to clarify molecular mechanism and treat PAs from the single-factor strategy model. The rapid development of multiomics and systems biology changed the paradigms from a traditional single-factor strategy to a multiparameter systematic strategy for effective management of PAs. A series of molecular alterations at the genome, transcriptome, proteome, peptidome, metabolome, and radiome levels are involved in pituitary tumorigenesis, and mutually associate into a complex molecular network system. Also, the center of multiomics is moving from structural genomics to phenomics, including proteomics and metabolomics in the medical sciences. Mass spectrometry (MS) has been extensively used in phenomics studies of human PAs to clarify molecular mechanisms, and to discover biomarkers and therapeutic targets/drugs. MS-based proteomics and proteoform studies play central roles in the multiomics strategy of PAs. This article reviews the status of multiomics, multiomics-based molecular pathway networks, molecular pathway network-based pattern biomarkers and therapeutic targets/drugs, and future perspectives for personalized, predeictive, and preventive (3P) medicine in PAs.
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Affiliation(s)
- Na Li
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
| | - Dominic M Desiderio
- The Charles B. Stout Neuroscience Mass Spectrometry Laboratory, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
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4
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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5
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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6
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Kořený L, Oborník M, Horáková E, Waller RF, Lukeš J. The convoluted history of haem biosynthesis. Biol Rev Camb Philos Soc 2021; 97:141-162. [PMID: 34472688 DOI: 10.1111/brv.12794] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 01/14/2023]
Abstract
The capacity of haem to transfer electrons, bind diatomic gases, and catalyse various biochemical reactions makes it one of the essential biomolecules on Earth and one that was likely used by the earliest forms of cellular life. Since the description of haem biosynthesis, our understanding of this multi-step pathway has been almost exclusively derived from a handful of model organisms from narrow taxonomic contexts. Recent advances in genome sequencing and functional studies of diverse and previously neglected groups have led to discoveries of alternative routes of haem biosynthesis that deviate from the 'classical' pathway. In this review, we take an evolutionarily broad approach to illuminate the remarkable diversity and adaptability of haem synthesis, from prokaryotes to eukaryotes, showing the range of strategies that organisms employ to obtain and utilise haem. In particular, the complex evolutionary histories of eukaryotes that involve multiple endosymbioses and horizontal gene transfers are reflected in the mosaic origin of numerous metabolic pathways with haem biosynthesis being a striking case. We show how different evolutionary trajectories and distinct life strategies resulted in pronounced tensions and differences in the spatial organisation of the haem biosynthesis pathway, in some cases leading to a complete loss of a haem-synthesis capacity and, rarely, even loss of a requirement for haem altogether.
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Affiliation(s)
- Luděk Kořený
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, U.K
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice (Budweis), 370 05, Czech Republic.,Faculty of Sciences, University of South Bohemia, Branišovská, České Budějovice (Budweis), 31, Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice (Budweis), 370 05, Czech Republic
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, U.K
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice (Budweis), 370 05, Czech Republic.,Faculty of Sciences, University of South Bohemia, Branišovská, České Budějovice (Budweis), 31, Czech Republic
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7
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Abstract
The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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8
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Fujishiro T, Ogawa S. The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis. Chem Sci 2021; 12:2172-2180. [PMID: 34163982 PMCID: PMC8179277 DOI: 10.1039/d0sc05439a] [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] [Indexed: 01/30/2023] Open
Abstract
The class II chelatase CfbA catalyzes Ni2+ insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni2+ and Co2+ remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni2+, Ni-SHC, and Co2+ were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni2+-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co2+ than Ni2+. Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni2+ and Co2+ by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni2+ insertion catalytic mechanism was proposed: Ni2+ insertion to SHC is promoted by the support of an acetate side chain of SHC.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Shimo-Okubo 255 Sakura Saitama 338-8570 Japan +81-48-858-9293
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Shimo-Okubo 255 Sakura Saitama 338-8570 Japan +81-48-858-9293
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9
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Kirschning A. The coenzyme/protein pair and the molecular evolution of life. Nat Prod Rep 2020; 38:993-1010. [PMID: 33206101 DOI: 10.1039/d0np00037j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Zentrum für Biomolekulare Wirkstoffchemie (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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10
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
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11
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Abstract
Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle and also modify its size, its side-chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1, and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review.
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Affiliation(s)
- Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
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12
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Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol 2018; 606:1-71. [PMID: 30097089 DOI: 10.1016/bs.mie.2018.06.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States.
