201
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Balo AR, Tao L, Britt RD. Characterizing SPASM/twitch Domain-Containing Radical SAM Enzymes by EPR Spectroscopy. APPLIED MAGNETIC RESONANCE 2021; 53:809-820. [PMID: 35509369 PMCID: PMC9012708 DOI: 10.1007/s00723-021-01406-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 06/14/2023]
Abstract
Owing to their importance, diversity and abundance of generated paramagnetic species, radical S-adenosylmethionine (rSAM) enzymes have become popular targets for electron paramagnetic resonance (EPR) spectroscopic studies. In contrast to prototypic single-domain and thus single-[4Fe-4S]-containing rSAM enzymes, there is a large subfamily of rSAM enzymes with multiple domains and one or two additional iron-sulfur cluster(s) called the SPASM/twitch domain-containing rSAM enzymes. EPR spectroscopy is a powerful tool that allows for the observation of the iron-sulfur clusters as well as potentially trappable paramagnetic reaction intermediates. Here, we review continuous-wave and pulse EPR spectroscopic studies of SPASM/twitch domain-containing rSAM enzymes. Among these enzymes, we will review in greater depth four well-studied enzymes, BtrN, MoaA, PqqE, and SuiB. Towards establishing a functional consensus of the additional architecture in these enzymes, we describe the commonalities between these enzymes as observed by EPR spectroscopy.
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Affiliation(s)
- Aidin R. Balo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - R. David Britt
- Department of Chemistry, University of California, Davis, CA 95616 USA
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202
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Chen C, Wang M, Lu H, Zhao B, Shi Z. Enabling the Use of Alkyl Thianthrenium Salts in Cross-Coupling Reactions by Copper Catalysis. Angew Chem Int Ed Engl 2021; 60:21756-21760. [PMID: 34378844 DOI: 10.1002/anie.202109723] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 02/03/2023]
Abstract
Alkyl groups are one of the most widely used groups in organic synthesis. Here, a a series of thianthrenium salts have been synthesized that act as reliable alkylation reagents and readily engage in copper-catalyzed Sonogashira reactions to build C(sp3 )-C(sp) bonds under mild photochemical conditions. Diverse alkyl thianthrenium salts, including methyl and disubstituted thianthrenium salts, are employed with great functional breadth, since sensitive Cl, Br, and I atoms, which are poorly tolerated in conventional approaches, are compatible. The generality of the developed alkyl reagents has also been demonstrated in copper-catalyzed Kumada reactions.
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Affiliation(s)
- Cheng Chen
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Minyan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Hongjian Lu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Binlin Zhao
- Department of Chemistry and Materials Science, College of Science, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhuangzhi Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China.,School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
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203
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Feng J, Shaik S, Wang B. Spin-Regulated Electron Transfer and Exchange-Enhanced Reactivity in Fe 4 S 4 -Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021; 60:20430-20436. [PMID: 34302311 DOI: 10.1002/anie.202107008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/06/2022]
Abstract
The [4Fe-4S]-dependent radical S-adenosylmethionine (SAM) proteins is one of large families of redox enzymes that are able to carry a panoply of challenging transformations. Despite the extensive studies of structure-function relationships of radical SAM (RS) enzymes, the electronic state-dependent reactivity of the [4Fe-4S] cluster in these enzymes remains elusive. Using combined MD simulations and QM/MM calculations, we deciphered the electronic state-dependent reactivity of the [4Fe-4S] cluster in Dph2, a key enzyme involved in the biosynthesis of diphthamide. Our calculations show that the reductive cleavage of the S-C(γ) bond is highly dependent on the electronic structure of [4Fe-4S]. Interestingly, the six electronic states can be classified into a low-energy and a high-energy groups, which are correlated with the net spin of Fe4 atom ligated to SAM. Due to the driving force of Fe4-C(γ) bonding, the net spin on the Fe4 moiety dictate the shift of the opposite spin electron from the Fe1-Fe2-Fe3 block to SAM. Such spin-regulated electron transfer results in the exchange-enhanced reactivity in the lower-energy group compared with those in the higher-energy group. This reactivity principle provides fundamental mechanistic insights into reactivities of [4Fe-4S] cluster in RS enzymes.
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Affiliation(s)
- Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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204
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Wang CH, DeBeer S. Structure, reactivity, and spectroscopy of nitrogenase-related synthetic and biological clusters. Chem Soc Rev 2021; 50:8743-8761. [PMID: 34159992 DOI: 10.1039/d1cs00381j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The reduction of dinitrogen (N2) is essential for its incorporation into nucleic acids and amino acids, which are vital to life on earth. Nitrogenases convert atmospheric dinitrogen to two ammonia molecules (NH3) under ambient conditions. The catalytic active sites of these enzymes (known as FeM-cofactor clusters, where M = Mo, V, Fe) are the sites of N2 binding and activation and have been a source of great interest for chemists for decades. In this review, recent studies on nitrogenase-related synthetic molecular complexes and biological clusters are discussed, with a focus on their reactivity and spectroscopic characterization. The molecular models that are discussed span from simple mononuclear iron complexes to multinuclear iron complexes and heterometallic iron complexes. In addition, recent work on the extracted biological cofactors is discussed. An emphasis is placed on how these studies have contributed towards our understanding of the electronic structure and mechanism of nitrogenases.
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Affiliation(s)
- Chen-Hao Wang
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
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205
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Chen C, Wang ZJ, Lu H, Zhao Y, Shi Z. Generation of non-stabilized alkyl radicals from thianthrenium salts for C-B and C-C bond formation. Nat Commun 2021; 12:4526. [PMID: 34312381 PMCID: PMC8313578 DOI: 10.1038/s41467-021-24716-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/24/2021] [Indexed: 01/01/2023] Open
Abstract
Sulfonium salts bearing a positively charged sulfur atom with three organic substituents have intrigued chemists for more than a century for their unusual structures and high chemical reactivity. These compounds are known to undergo facile single-electron reduction to emerge as a valuable and alternative source of aryl radicals for organic synthesis. However, the generation of non-stabilized alkyl radicals from sulfonium salts has been a challenge for several decades. Here we report the treatment of S-(alkyl) thianthrenium salts to generate non-stabilized alkyl radicals as key intermediates granting the controlled and selective outcome of the ensuing reactions under mild photoredox conditions. The value of these reagents has been demonstrated through the efficient construction of alkylboronates and other transformations, including heteroarylation, alkylation, alkenylation, and alkynylation. The developed method is practical, and provides the opportunity to convert C-OH bond to C-B and C-C bonds.
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Affiliation(s)
- Cheng Chen
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Zheng-Jun Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Hongjian Lu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
| | - Yue Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Zhuangzhi Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China. .,School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, China.
