1
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Santos AJDC, Dias RS, da Silva CHM, Vidigal PMP, de Sousa MP, da Silva CC, de Paula SO. Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir. Access Microbiol 2024; 6:000801.v3. [PMID: 39148687 PMCID: PMC11326445 DOI: 10.1099/acmi.0.000801.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.
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Affiliation(s)
- Adriele Jéssica do Carmo Santos
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Carlos Henrique Martins da Silva
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Pedro Marcus Pereira Vidigal
- Center for Biomolecules Analysis (NuBIOMOL), Federal University of Viçosa, Vila Gianetti, Campus Universitário, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Maíra Paula de Sousa
- Leopoldo Américo Miguez de Mello Research and Development Center, Petrobras, Av. Horácio Macedo, 950, Federal University of Rio de Janeiro, 21941-915, Rio de Janeiro, Brazil
| | - Cynthia Canedo da Silva
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Sérgio Oliveira de Paula
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, 36570-900, Viçosa, Minas Gerais, Brazil
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2
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Korotenko V, Zipse H. The stability of oxygen-centered radicals and its response to hydrogen bonding interactions. J Comput Chem 2024; 45:101-114. [PMID: 37747356 DOI: 10.1002/jcc.27221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/26/2023]
Abstract
The stability of various alkoxy/aryloxy/peroxy radicals, as well as TEMPO and triplet dioxygen (3 O2 ) has been explored at a variety of theoretical levels. Good correlations between RSEtheor and RSEexp are found for hybrid DFT methods, for compound schemes such as G3B3-D3, and also for DLPNO-CCSD(T) calculations. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have been probed by addition of a single solvating water molecule. While this water molecule always acts as a H-bond donor to the oxygen-centered radical itself, it can act as a H-bond donor or acceptor to the respective closed-shell parent.
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Affiliation(s)
| | - Hendrik Zipse
- Department of Chemistry, LMU Munich, Munich, Germany
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3
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Eastman KS, Mifflin MC, Oblad PF, Roberts AG, Bandarian V. A Promiscuous rSAM Enzyme Enables Diverse Peptide Cross-linking. ACS BIO & MED CHEM AU 2023; 3:480-493. [PMID: 38144258 PMCID: PMC10739248 DOI: 10.1021/acsbiomedchemau.3c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 12/26/2023]
Abstract
Ribosomally produced and post-translationally modified polypeptides (RiPPs) are a diverse group of natural products that are processed by a variety of enzymes to their biologically relevant forms. PapB is a member of the radical S-adenosyl-l-methionine (rSAM) superfamily that introduces thioether cross-links between Cys and Asp residues in the PapA RiPP. We report that PapB has high tolerance for variations in the peptide substrate. Our results demonstrate that branched side chains in the thiol- and carboxylate-containing residues are processed and that lengthening of these groups to homocysteine and homoglutamate does not impair the ability of PapB to form thioether cross-links. Remarkably, the enzyme can even cross-link a peptide substrate where the native Asp carboxylate moiety is replaced with a tetrazole. We show that variations to residues embedded between the thiol- and carboxylate-containing residues are tolerated by PapB, as peptides containing both bulky (e.g., Phe) and charged (e.g., Lys) side chains in both natural L- and unnatural D-forms are efficiently cross-linked. Diastereomeric peptides bearing (2S,3R)- and (2S,3S)-methylaspartate are processed by PapB to form cyclic thioethers with markedly different rates, suggesting the enzymatic hydrogen atom abstraction event for the native Asp-containing substrate is diastereospecific. Finally, we synthesized two diastereomeric peptide substrates bearing E- and Z-configured γ,δ-dehydrohomoglutamate and show that PapB promotes addition of the deoxyadenosyl radical (dAdo•) instead of hydrogen atom abstraction. In the Z-configured γ,δ-dehydrohomoglutamate substrate, a fraction of the dAdo-adduct peptide is thioether cross-linked. In both cases, there is evidence for product inhibition of PapB, as the dAdo-adducts likely mimic the native transition state where dAdo• is poised to abstract a substrate hydrogen atom. Collectively, these findings provide critical insights into the arrangement of reacting species in the active site of the PapB, reveal unusual promiscuity, and highlight the potential of PapB as a tool in the development peptide therapeutics.