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Elaine C Meng
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, United States
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Sara Calhoun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Graduate Program in Biophysics, University of California, San Francisco, CA, United States
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
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13
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Widner FJ, Lawrence AD, Deery E, Heldt D, Frank S, Gruber K, Wurst K, Warren MJ, Kräutler B. Total Synthesis, Structure, and Biological Activity of Adenosylrhodibalamin, the Non-Natural Rhodium Homologue of Coenzyme B12. Angew Chem Int Ed Engl 2016; 55:11281-6. [PMID: 27355790 PMCID: PMC5103170 DOI: 10.1002/anie.201603738] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/12/2022]
Abstract
B12 is unique among the vitamins as it is biosynthesized only by certain prokaryotes. The complexity of its synthesis relates to its distinctive cobalt corrin structure, which is essential for B12 biochemistry and renders coenzyme B12 (AdoCbl) so intriguingly suitable for enzymatic radical reactions. However, why is cobalt so fit for its role in B12 -dependent enzymes? To address this question, we considered the substitution of cobalt in AdoCbl with rhodium to generate the rhodium analogue 5'-deoxy-5'-adenosylrhodibalamin (AdoRbl). AdoRbl was prepared by de novo total synthesis involving both biological and chemical steps. AdoRbl was found to be inactive in vivo in microbial bioassays for methionine synthase and acted as an in vitro inhibitor of an AdoCbl-dependent diol dehydratase. Solution NMR studies of AdoRbl revealed a structure similar to that of AdoCbl. However, the crystal structure of AdoRbl revealed a conspicuously better fit of the corrin ligand for Rh(III) than for Co(III) , challenging the current views concerning the evolution of corrins.
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Affiliation(s)
- Florian J Widner
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI), Universität Innsbruck, 6020, Innsbruck, Austria.,Plant and Microbial Biology Department, University of California, Berkeley, CA, USA
| | | | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Dana Heldt
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Stefanie Frank
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften, Universität Graz, Austria
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck, Austria
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Bernhard Kräutler
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI), Universität Innsbruck, 6020, Innsbruck, Austria.
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14
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Widner FJ, Lawrence AD, Deery E, Heldt D, Frank S, Gruber K, Wurst K, Warren MJ, Kräutler B. Totalsynthese, Struktur und biologische Aktivität von Adenosylrhodibalamin, dem unnatürlichen Rhodiumhomologen von Coenzym B12. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603738] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Florian J. Widner
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI); Universität Innsbruck; 6020 Innsbruck Österreich
- Plant and Microbial Biology Department; University of California; Berkeley USA
| | - Andrew D. Lawrence
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Evelyne Deery
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Dana Heldt
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Stefanie Frank
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften; Universität Graz; Österreich
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische und Theoretische Chemie; Universität Innsbruck; Österreich
| | - Martin J. Warren
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Bernhard Kräutler
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI); Universität Innsbruck; 6020 Innsbruck Österreich
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Newton MS, Arcus VL, Patrick WM. Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes. J R Soc Interface 2016; 12:rsif.2015.0036. [PMID: 25926697 DOI: 10.1098/rsif.2015.0036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. In this review, we summarize experimental data that suggest a different reality. Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. Experiments to infer and resurrect ancient sequences suggest that some of the first organisms present on the Earth are likely to have possessed highly active enzymes. Reconciling these observations, we argue that rapid bursts of strong selection for increased catalytic efficiency are interspersed with much longer periods in which the catalytic power of an enzyme erodes, through neutral drift and selection for other properties such as cellular energy efficiency or regulation. Thus, many enzymes may have already passed their catalytic peaks.
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Affiliation(s)
- Matilda S Newton
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Vickery L Arcus
- School of Biology, University of Waikato, Hamilton, New Zealand
| | - Wayne M Patrick
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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16
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Bruska MK, Stiebritz MT, Reiher M. Binding of Reactive Oxygen Species at Fe-S Cubane Clusters. Chemistry 2015; 21:19081-9. [PMID: 26585994 DOI: 10.1002/chem.201503008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 01/05/2023]
Abstract
Reactive oxygen species (ROS) play an important role in the biochemistry of the cell and occur in degenerative processes as well as in signal transduction. Iron-sulfur proteins are particularly oxygen-sensitive and their inorganic cofactors frequently undergo ROS-induced decomposition reactions. As experimental knowledge about these processes is still incomplete we present here a quantum chemical study of the relative energetics for the binding of the most relevant ROS to [Fe4S4] clusters. We find that cubane clusters with one uncoordinated Fe atom (as found, for instance, in aconitase) bind all oxygen derivatives considered, whereas activation of triplet O2 to singlet O2 is required for binding to valence-saturated iron centers in these clusters. The radicals NO and OH feature the most exothermic binding energies to Fe atoms. Direct sulfoxidation of coordinating cysteine residues is only possible by OH or H2O2 as attacking agents. The thermodynamic picture of ROS binding to iron-sulfur clusters established here can serve as a starting point for studying reactivity-modulating effects of the cluster-embedding protein environment on ROS-induced decomposition of iron-sulfur proteins.
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Affiliation(s)
- Marta K Bruska
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland)
| | - Martin T Stiebritz
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland)
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland).