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206
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Biochemical Approaches to Probe the Role of the Auxiliary Iron-Sulfur Cluster of Lipoyl Synthase from Mycobacterium Tuberculosis. Methods Mol Biol 2021. [PMID: 34292556 DOI: 10.1007/978-1-0716-1605-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Lipoic acid is an essential sulfur-containing cofactor used by several multienzyme complexes involved in energy metabolism and the breakdown of certain amino acids. It is composed of n-octanoic acid with sulfur atoms appended at C6 and C8. Lipoic acid is biosynthesized de novo in its cofactor form, in which it is covalently bound in an amide linkage to a target lysyl residue on a lipoyl carrier protein (LCP). The n-octanoyl moiety of the cofactor is derived from type 2 fatty acid biosynthesis and is transferred to an LCP to afford an octanoyllysyl amino acid. Next, lipoyl synthase (LipA in bacteria) catalyzes the attachment of the two sulfur atoms to afford the intact cofactor. LipA is a radical S-adenosylmethionine (SAM) enzyme that contains two [4Fe-4S] clusters. One [4Fe-4S] cluster is used to facilitate a reductive cleavage of SAM to render the highly oxidizing 5'-deoxyadenosyl 5'-radical needed to abstract C6 and C8 hydrogen atoms to allow for sulfur attachment. By contrast, the second cluster is the sulfur source, necessitating its destruction during turnover. In Escherichia coli, this auxiliary cluster can be restored after each turnover by NfuA or IscU, which are two iron-sulfur cluster carrier proteins that are implicated in iron-sulfur cluster biogenesis. In this chapter, we describe methods for purifying and characterizing LipA and NfuA from Mycobacterium tuberculosis, a human pathogen for which endogenously synthesized lipoic acid is essential. These studies provide the foundation for assessing lipoic acid biosynthesis as a potential target for the design of novel antituberculosis agents.
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207
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Methods to Screen for Radical SAM Enzyme Crystallization Conditions. Methods Mol Biol 2021. [PMID: 34292557 DOI: 10.1007/978-1-0716-1605-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Radical S-adenosyl-L-methionine proteins most probably belong to the widest superfamily of metalloenzymes. Thanks to their ability to catalyze difficult reactions, combined with their involvement in the biosynthesis of numbers of natural products, they sound promising for various biotechnological applications. Their structural study is often limited because they are usually challenging to crystallize. This chapter presents protocols and equipment developed to quickly screen for crystallization conditions under anaerobic conditions, as exemplified by our recent study of the nitrogenase maturase NifB.
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208
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Benjdia A, Berteau O. Radical SAM Enzymes and Ribosomally-Synthesized and Post-translationally Modified Peptides: A Growing Importance in the Microbiomes. Front Chem 2021; 9:678068. [PMID: 34350157 PMCID: PMC8326336 DOI: 10.3389/fchem.2021.678068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
To face the current antibiotic resistance crisis, novel strategies are urgently required. Indeed, in the last 30 years, despite considerable efforts involving notably high-throughput screening and combinatorial libraries, only few antibiotics have been launched to the market. Natural products have markedly contributed to the discovery of novel antibiotics, chemistry and drug leads, with more than half anti-infective and anticancer drugs approved by the FDA being of natural origin or inspired by natural products. Among them, thanks to their modular structure and simple biosynthetic logic, ribosomally synthesized and posttranslationally modified peptides (RiPPs) are promising scaffolds. In addition, recent studies have highlighted the pivotal role of RiPPs in the human microbiota which remains an untapped source of natural products. In this review, we report on recent developments in radical SAM enzymology and how these unique biocatalysts have been shown to install complex and sometimes unprecedented posttranslational modifications in RiPPs with a special focus on microbiome derived enzymes.
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Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
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209
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Ye Y, Fu H, Hyster TK. Activation modes in biocatalytic radical cyclization reactions. J Ind Microbiol Biotechnol 2021; 48:6155068. [PMID: 33674826 PMCID: PMC8210684 DOI: 10.1093/jimb/kuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 12/17/2022]
Abstract
Radical cyclizations are essential reactions in the biosynthesis of secondary metabolites and the chemical synthesis of societally valuable molecules. In this review, we highlight the general mechanisms utilized in biocatalytic radical cyclizations. We specifically highlight cytochrome P450 monooxygenases (P450s) involved in the biosynthesis of mycocyclosin and vancomycin, nonheme iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGDs) used in the biosynthesis of kainic acid, scopolamine, and isopenicillin N, and radical S-adenosylmethionine (SAM) enzymes that facilitate the biosynthesis of oxetanocin A, menaquinone, and F420. Beyond natural mechanisms, we also examine repurposed flavin-dependent “ene”-reductases (ERED) for non-natural radical cyclization. Overall, these general mechanisms underscore the opportunity for enzymes to augment and enhance the synthesis of complex molecules using radical mechanisms.
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Affiliation(s)
- Yuxuan Ye
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Haigen Fu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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210
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Examining pathways of iron and sulfur acquisition, trafficking, deployment, and storage in mineral-grown methanogen cells. J Bacteriol 2021; 203:e0014621. [PMID: 34251867 PMCID: PMC8516115 DOI: 10.1128/jb.00146-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanogens have a high demand for iron (Fe) and sulfur (S); however, little is known of how they acquire, deploy, and store these elements and how this, in turn, affects their physiology. Methanogens were recently shown to reduce pyrite (FeS2) generating aqueous iron-sulfide (FeS(aq)) clusters that are likely assimilated as a source of Fe and S. Here, we compare the phenotype of Methanococcus voltae when grown with FeS2 or ferrous iron (Fe(II)) and sulfide (HS-). FeS2-grown cells are 33% smaller yet have 193% more Fe than Fe(II)/HS--grown cells. Whole cell EPR revealed similar distributions of paramagnetic Fe, although FeS2-grown cells showed a broad spectral feature attributed to intracellular thioferrate-like nanoparticles. Differential proteomic analyses showed similar expression of core methanogenesis enzymes, indicating that Fe and S source does not substantively alter the energy metabolism of cells. However, a homolog of the Fe(II) transporter FeoB and its putative transcriptional regulator DtxR were up-expressed in FeS2-grown cells, suggesting that cells sense Fe(II) limitation. Two homologs of IssA, a protein putatively involved in coordinating thioferrate nanoparticles, were also up-expressed in FeS2-grown cells. We interpret these data to indicate that, in FeS2-grown cells, DtxR cannot sense Fe(II) and therefore cannot down-regulate FeoB. We suggest this is due to the transport of Fe(II) complexed with sulfide (FeS(aq)) leading to excess Fe that is sequestered by IssA as a thioferrate-like species. This model provides a framework for the design of targeted experiments aimed at further characterizing Fe acquisition and homeostasis in M. voltae and other methanogens. IMPORTANCE FeS2 is the most abundant sulfide mineral in the Earth's crust and is common in environments inhabited by methanogenic archaea. FeS2 can be reduced by methanogens, yielding aqueous FeS(aq) clusters that are thought to be a source of Fe and S. Here, we show that growth of Methanococcus voltae on FeS2 results in smaller cell size and higher Fe content per cell, with Fe likely stored intracellularly as thioferrate-like nanoparticles. Fe(II) transporters and storage proteins were up-regulated in FeS2-grown cells. These responses are interpreted to result from cells incorrectly sensing Fe(II) limitation due to assimilation of Fe(II) as FeS(aq). These findings have implications for our understanding of how Fe/S availability influences methanogen physiology and the biogeochemical cycling of these elements.