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Affiliation(s)
- Karsten
A. S. Eastman
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Marcus C. Mifflin
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Paul F. Oblad
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Andrew G. Roberts
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
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4
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Benjdia A, Berteau O. B 12-dependent radical SAM enzymes: Ever expanding structural and mechanistic diversity. Curr Opin Struct Biol 2023; 83:102725. [PMID: 37931378 DOI: 10.1016/j.sbi.2023.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 11/08/2023]
Abstract
In the last decade, B12-dependent radical SAM enzymes have emerged as central biocatalysts in the biosynthesis of a myriad of natural products. Notably, these enzymes have been shown to catalyze carbon-carbon bond formation on unactivated carbon atoms leading to unusual methylations. Recently, structural studies have revealed unprecedented insights into the complex chemistry catalyzed by these enzymes. In this review, we cover recent advances in our understanding of B12-dependent radical SAM enzymes from a mechanistic and structural perspective. We discuss the unanticipated diversity of these enzymes which suggests evolutionary links between various biosynthetic and metabolic pathways from antibiotic to RiPP and methane biosynthesis.
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Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
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5
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Revealing intrinsic changes of DNA induced by spore photoproduct lesion through computer simulation. Biophys Chem 2023; 296:106992. [PMID: 36933500 DOI: 10.1016/j.bpc.2023.106992] [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: 11/03/2022] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
In bacterial endospores, a cross-linked thymine dimer, 5-thyminyl-5,6-dihydrothymine, commonly referred to as the spore photoproduct (SP), is found as the dominant DNA photo lesion under UV radiation. During spore germination, SP is faithfully repaired by the spore photoproduct lyase (SPL) for normal DNA replication to resume. Despite this general mechanism, the exact way in which SP modifies the duplex DNA structure so that the damaged site can be recognized by SPL to initiate the repair process is still unclear. A previous X-ray crystallographic study, which used a reverse transcriptase as a DNA host template, captured a protein-bound duplex oligonucleotide containing two SP lesions; the study showed shortened hydrogen bonds between the AT base pairs involved in the lesions and widened minor grooves near the damaged sites. However, it remains to be determined whether the results accurately reflect the conformation of SP-containing DNA (SP-DNA) in its fully hydrated pre-repair form. To uncover the intrinsic changes in DNA conformation caused by SP lesions, we performed molecular dynamics (MD) simulations of SP-DNA duplexes in aqueous solution, using the nucleic acid portion of the previously determined crystal structure as a template. After MD relaxation, our simulated SP-DNAs showed weakened hydrogen bonds at the damaged sites compared to those in the undamaged DNA. Our analyses of the MD trajectories revealed a range of local and global structural distortions of DNA induced by SP. Specifically, the SP region displays a greater tendency to adopt an A-like-DNA conformation, and curvature analysis revealed an increase in the global bending compared to the canonical B-DNA. Although these SP-induced DNA conformational changes are relatively minor, they may provide a sufficient structural basis for SP to be recognized by SPL during the lesion repair process.
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6
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Jäger C, Croft AK. If It Is Hard, It Is Worth Doing: Engineering Radical Enzymes from Anaerobes. Biochemistry 2022; 62:241-252. [PMID: 36121716 PMCID: PMC9850924 DOI: 10.1021/acs.biochem.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With a pressing need for sustainable chemistries, radical enzymes from anaerobes offer a shortcut for many chemical transformations and deliver highly sought-after functionalizations such as late-stage C-H functionalization, C-C bond formation, and carbon-skeleton rearrangements, among others. The challenges in handling these oxygen-sensitive enzymes are reflected in their limited industrial exploitation, despite what they may deliver. With an influx of structures and mechanistic understanding, the scope for designed radical enzymes to deliver wanted processes becomes ever closer. Combined with new advances in computational methods and workflows for these complex systems, the outlook for an increased use of radical enzymes in future processes is exciting.