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17
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Affiliation(s)
- Torsten Bruhn
- Institute
of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Christian Brückner
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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Dailey HA, Gerdes S. HemQ: An iron-coproporphyrin oxidative decarboxylase for protoheme synthesis in Firmicutes and Actinobacteria. Arch Biochem Biophys 2015; 574:27-35. [PMID: 25711532 DOI: 10.1016/j.abb.2015.02.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 02/05/2023]
Abstract
Genes for chlorite dismutase-like proteins are found widely among heme-synthesizing bacteria and some Archaea. It is now known that among the Firmicutes and Actinobacteria these proteins do not possess chlorite dismutase activity but instead are essential for heme synthesis. These proteins, named HemQ, are iron-coproporphyrin (coproheme) decarboxylases that catalyze the oxidative decarboxylation of coproheme III into protoheme IX. As purified, HemQs do not contain bound heme, but readily bind exogeneously supplied heme with low micromolar affinity. The heme-bound form of HemQ has low peroxidase activity and in the presence of peroxide the bound heme may be destroyed. Thus, it is possible that HemQ may serve a dual role as a decarboxylase in heme biosynthesis and a regulatory protein in heme homeostasis.
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Affiliation(s)
- Harry A Dailey
- Biomedical and Health Sciences Institute, Department of Microbiology and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Svetlana Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
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19
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20
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Bali S, Palmer DJ, Schroeder S, Ferguson SJ, Warren MJ. Recent advances in the biosynthesis of modified tetrapyrroles: the discovery of an alternative pathway for the formation of heme and heme d 1. Cell Mol Life Sci 2014; 71:2837-63. [PMID: 24515122 PMCID: PMC11113276 DOI: 10.1007/s00018-014-1563-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 12/19/2013] [Accepted: 01/10/2014] [Indexed: 02/05/2023]
Abstract
Hemes (a, b, c, and o) and heme d 1 belong to the group of modified tetrapyrroles, which also includes chlorophylls, cobalamins, coenzyme F430, and siroheme. These compounds are found throughout all domains of life and are involved in a variety of essential biological processes ranging from photosynthesis to methanogenesis. The biosynthesis of heme b has been well studied in many organisms, but in sulfate-reducing bacteria and archaea, the pathway has remained a mystery, as many of the enzymes involved in these characterized steps are absent. The heme pathway in most organisms proceeds from the cyclic precursor of all modified tetrapyrroles uroporphyrinogen III, to coproporphyrinogen III, which is followed by oxidation of the ring and finally iron insertion. Sulfate-reducing bacteria and some archaea lack the genetic information necessary to convert uroporphyrinogen III to heme along the "classical" route and instead use an "alternative" pathway. Biosynthesis of the isobacteriochlorin heme d 1, a cofactor of the dissimilatory nitrite reductase cytochrome cd 1, has also been a subject of much research, although the biosynthetic pathway and its intermediates have evaded discovery for quite some time. This review focuses on the recent advances in the understanding of these two pathways and their surprisingly close relationship via the unlikely intermediate siroheme, which is also a cofactor of sulfite and nitrite reductases in many organisms. The evolutionary questions raised by this discovery will also be discussed along with the potential regulation required by organisms with overlapping tetrapyrrole biosynthesis pathways.
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Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - David J. Palmer
- School of Biosciences, University of Kent, Kent, Canterbury, CT2 7NZ UK
| | - Susanne Schroeder
- School of Biosciences, University of Kent, Kent, Canterbury, CT2 7NZ UK
| | - Stuart J. Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Martin J. Warren
- School of Biosciences, University of Kent, Kent, Canterbury, CT2 7NZ UK
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21
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Adams NE, Thiaville JJ, Proestos J, Juárez-Vázquez AL, McCoy AJ, Barona-Gómez F, Iwata-Reuyl D, de Crécy-Lagard V, Maurelli AT. Promiscuous and adaptable enzymes fill "holes" in the tetrahydrofolate pathway in Chlamydia species. mBio 2014; 5:e01378-14. [PMID: 25006229 PMCID: PMC4161248 DOI: 10.1128/mbio.01378-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/03/2014] [Indexed: 11/20/2022] Open
Abstract
Folates are tripartite molecules comprising pterin, para-aminobenzoate (PABA), and glutamate moieties, which are essential cofactors involved in DNA and amino acid synthesis. The obligately intracellular Chlamydia species have lost several biosynthetic pathways for essential nutrients which they can obtain from their host but have retained the capacity to synthesize folate. In most bacteria, synthesis of the pterin moiety of folate requires the FolEQBK enzymes, while synthesis of the PABA moiety is carried out by the PabABC enzymes. Bioinformatic analyses reveal that while members of Chlamydia are missing the genes for FolE (GTP cyclohydrolase) and FolQ, which catalyze the initial steps in de novo synthesis of the pterin moiety, they have genes for the rest of the pterin pathway. We screened a chlamydial genomic library in deletion mutants of Escherichia coli to identify the "missing genes" and identified a novel enzyme, TrpFCtL2, which has broad substrate specificity. TrpFCtL2, in combination with GTP cyclohydrolase II (RibA), the first enzyme of riboflavin synthesis, provides a bypass of the first two canonical steps in folate synthesis catalyzed by FolE and