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211
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Lachowicz JC, Gizzi AS, Almo SC, Grove TL. Structural Insight into the Substrate Scope of Viperin and Viperin-like Enzymes from Three Domains of Life. Biochemistry 2021; 60:2116-2129. [PMID: 34156827 PMCID: PMC8672371 DOI: 10.1021/acs.biochem.0c00958] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Viperin is a member of the radical S-adenosylmethionine superfamily and has been shown to restrict the replication of a wide range of RNA and DNA viruses. We recently demonstrated that human viperin (HsVip) catalyzes the conversion of CTP to 3'-deoxy-3',4'-didehydro-CTP (ddhCTP or ddh-synthase), which acts as a chain terminator for virally encoded RNA-dependent RNA polymerases from several flaviviruses. Viperin homologues also exist in non-chordate eukaryotes (e.g., Cnidaria and Mollusca), numerous fungi, and members of the archaeal and eubacterial domains. Recently, it was reported that non-chordate and non-eukaryotic viperin-like homologues are also ddh-synthases and generate a diverse range of ddhNTPs, including the newly discovered ddhUTP and ddhGTP. Herein, we expand on the catalytic mechanism of mammalian, fungal, bacterial, and archaeal viperin-like enzymes with a combination of X-ray crystallography and enzymology. We demonstrate that, like mammalian viperins, these recently discovered viperin-like enzymes operate through the same mechanism and can be classified as ddh-synthases. Furthermore, we define the unique chemical and physical determinants supporting ddh-synthase activity and nucleotide selectivity, including the crystallographic characterization of a fungal viperin-like enzyme that utilizes UTP as a substrate and a cnidaria viperin-like enzyme that utilizes CTP as a substrate. Together, these results support the evolutionary conservation of the ddh-synthase activity and its broad phylogenetic role in innate antiviral immunity.
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Affiliation(s)
- Jake C Lachowicz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Anthony S Gizzi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
- Department of Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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212
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Yin Y, Ji X, Zhang Q. The Promiscuous Activity of the Radical
SAM
Enzyme
NosL
toward Two Unnatural Substrates. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yue Yin
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
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213
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Abstract
![]()
TYW1 is a radical S-adenosyl-l-methionine
(SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine-containing tRNAPhe, forming
4-demethylwyosine-containing tRNAPhe. Homologues of TYW1
are found in both archaea and eukarya; archaeal homologues consist
of a single domain, while eukaryal homologues contain a flavin binding
domain in addition to the radical SAM domain shared with archaeal
homologues. In this study, TYW1 from Saccharomyces cerevisiae (ScTYW1) was heterologously expressed in Escherichia coli and purified to homogeneity. ScTYW1 is purified with 0.54 ± 0.07 and 4.2 ± 1.9 equiv of
flavin mononucleotide (FMN) and iron, respectively, per mole of protein,
suggesting the protein is ∼50% replete with Fe–S clusters
and FMN. While both NADPH and NADH are sufficient for activity, significantly
more product is observed when used in combination with flavin nucleotides. ScTYW1 is the first example of a radical SAM flavoenzyme
that is active with NAD(P)H alone.
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Affiliation(s)
- Anthony P Young
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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214
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Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases. Cells 2021; 10:cells10071591. [PMID: 34202661 PMCID: PMC8307549 DOI: 10.3390/cells10071591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.
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215
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Zhang Y, Su D, Dzikovski B, Majer SH, Coleman R, Chandrasekaran S, Fenwick MK, Crane BR, Lancaster KM, Freed JH, Lin H. Dph3 Enables Aerobic Diphthamide Biosynthesis by Donating One Iron Atom to Transform a [3Fe-4S] to a [4Fe-4S] Cluster in Dph1-Dph2. J Am Chem Soc 2021; 143:9314-9319. [PMID: 34154323 PMCID: PMC8251694 DOI: 10.1021/jacs.1c03956] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All radical S-adenosylmethionine (radical-SAM) enzymes, including the noncanonical radical-SAM enzyme diphthamide biosynthetic enzyme Dph1-Dph2, require at least one [4Fe-4S](Cys)3 cluster for activity. It is well-known in the radical-SAM enzyme community that the [4Fe-4S](Cys)3 cluster is extremely air-sensitive and requires strict anaerobic conditions to reconstitute activity in vitro. Thus, how such enzymes function in vivo in the presence of oxygen in aerobic organisms is an interesting question. Working on yeast Dph1-Dph2, we found that consistent with the known oxygen sensitivity, the [4Fe-4S] cluster is easily degraded into a [3Fe-4S] cluster. Remarkably, the small iron-containing protein Dph3 donates one Fe atom to convert the [3Fe-4S] cluster in Dph1-Dph2 to a functional [4Fe-4S] cluster during the radical-SAM enzyme catalytic cycle. This mechanism to maintain radical-SAM enzyme activity in aerobic environments is likely general, and Dph3-like proteins may exist to keep other radical-SAM enzymes functional in aerobic environments.
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Affiliation(s)
- Yugang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Dan Su
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Rachael Coleman
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Siddarth Chandrasekaran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, United States
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216
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York A, Everhart A, Vitek MP, Gottschalk KW, Colton CA. Metabolism-Based Gene Differences in Neurons Expressing Hyperphosphorylated AT8- Positive (AT8+) Tau in Alzheimer's Disease. ASN Neuro 2021; 13:17590914211019443. [PMID: 34121475 PMCID: PMC8207264 DOI: 10.1177/17590914211019443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Metabolic adaptations in the brain are critical to the establishment and maintenance of normal cellular functions and to the pathological responses to disease processes. Here, we have focused on specific metabolic pathways that are involved in immune-mediated neuronal processes in brain using isolated neurons derived from human autopsy brain sections of normal individuals and individuals diagnosed as Alzheimer's disease (AD). Laser capture microscopy was used to select specific cell types in immune-stained thin brain sections followed by NanoString technology to identify and quantify differences in mRNA levels between age-matched control and AD neuronal samples. Comparisons were also made between neurons isolated from AD brain sections expressing pathogenic hyperphosphorylated AT8- positive (AT8+) tau and non-AT8+ AD neurons using double labeling techniques. The mRNA expression data showed unique patterns of metabolic pathway expression between the subtypes of captured neurons that involved membrane based solute transporters, redox factors, and arginine and methionine metabolic pathways. We also identified the expression levels of a novel metabolic gene, Radical-S-Adenosyl Domain1 (RSAD1) and its corresponding protein, Rsad1, that impact methionine usage and radical based reactions. Immunohistochemistry was used to identify specific protein expression levels and their cellular location in NeuN+ and AT8+ neurons. APOE4 vs APOE3 genotype-specific and sex-specific gene expression differences in these metabolic pathways were also observed when comparing neurons from individuals with AD to age-matched individuals.