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7
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Artificially sporulated Escherichia coli cells as a robust cell factory for interfacial biocatalysis. Nat Commun 2022; 13:3142. [PMID: 35668090 PMCID: PMC9170730 DOI: 10.1038/s41467-022-30915-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
The natural bacterial spores have inspired the development of artificial spores, through coating cells with protective materials, for durable whole-cell catalysis. Despite attractiveness, artificial spores developed to date are generally limited to a few microorganisms with their natural endogenous enzymes, and they have never been explored as a generic platform for widespread synthesis. Here, we report a general approach to designing artificial spores based on Escherichia coli cells with recombinant enzymes. The artificial spores are simply prepared by coating cells with polydopamine, which can withstand UV radiation, heating and organic solvents. Additionally, the protective coating enables living cells to stabilize aqueous-organic emulsions for efficient interfacial biocatalysis ranging from single reactions to multienzyme cascades. Furthermore, the interfacial system can be easily expanded to chemoenzymatic synthesis by combining artificial spores with metal catalysts. Therefore, this artificial-spore-based platform technology is envisioned to lay the foundation for next-generation cell factory engineering.
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8
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Zhou S, Wei WJ, Liao RZ. QM/MM Study of the Mechanism of the Noncanonical S-Cγ Bond Scission in S-Adenosylmethionine Catalyzed by the CmnDph2 Radical Enzyme. Top Catal 2022. [DOI: 10.1007/s11244-021-01420-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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10
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Feng JQ, Wang BJ. Super-exchange and exchange-enhanced reactivity in Fe4S4-mediated activation of SAM by radical SAM enzymes. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2108134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jian-qiang 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
| | - Bin-ju 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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11
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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. [DOI: 10.1002/ange.202107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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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12
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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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13
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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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14
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Huang R, Zhou PK. DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther 2021; 6:254. [PMID: 34238917 PMCID: PMC8266832 DOI: 10.1038/s41392-021-00648-7] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China.
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15
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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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16
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Pagnier A, Yang H, Jodts RJ, James CD, Shepard EM, Impano S, Broderick WE, Hoffman BM, Broderick JB. Radical SAM Enzyme Spore Photoproduct Lyase: Properties of the Ω Organometallic Intermediate and Identification of Stable Protein Radicals Formed during Substrate-Free Turnover. J Am Chem Soc 2020; 142:18652-18660. [PMID: 32966073 DOI: 10.1021/jacs.0c08585] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase is a radical S-adenosyl-l-methionine (SAM) enzyme with the unusual property that addition of SAM to the [4Fe-4S]1+ enzyme absent substrate results in rapid electron transfer to SAM with accompanying homolytic S-C5' bond cleavage. Herein, we demonstrate that this unusual reaction forms the organometallic intermediate Ω in which the unique Fe atom of the [4Fe-4S] cluster is bound to C5' of the 5'-deoxyadenosyl radical (5'-dAdo•). During catalysis, homolytic cleavage of the Fe-C5' bond liberates 5'-dAdo• for reaction with substrate, but here, we use Ω formation without substrate to determine the thermal stability of Ω. The reaction of Geobacillus thermodenitrificans SPL (GtSPL) with SAM forms Ω within ∼15 ms after mixing. By monitoring the decay of Ω through rapid freeze-quench trapping at progressively longer times we find an ambient temperature decay time of the Ω Fe-C5' bond of τ ≈ 5-6 s, likely shortened by enzymatic activation as is the case with the Co-C5' bond of B12. We have further used hand quenching at times up to 10 min, and thus with multiple SAM turnovers, to probe the fate of the 5'-dAdo• radical liberated by Ω. In the absence of substrate, Ω undergoes low-probability conversion to a stable protein radical. The WT enzyme with valine at residue 172 accumulates a Val•; mutation of Val172 to isoleucine or cysteine results in accumulation of an Ile• or Cys• radical, respectively. The structures of the radical in WT, V172I, and V172C variants have been established by detailed EPR/DFT analyses.