FolQ. Notably, TrpFCtL2 retains the phosphoribosyl anthranilate isomerase activity of the original annotation. Additionally, we independently confirmed the recent discovery of a novel enzyme, CT610, which uses an unknown precursor to synthesize PABA and complements E. coli mutants with deletions of pabA, pabB, or pabC. Thus, Chlamydia species have evolved a variant folate synthesis pathway that employs a patchwork of promiscuous and adaptable enzymes recruited from other biosynthetic pathways. Importance: Collectively, the involvement of TrpFCtL2 and CT610 in the tetrahydrofolate pathway completes our understanding of folate biosynthesis in Chlamydia. Moreover, the novel roles for TrpFCtL2 and CT610 in the tetrahydrofolate pathway are sophisticated examples of how enzyme evolution plays a vital role in the adaptation of obligately intracellular organisms to host-specific niches. Enzymes like TrpFCtL2 which possess an enzyme fold common to many other enzymes are highly versatile and possess the capacity to evolve to catalyze related reactions in two different metabolic pathways. The continued identification of unique enzymes such as these in bacterial pathogens is important for development of antimicrobial compounds, as drugs that inhibit such enzymes would likely not have any targets in the host or the host's normal microbial flora.
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Affiliation(s)
- Nancy E Adams
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, Maryland, USA
| | - Jennifer J Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - James Proestos
- Department of Chemistry, Portland State University, Portland, Oregon, USA
| | - Ana L Juárez-Vázquez
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Andrea J McCoy
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, Maryland, USA
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, Oregon, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Anthony T Maurelli
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, Maryland, USA
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Helliwell KE, Wheeler GL, Smith AG. Widespread decay of vitamin-related pathways: coincidence or consequence? Trends Genet 2013; 29:469-78. [DOI: 10.1016/j.tig.2013.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/09/2013] [Accepted: 03/25/2013] [Indexed: 02/03/2023]
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23
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Bruska MK, Stiebritz MT, Reiher M. Analysis of differences in oxygen sensitivity of Fe-S clusters. Dalton Trans 2013; 42:8729-35. [PMID: 23632881 DOI: 10.1039/c3dt50763g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Many but not all iron-sulphur clusters in metalloproteins are known to be sensitive to molecular oxygen with dramatic consequences for their biological function. We performed a systematic quantum chemical investigation that sheds light on the differences in oxygen sensitivity depending on charge and spin states of these clusters as well as on their spatial fixation by the enzyme's scaffold. We find that significant structural distortions are required to bind O2 exothermically to [Fe2S2] and [Fe3S4] clusters, while only small conformational changes allow for the thermodynamically favorable coordination of molecular oxygen to [Fe4S4] cubanes and [Fe4S3] clusters.
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Affiliation(s)
- Marta K Bruska
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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24
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25
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Soares ARM, Anderson DR, Chandrashaker V, Lindsey JS. Catalytic diversification upon metal scavenging in a prebiotic model for formation of tetrapyrrole macrocycles. NEW J CHEM 2013. [DOI: 10.1039/c3nj00498h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Soares ARM, Taniguchi M, Chandrashaker V, Lindsey JS. Primordial oil slick and the formation of hydrophobic tetrapyrrole macrocycles. ASTROBIOLOGY 2012; 12:1055-1068. [PMID: 23095096 PMCID: PMC3491618 DOI: 10.1089/ast.2012.0857] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 08/26/2012] [Indexed: 06/01/2023]
Abstract
The functional end products of the extant biosynthesis of tetrapyrrole macrocycles in photosynthetic organisms are hydrophobic: chlorophylls and bacteriochlorophylls. A model for the possible prebiogenesis of hydrophobic analogues of nature's photosynthetic pigments was investigated by reaction of acyclic reactants in five media: aqueous solution (pH 7, 60°C, 24 h); aqueous solution containing 0.1 M decanoic acid (which forms a turbid suspension of vesicles); or aqueous solution accompanied by dodecane, mesitylene, or a five-component organic mixture (each of which forms a phase-separated organic layer). The organic mixture was composed of equimolar quantities of decanoic acid, dodecane, mesitylene, naphthalene, and pentyl acetate. The reaction of 1,5-dimethoxy-3-methylpentan-2,4-dione and 1-aminobutan-2-one to give etioporphyrinogens was enhanced in the presence of decanoic acid, affording (following chemical oxidation) etioporphyrins (tetraethyltetramethylporphyrins) in yields of 1.4-10.8% across the concentration range of 3.75-120 mM. The yield of etioporphyrins was greater in the presence of the five-component organic mixture (6.6% at 120 mM) versus that with dodecane or mesitylene (2.1% or 2.9%, respectively). The reaction in aqueous solution with no added oil-slick constituents resulted in phase separation-where the organic reactants themselves form an upper organic layer-and the yield of etioporphyrins was 0.5-2.6%. Analogous reactions leading to uroporphyrins (hydrophilic, eight carboxylic acids) or coproporphyrins (four carboxylic acids) were unaffected by the presence of decanoic acid or dodecane, and all yields were at most ∼2% or ∼8%, respectively. Taken together, the results indicate a facile means for the formation of highly hydrophobic constituents of potential value for prebiotic photosynthesis.