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Affiliation(s)
- Audra York
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Angela Everhart
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael P Vitek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Kirby W Gottschalk
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Carol A Colton
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
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217
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Mitchell SC. Nutrition and sulfur. ADVANCES IN FOOD AND NUTRITION RESEARCH 2021; 96:123-174. [PMID: 34112351 DOI: 10.1016/bs.afnr.2021.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sulfur is unusual in that it is a mineral that may be taken into the body in both inorganic and organic combinations. It has been available within the environment throughout the development of lifeforms and as such has become integrated into virtually every aspect of biochemical function. It is essential for the nature and maintenance of structure, assists in communication within the organism, is vital as a catalytic assistant in intermediary metabolism and the mechanism of energy flow as well as being involved in internal defense against potentially damaging reactive species and invading foreign chemicals. Recent studies have suggested extended roles for sulfur-containing molecules within living systems. As such, questions have been raised as to whether or not humans are receiving sufficient sulfur within their diet. Sulfur appears to have been the "poor relation" with regards to mineral nutrition. This may be because of difficulties encountered over its multifarious functions, the many chemical guises in which it may be ingested and its complex biochemical interconversions once taken into the body. No established daily requirements have been determined, unlike many minerals, although suggestions have been proposed. Owing to its widespread distribution within dietary components its intake has almost been taken for granted. In the majority of individuals partaking of a balanced diet the supply is deemed adequate, but those opting for specialized or restrictive diets may experience occasional and low-level shortages. In these instances, the careful use of sulfur supplements may be of benefit.
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Affiliation(s)
- Stephen C Mitchell
- Faculty of Medicine, Imperial College London, London, England, United Kingdom.
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218
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Chatterjee B, Jena S, Chugh V, Weyhermüller T, Werlé C. A Molecular Iron-Based System for Divergent Bond Activation: Controlling the Reactivity of Aldehydes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00733] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Basujit Chatterjee
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34−36, 45470 Mülheim an der Ruhr, Germany
- Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Soumyashree Jena
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34−36, 45470 Mülheim an der Ruhr, Germany
- Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Vishal Chugh
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34−36, 45470 Mülheim an der Ruhr, Germany
- Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Thomas Weyhermüller
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Christophe Werlé
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34−36, 45470 Mülheim an der Ruhr, Germany
- Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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219
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Wang J, Ma S, Ding W, Chen T, Zhang Q. Mechanistic Study of Oxidoreductase
AprQ
Involved in Biosynthesis of Aminoglycoside Antibiotic Apramycin. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jinxiu Wang
- State Key Laboratory of Cryospheric Science, Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco‐Environment and Resources, Chinese Academy of Sciences Lanzhou Gansu 730000 China
- Department of Chemistry, Fudan University Shanghai 200433 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Suze Ma
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco‐Environment and Resources, Chinese Academy of Sciences Lanzhou Gansu 730000 China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai 200433 China
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220
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Trapping a cross-linked lysine-tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB. Proc Natl Acad Sci U S A 2021; 118:2101571118. [PMID: 34001621 DOI: 10.1073/pnas.2101571118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The radical S-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon-carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys-Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]2+ state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys-Trp radical (Lys-Trp•) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys-Trp• intermediate by the redox-tuned [4Fe-4S]2+ AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon-carbon bond-forming reactions.
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221
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Blue TC, Davis KM. Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics. Molecules 2021; 26:molecules26092590. [PMID: 33946806 PMCID: PMC8124187 DOI: 10.3390/molecules26092590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022] Open
Abstract
Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.
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222
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Rupnik K, Rettberg L, Tanifuji K, Rebelein JG, Ribbe MW, Hu Y, Hales BJ. An EPR and VTVH MCD spectroscopic investigation of the nitrogenase assembly protein NifB. J Biol Inorg Chem 2021; 26:403-410. [PMID: 33905031 DOI: 10.1007/s00775-021-01870-y] [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: 01/19/2021] [Accepted: 04/22/2021] [Indexed: 12/01/2022]
Abstract
NifB, a radical SAM enzyme, catalyzes the biosynthesis of the L cluster (Fe8S9C), a structural homolog and precursor to the nitrogenase active-site M cluster ([MoFe7S9C·R-homocitrate]). Sequence analysis shows that NifB contains the CxxCxxxC motif that is typically associated with the radical SAM cluster ([Fe4S4]SAM) involved in the binding of S-adenosylmethionine (SAM). In addition, NifB houses two transient [Fe4S4] clusters (K cluster) that can be fused into an 8Fe L cluster concomitant with the incorporation of an interstitial carbide ion, which is achieved through radical SAM chemistry initiated at the [Fe4S4]SAM cluster upon its interaction with SAM. Here, we report a VTVH MCD/EPR spectroscopic study of the L cluster biosynthesis on NifB, which focuses on the initial interaction of SAM with [Fe4S4]SAM in a variant NifB protein (MaNifBSAM) containing only the [Fe4S4]SAM cluster and no K cluster. Titration of MaNifBSAM with SAM reveals that [Fe4S4]SAM exists in two forms, labeled [Formula: see text] and [Formula: see text]. It is proposed that these forms are involved in the synthesis of the L cluster. Of the two cluster types, only [Formula: see text] initially interacts with SAM, resulting in the generation of Z, an S = ½ paramagnetic [Fe4S4]SAM/SAM complex.
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Affiliation(s)
- Kresimir Rupnik
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Lee Rettberg
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA. .,Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA.
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.
| | - Brian J Hales
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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223
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Yeh YC, Kim HJ, Liu HW. Mechanistic Investigation of 1,2-Diol Dehydration of Paromamine Catalyzed by the Radical S-Adenosyl-l-methionine Enzyme AprD4. J Am Chem Soc 2021; 143:5038-5043. [PMID: 33784078 DOI: 10.1021/jacs.1c00076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AprD4 is a radical S-adenosyl-l-methionine (SAM) enzyme catalyzing C3'-deoxygenation of paromamine to form 4'-oxo-lividamine. It is the only 1,2-diol dehydratase in the radical SAM enzyme superfamily that has been identified and characterized in vitro. The AprD4 catalyzed 1,2-diol dehydration is a key step in the biosynthesis of several C3'-deoxy-aminoglycosides. While the regiochemistry of the hydrogen atom abstraction catalyzed by AprD4 has been established, the mechanism of the subsequent chemical transformation remains not fully understood. To investigate the mechanism, several substrate analogues were synthesized and their fates upon incubation with AprD4 were analyzed. The results support a mechanism involving formation of a ketyl radical intermediate followed by direct elimination of the C3'-hydroxyl group rather than that of a gem-diol intermediate generated via 1,2-migration of the C3'-hydroxyl group to C4'. The stereochemistry of hydrogen atom incorporation after radical-mediated dehydration was also established.
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Affiliation(s)
- Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hak Joong Kim
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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224
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Moosmann B, Schindeldecker M, Hajieva P. Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation. Biol Chem 2021; 401:213-231. [PMID: 31318686 DOI: 10.1515/hsz-2019-0232] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.