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Affiliation(s)
- Adrien Pagnier
- 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
| | - Christopher D James
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - Stella Impano
- 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
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
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17
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Zhai Y, Tian J, Ping R, Xiu H, Xiang Q, Shen R, Wang Z. Effects of ultraviolet-C light-emitting diodes at 275 nm on inactivation of Alicyclobacillusacidoterrestris vegetative cells and its spores as well as the quality attributes of orange juice. FOOD SCI TECHNOL INT 2020; 27:334-343. [PMID: 32954800 DOI: 10.1177/1082013220957529] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Alicyclobacillus acidoterrestris is a thermoacidophilic, spore-forming bacillus. A. acidoterrestris and its spores can survive in pasteurized juices and cause microbial spoilage. In this work, the effects of ultraviolet-C light-emitting diodes at 275 nm on the inactivation of A. acidoterrestris vegetative cells and its spores in commercial pasteurized orange juice were studied. Meanwhile, the effects of ultraviolet-C light-emitting diodes on the quality attributes of the orange juice were also investigated. The quantities of A. acidoterrestris vegetative cells and its spores inoculated in orange juice were reduced by 6.04 and 2.49 log10 CFU/mL after ultraviolet-C light-emitting diode treatment at 220 mJ/cm2, respectively. The Weibull and Weibull plus tail models were satisfactorily fitted to estimate the reductions of A. acidoterrestris vegetative cells and its spores in orange juice, respectively. Physicochemical properties (pH, titratable acidity, total soluble solids, and clarity) of orange juice did not change significantly after exposure to ultraviolet-C light-emitting diodes. However, the total phenolic content of orange juice decreased with increasing fluence. In addition, ultraviolet-C light-emitting diode treatment at a higher fluence led to a noticeable color difference. These results indicate that ultraviolet-C light-emitting diode treatment has a potential application in the juice processing industry.
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Affiliation(s)
- Yafei Zhai
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, PR China.,Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou, PR China.,Henan Collaborative Innovation Center of Food Production and Safety, Zhengzhou, PR China
| | - Jiali Tian
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, PR China
| | - Ruonan Ping
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, PR China
| | - Hongxia Xiu
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, PR China
| | - Qisen Xiang
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, PR China.,Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou, PR China.,Henan Collaborative Innovation Center of Food Production and Safety, Zhengzhou, PR China
| | - Ruiling Shen
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, PR China.,Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou, PR China.,Henan Collaborative Innovation Center of Food Production and Safety, Zhengzhou, PR China
| | - Zhangcun Wang
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, PR China.,Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou, PR China.,Henan Collaborative Innovation Center of Food Production and Safety, Zhengzhou, PR China
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18
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Kumar G, Srinivasan N, Sandhya S. Artificial protein sequences enable recognition of vicinal and distant protein functional relationships. Proteins 2020; 88:1688-1700. [PMID: 32725917 DOI: 10.1002/prot.25986] [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: 04/14/2020] [Revised: 06/29/2020] [Accepted: 07/26/2020] [Indexed: 11/07/2022]
Abstract
High divergence in protein sequences makes the detection of distant protein relationships through homology-based approaches challenging. Grouping protein sequences into families, through similarities in either sequence or 3-D structure, facilitates in the improved recognition of protein relationships. In addition, strategically designed protein-like sequences have been shown to bridge distant structural domain families by serving as artificial linkers. In this study, we have augmented a search database of known protein domain families with such designed sequences, with the intention of providing functional clues to domain families of unknown structure. When assessed using representative query sequences from each family, we obtain a success rate of 94% in protein domain families of known structure. Further, we demonstrate that the augmented search space enabled fold recognition for 582 families with no structural information available a priori. Additionally, we were able to provide reliable functional relationships for 610 orphan families. We discuss the application of our method in predicting functional roles through select examples for DUF4922, DUF5131, and DUF5085. Our approach also detects new associations between families that were previously not known to be related, as demonstrated through new sub-groups of the RNA polymerase domain among three distinct RNA viruses. Taken together, designed sequences-augmented search databases direct the detection of meaningful relationships between distant protein families. In turn, they enable fold recognition and offer reliable pointers to potential functional sites that may be probed further through direct mutagenesis studies.