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Affiliation(s)
- Ana R M Soares
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, USA
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27
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Abstract
Vitamin B12 (cobalamin) is a cobalt-containing modified tetrapyrrole that is an essential nutrient for higher animals. Its biosynthesis is restricted to certain bacteria and requires approximately 30 enzymatic steps for its complete de novo construction. Remarkably, two distinct biosynthetic pathways exist, which are termed the aerobic and anaerobic routes. The anaerobic pathway has yet to be fully characterized due to the inherent instability of its oxygen-sensitive intermediates. Bacillus megaterium, a bacterium previously used for the commercial production of cobalamin, has a complete anaerobic pathway and this organism is now being used to investigate the anaerobic B12 pathway through the application of recent advances in recombinant protein production. The present paper provides a summary of recent findings in the anaerobic pathway and future perspectives.
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28
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Goncearenco A, Berezovsky IN. Exploring the evolution of protein function in Archaea. BMC Evol Biol 2012; 12:75. [PMID: 22646318 PMCID: PMC3458885 DOI: 10.1186/1471-2148-12-75] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/24/2012] [Indexed: 11/21/2022] Open
Abstract
Background Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides. Results We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes. Conclusions Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Unit, Uni Research, University of Bergen, N-5008 Bergen, Norway
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29
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Nath N, Mitchell JBO. Is EC class predictable from reaction mechanism? BMC Bioinformatics 2012; 13:60. [PMID: 22530800 PMCID: PMC3368749 DOI: 10.1186/1471-2105-13-60] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 04/24/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism in descriptors, and also three approaches that encode only the overall chemical reaction. Both cross-validation and also an external test set are used. RESULTS The three descriptor sets encoding overall chemical transformation perform better than the two descriptions of mechanism. SVM and RF models perform comparably well; kNN is less successful. Oxidoreductases and hydrolases are relatively well predicted by all types of descriptor; isomerases are well predicted by overall reaction descriptors but not by mechanistic ones. CONCLUSIONS Our results suggest that pairs of similar enzyme reactions tend to proceed by different mechanisms. Oxidoreductases, hydrolases, and to some extent isomerases and ligases, have clear chemical signatures, making them easier to predict than transferases and lyases. We find evidence that isomerases as a class are notably mechanistically diverse and that their one shared property, of substrate and product being isomers, can arise in various unrelated ways.The performance of the different machine learning algorithms is in line with many cheminformatics applications, with SVM and RF being roughly equally effective. kNN is less successful, given the role that non-local information plays in successful classification. We note also that, despite a lack of clarity in the literature, EC number prediction is not a single problem; the challenge of predicting protein function from available sequence data is quite different from assigning an EC classification from a cheminformatics representation of a reaction.
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Affiliation(s)
- Neetika Nath
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, Purdie Building, University of St Andrews, North Haugh, St Andrews, Scotland KY16 9ST, UK
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Peretó J. Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks. Chem Soc Rev 2012; 41:5394-403. [PMID: 22508108 DOI: 10.1039/c2cs35054h] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The origin of life on Earth was a chemical affair. So how did primitive biochemical systems originate from geochemical and cosmochemical processes on the young planet? Contemporary research into the origins of life subscribes to the Darwinian principle of material causes operating in an evolutionary context, as advocated by A. I. Oparin and J. B. S. Haldane in the 1920s. In its simplest form (e.g., a bacterial cell) extant biological complexity relies on the functional integration of metabolic networks and replicative genomes inside a lipid boundary. Different research programmes have explored the prebiotic plausibility of each of these autocatalytic subsystems and combinations thereof: self-maintained networks of small molecules, template chemistry, and self-reproductive vesicles. This tutorial review focuses on the debates surrounding the origin of metabolism and offers a brief overview of current studies on the evolution of metabolic networks. I suggest that a leitmotif in the origin and evolution of metabolism is the role played by catalysers' substrate ambiguity and multifunctionality.
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Affiliation(s)
- Juli Peretó
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Departament de Bioquímica i Biologia Molecular, Universitat de València, C. Jose Beltran 2, 46980 Paterna, Spain.