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Affiliation(s)
- Bernd Moosmann
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Mario Schindeldecker
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Parvana Hajieva
- Cellular Adaptation Group, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
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225
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A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical SAM protein MoaA for the synthesis of active molybdoenzymes. J Bacteriol 2021; 203:e0008621. [PMID: 33782054 DOI: 10.1128/jb.00086-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them were characterized in detail in Escherichia coli, namely IscA, SufA and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli Our studies include the identification of the A-type carrier proteins ErpA and IscA involved in [4Fe-4S] cluster insertion into the S-adenosyl-methionine dependent radical SAM protein MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth of nitrate respiration, based on low gene expression levels.IMPORTANCEUnderstanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics and gene regulation. Still remaining critical gaps in our knowledge are how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SusA and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.
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226
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Przybyla-Toscano J, Christ L, Keech O, Rouhier N. Iron-sulfur proteins in plant mitochondria: roles and maturation. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2014-2044. [PMID: 33301571 DOI: 10.1093/jxb/eraa578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/05/2020] [Indexed: 05/22/2023]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe-S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe-S proteins. Several other proteins or complexes present in the matrix require Fe-S clusters as well, or depend either on Fe-S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe-S proteins. In this review, we have listed and discussed the Fe-S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe-S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe-S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.
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Affiliation(s)
- Jonathan Przybyla-Toscano
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Loïck Christ
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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227
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Quorum Sensing in Streptococcus mutans Regulates Production of Tryglysin, a Novel RaS-RiPP Antimicrobial Compound. mBio 2021; 12:mBio.02688-20. [PMID: 33727351 PMCID: PMC8092268 DOI: 10.1128/mbio.02688-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria interact and compete with a large community of organisms in their natural environment. Streptococcus mutans is one such organism, and it is an important member of the oral microbiota. We found that S. mutans uses a quorum-sensing system to regulate production of a novel posttranslationally modified peptide capable of inhibiting growth of several streptococcal species. The genus Streptococcus encompasses a large bacterial taxon that commonly colonizes mucosal surfaces of vertebrates and is capable of disease etiologies originating from diverse body sites, including the respiratory, digestive, and reproductive tracts. Identifying new modes of treating infections is of increasing importance, as antibiotic resistance has escalated. Streptococcus mutans is an important opportunistic pathogen that is an agent of dental caries and is capable of systemic diseases such as endocarditis. As such, understanding how it regulates virulence and competes in the oral niche is a priority in developing strategies to defend from these pathogens. We determined that S. mutans UA159 possesses a bona fide short hydrophobic peptide (SHP)/Rgg quorum-sensing system that regulates a specialized biosynthetic operon featuring a radical-SAM (S-adenosyl-l-methionine) (RaS) enzyme and produces a ribosomally synthesized and posttranslationally modified peptide (RiPP). The pairing of SHP/Rgg regulatory systems with RaS biosynthetic operons is conserved across streptococci, and a locus similar to that in S. mutans is found in Streptococcus ferus, an oral streptococcus isolated from wild rats. We identified the RaS-RiPP product from this operon and solved its structure using a combination of analytical methods; we term these RiPPs tryglysin A and B for the unusual Trp-Gly-Lys linkage. We report that tryglysins specifically inhibit the growth of other streptococci, but not other Gram-positive bacteria such as Enterococcus faecalis or Lactococcus lactis. We predict that tryglysin is produced by S. mutans in its oral niche, thus inhibiting the growth of competing species, including several medically relevant streptococci.
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228
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Meyer S, Häfliger J, Schäfer M, Molloy JJ, Daniliuc CG, Gilmour R. A Chiral Pentafluorinated Isopropyl Group via Iodine(I)/(III) Catalysis. Angew Chem Int Ed Engl 2021; 60:6430-6434. [PMID: 33427355 PMCID: PMC7986799 DOI: 10.1002/anie.202015946] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/08/2021] [Indexed: 12/15/2022]
Abstract
An I(I)/(III) catalysis strategy to construct an enantioenriched fluorinated isostere of the i Pr group is reported. The difluorination of readily accessible α-CF3 -styrenes is enabled by the in situ generation of a chiral ArIF2 species to forge a stereocentre with the substituents F, CH2 F and CF3 (up to 95 %, >20:1 vicinal:geminal difluorination). The replacement of the metabolically labile benzylic proton results in a highly preorganised scaffold as was determined by X-ray crystallography (π→σ* and stereoelectronic gauche σ→σ* interactions). A process of catalyst editing is disclosed in which preliminary validation of enantioselectivity is placed on a structural foundation.
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Affiliation(s)
- Stephanie Meyer
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - Joel Häfliger
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - Michael Schäfer
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - John J. Molloy
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - Constantin G. Daniliuc
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - Ryan Gilmour
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
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229
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Cheng J, Ji W, Ma S, Ji X, Deng Z, Ding W, Zhang Q. Characterization and Mechanistic Study of the Radical SAM Enzyme ArsS Involved in Arsenosugar Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jinduo Cheng
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Wenjuan Ji
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Suze Ma
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
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230
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Cheng J, Ji W, Ma S, Ji X, Deng Z, Ding W, Zhang Q. Characterization and Mechanistic Study of the Radical SAM Enzyme ArsS Involved in Arsenosugar Biosynthesis. Angew Chem Int Ed Engl 2021; 60:7570-7575. [PMID: 33427387 DOI: 10.1002/anie.202015177] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/07/2021] [Indexed: 12/18/2022]
Abstract
Arsenosugars are a group of arsenic-containing ribosides that are found predominantly in marine algae but also in terrestrial organisms. It has been proposed that arsenosugar biosynthesis involves a key intermediate 5'-deoxy-5'-dimethylarsinoyl-adenosine (DDMAA), but how DDMAA is produced remains elusive. Now, we report characterization of ArsS as a DDMAA synthase, which catalyzes a radical S-adenosylmethionine (SAM)-mediated alkylation (adenosylation) of dimethylarsenite (DMAsIII ) to produce DDMAA. This radical-mediated reaction is redox neutral, and multiple turnover can be achieved without external reductant. Phylogenomic and biochemical analyses revealed that DDMAA synthases are widespread in distinct bacterial phyla with similar catalytic efficiencies; these enzymes likely originated from cyanobacteria. This study reveals a key step in arsenosugar biosynthesis and also a new paradigm in radical SAM chemistry, highlighting the catalytic diversity of this superfamily of enzymes.
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Affiliation(s)
- Jinduo Cheng
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Wenjuan Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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231
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Impano S, Yang H, Shepard EM, Swimley R, Pagnier A, Broderick WE, Hoffman BM, Broderick JB. S-Adenosyl-l-ethionine is a Catalytically Competent Analog of S-Adenosyl-l-methione (SAM) in the Radical SAM Enzyme HydG. Angew Chem Int Ed Engl 2021; 60:4666-4672. [PMID: 33935588 PMCID: PMC8081114 DOI: 10.1002/anie.202014337] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 01/02/2023]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes initiate biological radical reactions with the 5'-deoxyadenosyl radical (5'-dAdo•). A [4Fe-4S]+ cluster reductively cleaves SAM to form the Ω organometallic intermediate in which the 5'-deoxyadenosyl moiety is directly bound to the unique iron of the [4Fe-4S] cluster, with subsequent liberation of 5'-dAdo•. Here we present synthesis of the SAM analog S-adenosyl-l-ethionine (SAE) and show SAE is a mechanistically-equivalent SAM-alternative for HydG, both supporting enzymatic turnover of substrate tyrosine and forming the organometallic intermediate Ω. Photolysis of SAE bound to HydG forms an ethyl radical trapped in the active site. The ethyl radical withstands prolonged storage at 77 K and its EPR signal is only partially lost upon annealing at 100 K, making it significantly less reactive than the methyl radical formed by SAM photolysis. Upon annealing above 77K, the ethyl radical adds to the [4Fe-4S]2+ cluster, generating an ethyl-[4Fe-4S]3+ organometallic species termed ΩE.