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Affiliation(s)
- Gayatri Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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19
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20
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Balty C, Guillot A, Fradale L, Brewee C, Boulay M, Kubiak X, Benjdia A, Berteau O. Ruminococcin C, an anti-clostridial sactipeptide produced by a prominent member of the human microbiota Ruminococcus gnavus. J Biol Chem 2019; 294:14512-14525. [PMID: 31337708 PMCID: PMC6779426 DOI: 10.1074/jbc.ra119.009416] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Indexed: 11/06/2022] Open
Abstract
The human microbiota plays a central role in human physiology. This complex ecosystem is a promising but untapped source of bioactive compounds and antibiotics that are critical for its homeostasis. However, we still have a very limited knowledge of its metabolic and biosynthetic capabilities. Here we investigated an enigmatic biosynthetic gene cluster identified previously in the human gut symbiont Ruminococcus gnavus. This gene cluster which encodes notably for peptide precursors and putative radical SAM enzymes, has been proposed to be responsible for the biosynthesis of ruminococcin C (RumC), a ribosomally synthesized and posttranslationally modified peptide (RiPP) with potent activity against the human pathogen Clostridium perfringens. By combining in vivo and in vitro approaches, including recombinant expression and purification of the respective peptides and proteins, enzymatic assays, and LC-MS analyses, we determined that RumC is a sulfur-to–α-carbon thioether-containing peptide (sactipeptide) with an unusual architecture. Moreover, our results support that formation of the thioether bridges follows a processive order, providing mechanistic insights into how radical SAM (AdoMet) enzymes install posttranslational modifications in RiPPs. We also found that the presence of thioether bridges and removal of the leader peptide are required for RumC's antimicrobial activity. In summary, our findings provide evidence that production of the anti-Clostridium peptide RumC depends on an R. gnavus operon encoding five potential RumC precursor peptides and two radical SAM enzymes, uncover key RumC structural features, and delineate the sequence of posttranslational modifications leading to its formation and antimicrobial activity.
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Affiliation(s)
- Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Laura Fradale
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Mylène Boulay
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xavier Kubiak
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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21
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Miller SA, Bandarian V. Analysis of Electrochemical Properties of S-Adenosyl-l-methionine and Implications for Its Role in Radical SAM Enzymes. J Am Chem Soc 2019; 141:11019-11026. [PMID: 31283208 PMCID: PMC7059804 DOI: 10.1021/jacs.9b00933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
S-Adenosyl-l-methionine (SAM) is the
central cofactor in the radical SAM enzyme superfamily, responsible
for a vast number of transformations in primary and secondary metabolism.
In nearly all of these reactions, the reductive cleavage of SAM is
proposed to produce a reactive species, 5′-deoxyadenosyl radical,
which initiates catalysis. While the mechanistic details in many cases
are well-understood, the reductive cleavage of SAM remains elusive.
In this manuscript, we have measured the solution peak potential of
SAM to be ∼−1.4 V (v SHE) and show that under controlled
potential conditions, it undergoes irreversible fragmentation to the
5′-deoxyadenosyl radical. While the radical intermediate is
not directly observed, its presence as an initial intermediate is
inferred by the formation of 8,5′-cycloadenosine and by H atom
incorporation into 5′-deoxyadenosine from solvent exchangeable
site. Similarly, 2-aminobutyrate is also observed under electrolysis
conditions. The implications of these results in the context of the
reductive cleavage of SAM by radical SAM enzymes are discussed.
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Affiliation(s)
- Sven A Miller
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Vahe Bandarian
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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22
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Barton JK, Silva RMB, O'Brien E. Redox Chemistry in the Genome: Emergence of the [4Fe4S] Cofactor in Repair and Replication. Annu Rev Biochem 2019; 88:163-190. [PMID: 31220976 PMCID: PMC6590699 DOI: 10.1146/annurev-biochem-013118-110644] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many DNA-processing enzymes have been shown to contain a [4Fe4S] cluster, a common redox cofactor in biology. Using DNA electrochemistry, we find that binding of the DNA polyanion promotes a negative shift in [4Fe4S] cluster potential, which corresponds thermodynamically to a ∼500-fold increase in DNA-binding affinity for the oxidized [4Fe4S]3+ cluster versus the reduced [4Fe4S]2+ cluster. This redox switch can be activated from a distance using DNA charge transport (DNA CT) chemistry. DNA-processing proteins containing the [4Fe4S] cluster are enumerated, with possible roles for the redox switch highlighted. A model is described where repair proteins may signal one another using DNA-mediated charge transport as a first step in their search for lesions. The redox switch in eukaryotic DNA primases appears to regulate polymerase handoff, and in DNA polymerase δ, the redox switch provides a means to modulate replication in response to oxidative stress. We thus describe redox signaling interactions of DNA-processing [4Fe4S] enzymes, as well as the most interesting potential players to consider in delineating new DNA-mediated redox signaling networks.