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31
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Taniguchi M, Soares ARM, Chandrashaker V, Lindsey JS. A tandem combinatorial model for the prebiogenesis of diverse tetrapyrrole macrocycles. NEW J CHEM 2012. [DOI: 10.1039/c2nj21050a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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32
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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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33
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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34
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Jaffe EK, Lawrence SH. Allostery and the dynamic oligomerization of porphobilinogen synthase. Arch Biochem Biophys 2011; 519:144-53. [PMID: 22037356 DOI: 10.1016/j.abb.2011.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 10/16/2022]
Abstract
The structural basis for allosteric regulation of porphobilinogen synthase (PBGS) is modulation of a quaternary structure equilibrium between octamer and hexamer (via dimers), which is represented schematically as 8mer ⇔ 2mer ⇔ 2mer∗⇔ 6mer∗. The "∗" represents a reorientation between two domains of each subunit that occurs in the dissociated state because it is sterically forbidden in the larger multimers. Allosteric effectors of PBGS are both intrinsic and extrinsic and are phylogenetically variable. In some species this equilibrium is modulated intrinsically by magnesium which binds at a site specific to the 8mer. In other species this equilibrium is modulated intrinsically by pH with the guanidinium group of an arginine being spatially equivalent to the allosteric magnesium ion. In humans, disease associated variants all shift the equilibrium toward the 6mer∗ relative to wild type. The 6mer∗ has a surface cavity that is not present in the 8mer and is proposed as a small molecule allosteric binding site. In silico and in vitro approaches have revealed species-specific allosteric PBGS inhibitors that stabilize the 6mer∗. Some of these inhibitors are drugs in clinical use leading to the hypothesis that extrinsic allosteric inhibition of human PBGS could be a mechanism for drug side effects.
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Affiliation(s)
- Eileen K Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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35
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Molecular hijacking of siroheme for the synthesis of heme and d1 heme. Proc Natl Acad Sci U S A 2011; 108:18260-5. [PMID: 21969545 DOI: 10.1073/pnas.1108228108] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modified tetrapyrroles such as chlorophyll, heme, siroheme, vitamin B(12), coenzyme F(430), and heme d(1) underpin a wide range of essential biological functions in all domains of life, and it is therefore surprising that the syntheses of many of these life pigments remain poorly understood. It is known that the construction of the central molecular framework of modified tetrapyrroles is mediated via a common, core pathway. Herein a further branch of the modified tetrapyrrole biosynthesis pathway is described in denitrifying and sulfate-reducing bacteria as well as the Archaea. This process entails the hijacking of siroheme, the prosthetic group of sulfite and nitrite reductase, and its processing into heme and d(1) heme. The initial step in these transformations involves the decarboxylation of siroheme to give didecarboxysiroheme. For d(1) heme synthesis this intermediate has to undergo the replacement of two propionate side chains with oxygen functionalities and the introduction of a double bond into a further peripheral side chain. For heme synthesis didecarboxysiroheme is converted into Fe-coproporphyrin by oxidative loss of two acetic acid side chains. Fe-coproporphyrin is then transformed into heme by the oxidative decarboxylation of two propionate side chains. The mechanisms of these reactions are discussed and the evolutionary significance of another role for siroheme is examined.
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36
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Jaffe EK, Shanmugam D, Gardberg A, Dieterich S, Sankaran B, Stewart LJ, Myler PJ, Roos DS. Crystal structure of Toxoplasma gondii porphobilinogen synthase: insights on octameric structure and porphobilinogen formation. J Biol Chem 2011; 286:15298-307. [PMID: 21383008 PMCID: PMC3083160 DOI: 10.1074/jbc.m111.226225] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/03/2011] [Indexed: 11/06/2022] Open
Abstract
Porphobilinogen synthase (PBGS) is essential for heme biosynthesis, but the enzyme of the protozoan parasite Toxoplasma gondii (TgPBGS) differs from that of its human host in several important respects, including subcellular localization, metal ion dependence, and quaternary structural dynamics. We have solved the crystal structure of TgPBGS, which contains an octamer in the crystallographic asymmetric unit. Crystallized in the presence of substrate, each active site contains one molecule of the product porphobilinogen. Unlike prior structures containing a substrate-derived heterocycle directly bound to an active site zinc ion, the product-bound TgPBGS active site contains neither zinc nor magnesium, placing in question the common notion that all PBGS enzymes require an active site metal ion. Unlike human PBGS, the TgPBGS octamer contains magnesium ions at the intersections between pro-octamer dimers, which are presumed to function in allosteric regulation. TgPBGS includes N- and C-terminal regions that differ considerably from previously solved crystal structures. In particular, the C-terminal extension found in all apicomplexan PBGS enzymes forms an intersubunit β-sheet, stabilizing a pro-octamer dimer and preventing formation of hexamers that can form in human PBGS. The TgPBGS structure suggests strategies for the development of parasite-selective PBGS inhibitors.