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Affiliation(s)
- Stella Impano
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL. USA 60208
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Ryan Swimley
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - William E Broderick
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Brian M Hoffman
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
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232
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Zhong A, Lee YH, Liu YN, Liu HW. Biosynthesis of Oxetanocin-A Includes a B 12-Dependent Radical SAM Enzyme That Can Catalyze both Oxidative Ring Contraction and the Demethylation of SAM. Biochemistry 2021; 60:537-546. [PMID: 33560833 PMCID: PMC7904626 DOI: 10.1021/acs.biochem.0c00915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxetanocin-A is an antitumor, antiviral, and antibacterial nucleoside. It is biosynthesized via the oxidative ring contraction of a purine nucleoside co-opted from primary metabolism. This reaction is catalyzed by a B12-dependent radical S-adenosyl-l-methionine (SAM) enzyme, OxsB, and a phosphohydrolase, OxsA. Previous experiments showed that the product of the OxsB/OxsA-catalyzed reaction is an oxetane aldehyde produced alongside an uncharacterized byproduct. Experiments reported herein reveal that OxsB/OxsA complex formation is crucial for the ring contraction reaction and that reduction of the aldehyde intermediate is catalyzed by a nonspecific dehydrogenase from the general cellular pool. In addition, the byproduct is identified as a 1,3-thiazinane adduct between the aldehyde and l-homocysteine. While homocysteine was never included in the OxsB/OxsA assays, the data suggest that it can be generated from SAM via S-adenosyl-l-homocysteine (SAH). Further study revealed that conversion of SAM to SAH is facilitated by OxsB; however, the subsequent conversion of SAH to homocysteine is due to protein contaminants that co-purify with OxsA. Nevertheless, the observed demethylation of SAM to SAH suggests possible methyltransferase activity of OxsB, and substrate methylation was indeed detected in the OxsB-catalyzed reaction. This work is significant because it not only completes the description of the oxetanocin-A biosynthetic pathway but also suggests that OxsB may be capable of methyltransferase activity.
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Affiliation(s)
- Aoshu Zhong
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yung-nan Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
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233
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Meyer S, Häfliger J, Schäfer M, Molloy JJ, Daniliuc CG, Gilmour R. Eine chirale pentafluorierte Isopropylgruppe durch Iod(I)/(III)‐Katalyse. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015946] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Stephanie Meyer
- Organisch Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstraße 36 48149 Münster Deutschland
| | - Joel Häfliger
- Organisch Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstraße 36 48149 Münster Deutschland
| | - Michael Schäfer
- Organisch Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstraße 36 48149 Münster Deutschland
| | - John J. Molloy
- Organisch Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstraße 36 48149 Münster Deutschland
| | - Constantin G. Daniliuc
- Organisch Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstraße 36 48149 Münster Deutschland
| | - Ryan Gilmour
- Organisch Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstraße 36 48149 Münster Deutschland
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234
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Knox HL, Chen PYT, Blaszczyk AJ, Mukherjee A, Grove TL, Schwalm EL, Wang B, Drennan CL, Booker SJ. Structural basis for non-radical catalysis by TsrM, a radical SAM methylase. Nat Chem Biol 2021; 17:485-491. [PMID: 33462497 PMCID: PMC7990684 DOI: 10.1038/s41589-020-00717-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
TsrM methylates C2 of the indole ring of L-tryptophan (Trp) during the biosynthesis of the quinaldic acid moiety of thiostrepton. It is annotated as a cobalamin-dependent radical S-adenosylmethionine (SAM) methylase; however, TsrM does not reductively cleave SAM to the universal 5ʹ-deoxyadenosyl 5ʹ-radical intermediate, a hallmark of radical-SAM (RS) enzymes. Herein, we report structures of TsrM from Kitasatospora setae, the first of a cobalamin-dependent radical SAM methylase. Unexpectedly, the structures show an essential arginine residue that resides in the proximal coordination sphere of the cobalamin cofactor and a [4Fe–4S] cluster that is ligated by a glutamyl residue and three cysteines in a canonical CxxxCxxC RS motif. Structures in the presence of substrates suggest a substrate-assisted mechanism of catalysis, wherein the carboxylate group of SAM serves as a general base to deprotonate N1 of the tryptophan substrate, facilitating formation of a C2 carbanion. The first crystal structures of a cobalamin-dependent radical SAM methylase reveal an unexpected mode of methylation.
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Affiliation(s)
- Hayley L Knox
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Anthony J Blaszczyk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.,Catalent Pharma Solutions, Gaithersburg, MD, USA
| | - Arnab Mukherjee
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Erica L Schwalm
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.,Merck & Co., Inc., Rahway, NJ, USA
| | - Bo Wang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. .,Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA.
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235
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Impano S, Yang H, Shepard EM, Swimley R, Pagnier A, Broderick WE, Hoffman BM, Broderick JB. S
‐Adenosyl‐
l
‐ethionine is a Catalytically Competent Analog of
S
‐Adenosyl‐
l
‐methionine (SAM) in the Radical SAM Enzyme HydG. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Stella Impano
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Hao Yang
- Department of Chemistry Northwestern University Evanston IL 60208 USA
| | - Eric M. Shepard
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Ryan Swimley
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - William E. Broderick
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Brian M. Hoffman
- Department of Chemistry Northwestern University Evanston IL 60208 USA
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
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236
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Impano S, Yang H, Jodts RJ, Pagnier A, Swimley R, McDaniel EC, Shepard EM, Broderick WE, Broderick JB, Hoffman BM. Active-Site Controlled, Jahn-Teller Enabled Regioselectivity in Reductive S-C Bond Cleavage of S-Adenosylmethionine in Radical SAM Enzymes. J Am Chem Soc 2021; 143:335-348. [PMID: 33372786 PMCID: PMC7934139 DOI: 10.1021/jacs.0c10925] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Catalysis by canonical radical S-adenosyl-l-methionine (SAM) enzymes involves electron transfer (ET) from [4Fe-4S]+ to SAM, generating an R3S0 radical that undergoes regioselective homolytic reductive cleavage of the S-C5' bond to generate the 5'-dAdo· radical. However, cryogenic photoinduced S-C bond cleavage has regioselectively yielded either 5'-dAdo· or ·CH3, and indeed, each of the three SAM S-C bonds can be regioselectively cleaved in an RS enzyme. This diversity highlights a longstanding central question: what controls regioselective homolytic S-C bond cleavage upon SAM reduction? We here provide an unexpected answer, founded on our observation that photoinduced S-C bond cleavage in multiple canonical RS enzymes reveals two enzyme classes: in one, photolysis forms 5'-dAdo·, and in another it forms ·CH3. The identity of the cleaved S-C bond correlates with SAM ribose conformation but not with positioning and orientation of the sulfonium center relative to the [4Fe-4S] cluster. We have recognized the reduced-SAM R3S0 radical is a (2E) state with its antibonding unpaired electron in an orbital doublet, which renders R3S0 Jahn-Teller (JT)-active and therefore subject to vibronically induced distortion. Active-site forces induce a JT distortion that localizes the odd electron in a single priority S-C antibond, which undergoes regioselective cleavage. In photolytic cleavage those forces act through control of the ribose conformation and are transmitted to the sulfur via the S-C5' bond, but during catalysis thermally induced conformational changes that enable ET from a cluster iron generate dominant additional forces that specifically select S-C5' for cleavage. This motion also can explain how 5'-dAdo· subsequently forms the organometallic intermediate Ω.