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Affiliation(s)
- Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Rebekah M B Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Elizabeth O'Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
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23
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Bridwell-Rabb J, Grell TAJ, Drennan CL. A Rich Man, Poor Man Story of S-Adenosylmethionine and Cobalamin Revisited. Annu Rev Biochem 2019; 87:555-584. [PMID: 29925255 DOI: 10.1146/annurev-biochem-062917-012500] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
S-adenosylmethionine (AdoMet) has been referred to as both "a poor man's adenosylcobalamin (AdoCbl)" and "a rich man's AdoCbl," but today, with the ever-increasing number of functions attributed to each cofactor, both appear equally rich and surprising. The recent characterization of an organometallic species in an AdoMet radical enzyme suggests that the line that differentiates them in nature will be constantly challenged. Here, we compare and contrast AdoMet and cobalamin (Cbl) and consider why Cbl-dependent AdoMet radical enzymes require two cofactors that are so similar in their reactivity. We further carry out structural comparisons employing the recently determined crystal structure of oxetanocin-A biosynthetic enzyme OxsB, the first three-dimensional structural data on a Cbl-dependent AdoMet radical enzyme. We find that the structural motifs responsible for housing the AdoMet radical machinery are largely conserved, whereas the motifs responsible for binding additional cofactors are much more varied.
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Affiliation(s)
- Jennifer Bridwell-Rabb
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Present address: Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Tsehai A J Grell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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24
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Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol 2018; 606:1-71. [PMID: 30097089 DOI: 10.1016/bs.mie.2018.06.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States.
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Elaine C Meng
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, United States
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Sara Calhoun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Graduate Program in Biophysics, University of California, San Francisco, CA, United States
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
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25
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Grell TJ, Young AP, Drennan CL, Bandarian V. Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1. J Am Chem Soc 2018; 140:6842-6852. [PMID: 29792696 PMCID: PMC5994729 DOI: 10.1021/jacs.8b01493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 12/03/2022]
Abstract
TYW1 is a radical S-adenosyl-l-methionine (SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine to form the posttranscriptional modification, 4-demethylwyosine, in situ on transfer RNA (tRNA). Two mechanisms have been proposed for this transformation, with one of the possible mechanisms invoking a Schiff base intermediate formed between a conserved lysine residue and pyruvate. Utilizing a combination of mass spectrometry and X-ray crystallography, we have obtained evidence to support the formation of a Schiff base lysine adduct in TYW1. When 13C labeled pyruvate is used, the mass shift of the adduct matches that of the labeled pyruvate, indicating that pyruvate is the source of the adduct. Furthermore, a crystal structure of TYW1 provides visualization of the Schiff base lysine-pyruvate adduct, which is positioned directly adjacent to the auxiliary [4Fe-4S] cluster. The adduct coordinates the unique iron of the auxiliary cluster through the lysine nitrogen and a carboxylate oxygen, reminiscent of how the radical SAM [4Fe-4S] cluster is coordinated by SAM. The structure provides insight into the binding site for tRNA and further suggests how radical SAM chemistry can be combined with Schiff base chemistry for RNA modification.
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Affiliation(s)
- Tsehai
A. J. Grell
- Department
of Chemistry, Department of Biology, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony P. Young
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Department of Biology, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vahe Bandarian
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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26
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Parent A, Benjdia A, Guillot A, Kubiak X, Balty C, Lefranc B, Leprince J, Berteau O. Mechanistic Investigations of PoyD, a Radical S-Adenosyl-l-methionine Enzyme Catalyzing Iterative and Directional Epimerizations in Polytheonamide A Biosynthesis. J Am Chem Soc 2018; 140:2469-2477. [PMID: 29253341 PMCID: PMC5824343 DOI: 10.1021/jacs.7b08402] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of bioactive peptides. Among RiPPs, the bacterial toxin polytheonamide A is characterized by a unique set of post-translational modifications catalyzed by novel radical S-adenosyl-l-methionine (SAM) enzymes. Here we show that the radical SAM enzyme PoyD catalyzes in vitro polytheonamide epimerization in a C-to-N directional manner. By combining mutagenesis experiments with labeling studies and investigating the enzyme substrate promiscuity, we deciphered in detail the mechanism of PoyD. We notably identified a critical cysteine residue as a likely key H atom donor and demonstrated that PoyD belongs to a distinct family of radical SAM peptidyl epimerases. In addition, our study shows that the core peptide directly influences the epimerization pattern allowing for production of peptides with unnatural epimerization patterns.