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Affiliation(s)
- Eileen K. Jaffe
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | | | - Anna Gardberg
- Emerald BioStructures, Inc., Bainbridge Island, Washington 98110
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | - Shellie Dieterich
- Emerald BioStructures, Inc., Bainbridge Island, Washington 98110
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | | | - Lance J. Stewart
- Emerald BioStructures, Inc., Bainbridge Island, Washington 98110
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | - Peter J. Myler
- the Seattle Biomedical Research Institute, Seattle, Washington 98109 and the Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, Washington 98195, and
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | - David S. Roos
- the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Vey JL, Drennan CL. Structural insights into radical generation by the radical SAM superfamily. Chem Rev 2011; 111:2487-506. [PMID: 21370834 PMCID: PMC5930932 DOI: 10.1021/cr9002616] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica L Vey
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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38
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Seyedarabi A, Hutchison T, To TT, Deery E, Brindley A, Warren MJ, Pickersgill RW. Cloning, purification and preliminary crystallographic analysis of cobalamin methyltransferases from Rhodobacter capsulatus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1652-6. [PMID: 21139217 DOI: 10.1107/s1744309110042910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 10/21/2010] [Indexed: 11/10/2022]
Abstract
Of the 30 biosynthetic steps necessary for the production of cobalamin (vitamin B12), eight involve the addition of S-adenosylmethionine-derived methyl groups to the tetrapyrrole framework. These eight methyl additions are catalysed by six canonical methyltransferase domains and one noncanonical methyltransferase domain. Recombinant forms of four methyltransferases from Rhodobacter capsulatus, CobJ, CobM, CobF and CobL, and of the C-terminal noncanonical domain of CobL (CobL-C) have been crystallized, some in more than one crystal form. Most of the crystals diffracted to beyond 2.5 Å resolution and all are suitable for structure determination. Crystals of CobM and CobJ, which are involved in ring contraction, and of CobL, which is involved in two methylations and decarboxylation, are reported for the first time.
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Affiliation(s)
- Arefeh Seyedarabi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England
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39
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Nawarathne IN, Walker KD. Point mutations (Q19P and N23K) increase the operational solubility of a 2alpha-O-benzoyltransferase that conveys various acyl groups from CoA to a taxane acceptor. JOURNAL OF NATURAL PRODUCTS 2010; 73:151-159. [PMID: 20108947 DOI: 10.1021/np900524d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Two site-directed mutations within the wild-type 2-O-benzoyltransferase (tbt) cDNA, from Taxus cuspidata plants, yielded an encoded protein containing replacement amino acids at Q19P and N23K that map to a solvent-exposed loop region. The likely significant changes in the biophysical properties invoked by these mutations caused the overexpressed, modified TBT (mTBT) to partition into the soluble enzyme fraction about 5-fold greater than the wild-type enzyme. Sufficient protein could now be acquired to examine the scope of the substrate specificity of mTBT by incubation with 7,13-O,O-diacetyl-2-O-debenzoylbaccatin III that was mixed individually with various substituted benzoyls, alkanoyls, and (E)-butenoyl CoA donors. The mTBT catalyzed the conversion of each 7,13-O,O-diacetyl-2-O-debenzoylbaccatin III to several 7,13-O,O-diacetyl-2-O-acyl-2-O-debenzoylbaccatin III analogues. The relative catalytic efficiency of mTBT with the 7,13-O,O-diacetyl-2-O-debenzoyl surrogate substrate and heterole carbonyl CoA substrates was slightly greater than with the natural aroyl substrate benzoyl CoA, while substituted benzoyl CoA thioesters were less productive. Short-chain hydrocarbon carbonyl and cyclohexanoyl CoA thioesters were also productive, where C(4) substrates were transferred by mTBT with approximately 10- to 17-fold greater catalytic efficiency compared to the transfer of benzoyl. The described broad specificity of mTBT suggests that a plethora of 2-O-acyl variants of the antimitotic paclitaxel can be assembled through biocatalytic sequences.
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Affiliation(s)
- Irosha N Nawarathne
- Department of Chemistry and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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40
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Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 2009; 325:1544-9. [PMID: 19762644 PMCID: PMC2833182 DOI: 10.1126/science.1174671] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.