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Affiliation(s)
- Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Ryan Swimley
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Elizabeth C McDaniel
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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237
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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238
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Rapp J, Rath P, Kilian J, Brilisauer K, Grond S, Forchhammer K. A bioactive molecule made by unusual salvage of radical SAM enzyme byproduct 5-deoxyadenosine blurs the boundary of primary and secondary metabolism. J Biol Chem 2021; 296:100621. [PMID: 33811856 PMCID: PMC8102628 DOI: 10.1016/j.jbc.2021.100621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
5-Deoxyadenosine (5dAdo) is the byproduct of many radical S-adenosyl-l-methionine enzyme reactions in all domains of life. 5dAdo is also an inhibitor of the radical S-adenosyl-l-methionine enzymes themselves, making it necessary for cells to construct pathways to recycle or dispose of this toxic metabolite. However, the specific pathways involved have long remained unexplored. Recent research demonstrated a growth advantage in certain organisms by using 5dAdo or intermediates as a sole carbon source and elucidated the corresponding salvage pathway. We now provide evidence using supernatant analysis by GC-MS for another 5dAdo recycling route. Specifically, in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus), the activity of promiscuous enzymes leads to the synthesis and excretion first of 5-deoxyribose and subsequently of 7-deoxysedoheptulose. 7-Deoxysedoheptulose is an unusual deoxy-sugar, which acts as an antimetabolite of the shikimate pathway, thereby exhibiting antimicrobial and herbicidal activity. This strategy enables organisms with small genomes and lacking canonical gene clusters for the synthesis of secondary metabolites, like S. elongatus, to produce antimicrobial compounds from primary metabolism and enzymatic promiscuity. Our findings challenge the view of bioactive molecules as sole products of secondary metabolite gene clusters and expand the range of compounds that microorganisms can deploy to compete for their ecological niche.
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Affiliation(s)
- Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Pascal Rath
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Joachim Kilian
- Center for Plant Molecular Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Klaus Brilisauer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany.
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239
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Computing Proton-Coupled Redox Potentials of Fluorotyrosines in a Protein Environment. J Phys Chem B 2020; 125:128-136. [PMID: 33378205 DOI: 10.1021/acs.jpcb.0c09974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation of tyrosine to form the neutral tyrosine radical via proton-coupled electron transfer is essential for a wide range of biological processes. The precise measurement of the proton-coupled redox potentials of tyrosine (Y) in complex protein environments is challenging mainly because of the highly oxidizing and reactive nature of the radical state. Herein, a computational strategy is presented for predicting proton-coupled redox potentials in a protein environment. In this strategy, both the reduced Y-OH and oxidized Y-O• forms of tyrosine are sampled with molecular dynamics using a molecular mechanical force field. For a large number of conformations, a quantum mechanical/molecular mechanical (QM/MM) electrostatic embedding scheme is used to compute the free-energy differences between the reduced and oxidized forms, including the zero-point energy and entropic contributions as well as the impact of the protein electrostatic environment. This strategy is applied to a series of fluorinated tyrosine derivatives embedded in a de novo α-helical protein denoted as α3Y. The force fields for both the reduced and oxidized forms of these noncanonical fluorinated tyrosine residues are parameterized for general use. The calculated relative proton-coupled redox potentials agree with experimentally measured values with a mean unsigned error of 24 mV. Analysis of the simulations illustrates that hydrogen-bonding interactions between tyrosine and water increase the redox potentials by ∼100-250 mV, with significant variations because of the fluctuating protein environment. This QM/MM approach enables the calculation of proton-coupled redox potentials of tyrosine and other residues such as tryptophan in a variety of protein systems.
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240
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Fontecilla-Camps JC. Primordial bioenergy sources: The two facets of adenosine triphosphate. J Inorg Biochem 2020; 216:111347. [PMID: 33450675 DOI: 10.1016/j.jinorgbio.2020.111347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H+ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.
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241
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Wilkens D, Meusinger R, Hein S, Simon J. Sequence analysis and specificity of distinct types of menaquinone methyltransferases indicate the widespread potential of methylmenaquinone production in bacteria and archaea. Environ Microbiol 2020; 23:1407-1421. [PMID: 33264482 DOI: 10.1111/1462-2920.15344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
Menaquinone (MK) serves as an essential membranous redox mediator in various electron transport chains of aerobic and anaerobic respiration. In addition, the composition of the quinone/quinol pool has been widely used as a biomarker in microbial taxonomy. The HemN-like class C radical SAM methyltransferases (RSMTs) MqnK, MenK and MenK2 have recently been shown to facilitate specific menaquinone methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesize 8-methylmenaquinone, 7-methylmenaquinone and 7,8-dimethylmenaquinone. However, the vast majority of protein sequences from the MqnK/MenK/MenK2 family belong to organisms, whose capacity to produce methylated menaquinones has not been investigated biochemically. Here, representative putative menK and menK2 genes from Collinsella tanakaei and Ferrimonas marina were individually expressed in Escherichia coli (wild-type or ubiE deletion mutant) and the corresponding cells were found to produce methylated derivatives of the endogenous MK and 2-demethylmenaquinone. Cluster and phylogenetic analyses of 828 (methyl)menaquinone methyltransferase sequences revealed signature motifs that allowed to discriminate enzymes of the MqnK/MenK/MenK2 family from other radical SAM enzymes and to identify C-7-specific menaquinone methyltransferases of the MenK2 subfamily. This study will help to predict the methylation status of the quinone/quinol pool of a microbial species (or even a microbial community) from its (meta)genome and contribute to the future design of microbial quinone/quinol pools in a Synthetic Biology approach.
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Affiliation(s)
- Dennis Wilkens
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany
| | - Reinhard Meusinger
- Department of Chemistry, Macromolecular Chemistry, Technical University of Darmstadt, Alarich-Weiss-Str. 4, Darmstadt, 64287, Germany
| | - Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, 64283, Germany
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242
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Mg-protoporphyrin IX monomethyl ester cyclase from Rhodobacter capsulatus: radical SAM-dependent synthesis of the isocyclic ring of bacteriochlorophylls. Biochem J 2020; 477:4635-4654. [DOI: 10.1042/bcj20200761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 11/17/2022]
Abstract
During bacteriochlorophyll a biosynthesis, the oxygen-independent conversion of Mg-protoporphyrin IX monomethyl ester (Mg-PME) to protochlorophyllide (Pchlide) is catalyzed by the anaerobic Mg-PME cyclase termed BchE. Bioinformatics analyses in combination with pigment studies of cobalamin-requiring Rhodobacter capsulatus mutants indicated an unusual radical S-adenosylmethionine (SAM) and cobalamin-dependent BchE catalysis. However, in vitro biosynthesis of the isocyclic ring moiety of bacteriochlorophyll using purified recombinant BchE has never been demonstrated. We established a spectroscopic in vitro activity assay which was subsequently validated by HPLC analyses and H218O isotope label transfer onto the carbonyl-group (C-131-oxo) of the isocyclic ring of Pchlide. The reaction product was further converted to chlorophyllide in the presence of light-dependent Pchlide reductase. BchE activity was stimulated by increasing concentrations of NADPH or SAM, and inhibited by S-adenosylhomocysteine. Subcellular fractionation experiments revealed that membrane-localized BchE requires an additional, heat-sensitive cytosolic component for activity. BchE catalysis was not sustained in chimeric experiments when a cytosolic extract from E. coli was used as a substitute. Size-fractionation of the soluble R. capsulatus fraction indicated that enzymatic activity relies on a specific component with an estimated molecular mass between 3 and 10 kDa. A structure guided site-directed mutagenesis approach was performed on the basis of a three-dimensional homology model of BchE. A newly established in vivo complementation assay was used to investigate 24 BchE mutant proteins. Potential ligands of the [4Fe-4S] cluster (Cys204, Cys208, Cys211), of SAM (Phe210, Glu308 and Lys320) and of the proposed cobalamin cofactor (Asp248, Glu249, Leu29, Thr71, Val97) were identified.
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243
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Liu G, Sil D, Maio N, Tong WH, Bollinger JM, Krebs C, Rouault TA. Heme biosynthesis depends on previously unrecognized acquisition of iron-sulfur cofactors in human amino-levulinic acid dehydratase. Nat Commun 2020; 11:6310. [PMID: 33298951 PMCID: PMC7725820 DOI: 10.1038/s41467-020-20145-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/06/2020] [Indexed: 12/18/2022] Open
Abstract
Heme biosynthesis and iron-sulfur cluster (ISC) biogenesis are two major mammalian metabolic pathways that require iron. It has long been known that these two pathways interconnect, but the previously described interactions do not fully explain why heme biosynthesis depends on intact ISC biogenesis. Herein we identify a previously unrecognized connection between these two pathways through our discovery that human aminolevulinic acid dehydratase (ALAD), which catalyzes the second step of heme biosynthesis, is an Fe-S protein. We find that several highly conserved cysteines and an Ala306-Phe307-Arg308 motif of human ALAD are important for [Fe4S4] cluster acquisition and coordination. The enzymatic activity of human ALAD is greatly reduced upon loss of its Fe-S cluster, which results in reduced heme biosynthesis in human cells. As ALAD provides an early Fe-S-dependent checkpoint in the heme biosynthetic pathway, our findings help explain why heme biosynthesis depends on intact ISC biogenesis. Heme biosynthesis depends on iron-sulfur (Fe-S) cluster biogenesis but the molecular connection between these pathways is not fully understood. Here, the authors show that the heme biosynthesis enzyme ALAD contains an Fe-S cluster, disruption of which reduces ALAD activity and heme production in human cells.
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Affiliation(s)
- Gang Liu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nunziata Maio
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Wing-Hang Tong
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - J Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Tracey Ann Rouault
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Balty C, Guillot A, Fradale L, Brewee C, Lefranc B, Herrero C, Sandström C, Leprince J, Berteau O, Benjdia A. Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes. J Biol Chem 2020; 295:16665-16677. [PMID: 32972973 PMCID: PMC8188230 DOI: 10.1074/jbc.ra120.015371] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether-containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC-MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.
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Affiliation(s)
- Clémence Balty
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Laura Fradale
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Benjamin Lefranc
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | | | - Corine Sandström
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jérôme Leprince
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
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246
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Zhu W, Klinman JP. Biogenesis of the peptide-derived redox cofactor pyrroloquinoline quinone. Curr Opin Chem Biol 2020; 59:93-103. [PMID: 32731194 PMCID: PMC7736144 DOI: 10.1016/j.cbpa.2020.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes that also plays beneficial roles in organisms from other kingdoms. We review recent developments on the pathway of PQQ biogenesis, focusing on the mechanisms of PqqE, PqqF/G, and PqqB. These advances may shed light on other, uncharacterized biosynthetic pathways.
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Affiliation(s)
- Wen Zhu
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA
| | - Judith P Klinman
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720-3220, USA.
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247
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Kang W, Rettberg LA, Stiebritz MT, Jasniewski AJ, Tanifuji K, Lee CC, Ribbe MW, Hu Y. X‐Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM‐Dependent Carbide Insertion During Nitrogenase Cofactor Assembly. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wonchull Kang
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Lee A. Rettberg
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Martin T. Stiebritz
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Andrew J. Jasniewski
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Markus W. Ribbe
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
- Department of Chemistry University of California, Irvine Irvine CA 92697-2025 USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
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Kang W, Rettberg LA, Stiebritz MT, Jasniewski AJ, Tanifuji K, Lee CC, Ribbe MW, Hu Y. X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly. Angew Chem Int Ed Engl 2020; 60:2364-2370. [PMID: 33035363 DOI: 10.1002/anie.202011367] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/27/2020] [Indexed: 12/13/2022]
Abstract
NifB is an essential radical SAM enzyme required for the assembly of an 8Fe core of the nitrogenase cofactor. Herein, we report the X-ray crystal structures of Methanobacterium thermoautotrophicum NifB without (apo MtNifB) and with (holo MtNifB) a full complement of three [Fe4 S4 ] clusters. Both apo and holo MtNifB contain a partial TIM barrel core, but unlike apo MtNifB, holo MtNifB is fully assembled and competent in cofactor biosynthesis. The radical SAM (RS)-cluster is coordinated by three Cys, and the adjacent K1- and K2-clusters, representing the precursor to an 8Fe cofactor core, are each coordinated by one His and two Cys. Prediction of substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of SAM between the RS- and K2-clusters and putative paths for entry of SAM and exit of products of SAM cleavage, thereby providing important mechanistic insights into the radical SAM-dependent carbide insertion concomitant with cofactor core formation.
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Affiliation(s)
- Wonchull Kang
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Lee A Rettberg
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Martin T Stiebritz
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
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Bím D, Alonso-Gil S, Srnec M. From Synthetic to Biological Fe 4 S 4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes. Chempluschem 2020; 85:2534-2541. [PMID: 33245201 DOI: 10.1002/cplu.202000663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Indexed: 11/10/2022]
Abstract
By employing the computational protocol for calculation of reduction potentials of the Fe4 S4 -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe4 S4 , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.
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Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
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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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