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Affiliation(s)
- Ying Zhang
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
| | - Ines Thiele
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093-0412, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Zhanwen Li
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Krzysztof Ginalski
- Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, Structure Determination Core, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - John Wooley
- Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, Crystallomics Core, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bernhard Palsson
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093-0412, USA
| | - Andrei Osterman
- Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Adam Godzik
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093, USA
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41
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Caetano-Anollés G, Yafremava LS, Gee H, Caetano-Anollés D, Kim HS, Mittenthal JE. The origin and evolution of modern metabolism. Int J Biochem Cell Biol 2008; 41:285-97. [PMID: 18790074 DOI: 10.1016/j.biocel.2008.08.022] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 08/09/2008] [Accepted: 08/11/2008] [Indexed: 10/21/2022]
Abstract
One fundamental goal of current research is to understand how complex biomolecular networks took the form that we observe today. Cellular metabolism is probably one of the most ancient biological networks and constitutes a good model system for the study of network evolution. While many evolutionary models have been proposed, a substantial body of work suggests metabolic pathways evolve fundamentally by recruitment, in which enzymes are drawn from close or distant regions of the network to perform novel chemistries or use different substrates. Here we review how structural and functional genomics has impacted our knowledge of evolution of modern metabolism and describe some approaches that merge evolutionary and structural genomics with advances in bioinformatics. These include mining the data on structure and function of enzymes for salient patterns of enzyme recruitment. Initial studies suggest modern metabolism originated in enzymes of nucleotide metabolism harboring the P-loop hydrolase fold, probably in pathways linked to the purine metabolic subnetwork. This gateway of recruitment gave rise to pathways related to the synthesis of nucleotides and cofactors for an ancient RNA world. Once the TIM beta/alpha-barrel fold architecture was discovered, it appears metabolic activities were recruited explosively giving rise to subnetworks related to carbohydrate and then amino acid metabolism. Remarkably, recruitment occurred in a layered system reminiscent of Morowitz's prebiotic shells, supporting the notion that modern metabolism represents a palimpsest of ancient metabolic chemistries.
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Abstract
Cells require metal ions as cofactors for the assembly of metalloproteins. Principally one has to distinguish between metal ions that are directly incorporated into their cognate sites on proteins and those metal ions that have to become part of prosthetic groups, cofactors or complexes prior to insertion of theses moieties into target proteins. Molybdenum is only active as part of the molybdenum cofactor, iron can be part of diverse Fe-S clusters or of the heme group, while copper ions are directly delivered to their targets. We will focus in greater detail on molybdenum metabolism because molybdenum metabolism is a good example for demonstrating the role and the network of metals in metabolism: each of the three steps in the pathway of molybdenum cofactor formation depends on a different metal (iron, copper, molybdenum) and also the enzymes finally harbouring the molybdenum cofactor need additional metal-containing groups to function (iron sulfur-clusters, heme-iron).
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Affiliation(s)
- Ralf R Mendel
- Department of Plant Biology, Technical University of Braunschweig, 38106, Braunschweig, Germany.
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44
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Marquet A, Bui BTS, Smith AG, Warren MJ. Iron–sulfur proteins as initiators of radical chemistry. Nat Prod Rep 2007; 24:1027-40. [PMID: 17898896 DOI: 10.1039/b703109m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-sulfur proteins are very versatile biological entities for which many new functions are continuously being unravelled. This review focus on their role in the initiation of radical chemistry, with special emphasis on radical-SAM enzymes, since several members of the family catalyse key steps in the biosynthetic pathways of cofactors such as biotin, lipoate, thiamine, heme and the molybdenum cofactor. It will also include other examples to show the chemical logic which is emerging from the presently available data on this family of enzymes. The common step in all the (quite different) reactions described here is the monoelectronic reductive cleavage of SAM by a reduced [4Fe-4S](1+) cluster, producing methionine and a highly oxidising deoxyadenosyl radical, which can initiate chemically difficult reactions. This set of enzymes, which represent a means to perform oxidation under reductive conditions, are often present in anaerobic organisms. Some other, non-SAM-dependent, radical reactions obeying the same chemical logic are also covered.
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Affiliation(s)
- Andrée Marquet
- Université Pierre et Marie Curie-Paris 6, CNRS UMR 7613, (Synthèse, Structure et Fonction de Molécules Bioactives), Paris, France.
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45
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Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ. Evolution of enzymes and pathways for the biosynthesis of cofactors. Nat Prod Rep 2007; 24:972-87. [PMID: 17898893 DOI: 10.1039/b703107f] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The evolution of metabolic pathways is discussed with reference to the biosynthesis of a number of vitamins and cofactors. Retrograde and patchwork models are highlighted and their relevance to our knowledge of pathway processes and enzymes is examined. Pathway complexity is explained in terms of the acquisition of broad specificity enzymes.
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Affiliation(s)
- Gemma L Holliday
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK CB10 1SD.
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46
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Webb ME, Marquet A, Mendel RR, Rébeillé F, Smith AG. Elucidating biosynthetic pathways for vitamins and cofactors. Nat Prod Rep 2007; 24:988-1008. [PMID: 17898894 DOI: 10.1039/b703105j] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The elucidation of the pathways to the water-soluble vitamins and cofactors has provided many biochemical and chemical challenges. This is a reflection both of their complex chemical nature, and the fact that they are often made in small amounts, making detection of the enzyme activities and intermediates difficult. Here we present an orthogonal review of how these challenges have been overcome using a combination of methods, which are often ingenious. We make particular reference to some recent developments in the study of biotin, pantothenate, folate, pyridoxol, cobalamin, thiamine, riboflavin and molybdopterin biosynthesis.
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Affiliation(s)
- Michael E Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
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