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Affiliation(s)
- Aubérie Parent
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Xavier Kubiak
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Benjamin Lefranc
- Inserm U1239, PRIMACEN, University of Rouen Normandy , 76000 Rouen, France
| | - Jérôme Leprince
- Inserm U1239, PRIMACEN, University of Rouen Normandy , 76000 Rouen, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
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27
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Wilcoxen J, Bruender NA, Bandarian V, Britt RD. A Radical Intermediate in Bacillus subtilis QueE during Turnover with the Substrate Analogue 6-Carboxypterin. J Am Chem Soc 2018; 140:1753-1759. [PMID: 29303575 DOI: 10.1021/jacs.7b10860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
7-Carboxy-7-deazaguanine (CDG) synthase (QueE), a member of the radical S-deoxyadenosyl-l-methionine (SAM) superfamily of enzymes, catalyzes a radical-mediated ring rearrangement required to convert 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) into CDG, forming the 7-dezapurine precursor to all pyrrolopyrimidine metabolites. Members of the radical SAM superfamily bind SAM to a [4Fe-4S] cluster, leveraging the reductive cleavage of SAM by the cluster to produce a highly reactive 5'-deoxyadenosyl radical which initiates chemistry by H atom abstraction from the substrate. QueE has recently been shown to use 6-carboxypterin (6-CP) as an alternative substrate, forming 6-deoxyadenosylpterin as the product. This reaction has been proposed to occur by radical addition between 5'-dAdo· and 6-CP, which upon oxidative decarboxylation yields the modified pterin. Here, we present spectroscopic evidence for a 6-CP-dAdo radical. The structure of this intermediate is determined by characterizing its electronic structure by continuous wave and pulse electron paramagnetic resonance spectroscopy.
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Affiliation(s)
- Jarett Wilcoxen
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Nathan A Bruender
- Department of Chemistry and Biochemistry, St. Cloud State University , St. Cloud, Minnesota 56301, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
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28
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Saha A, Kizaki S, Han JH, Yu Z, Sugiyama H. UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258. Bioorg Med Chem 2018; 26:37-40. [PMID: 29170027 DOI: 10.1016/j.bmc.2017.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/15/2023]
Abstract
Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to BrU caused DNA cleavage preferentially at self-complementary 5'-AABrUBrU-3' sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA.
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Affiliation(s)
- Abhijit Saha
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Seiichiro Kizaki
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Ji Hoon Han
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Zutao Yu
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo, Kyoto 606-8502, Japan.
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29
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Benjdia A, Balty C, Berteau O. Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Front Chem 2017; 5:87. [PMID: 29167789 PMCID: PMC5682303 DOI: 10.3389/fchem.2017.00087] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/11/2017] [Indexed: 11/13/2022] Open
Abstract
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.
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Affiliation(s)
- Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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30
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Zhang J, Yan S, Liu X, Gan L, Wu Z, Gong Y, Huang M, Zhang X, Guo W. Gender-related prognostic value and genomic pattern of intra-tumor heterogeneity in colorectal cancer. Carcinogenesis 2017; 38:837-846. [PMID: 28531253 PMCID: PMC5862243 DOI: 10.1093/carcin/bgx046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 05/12/2017] [Indexed: 01/21/2023] Open
Abstract
Intra-tumor heterogeneity (ITH) is crucial in tumorigenesis and resistance to target therapy. Here, we used mutant-allele tumor heterogeneity (MATH) to measure ITH based on next-generation sequencing data and high MATH was proven as an independent risk prognostic factor in male CRC patients in both a training set of 284 colorectal cancer (CRC) patients with from The Cancer Genome Atlas (TCGA) and a validating set of 187 CRC patients from International Cancer Genome Consortium (ICGC). Further, the genomic pattern according to MATH demonstrated that mutation rates of TP53, IRF5 and KRAS were independently associated with MATH, and the latter two were only significant in male patients. As MATH increased, the fraction of somatic copy number alteration (SCNA) elevated. Moreover, more SCNA events was independently associated with MATH in male than in female. WNT pathway, TGF-β pathway and DNA repair deficiency was enriched in high MATH group and the latter two showed up only in male patients. In summary, we reveal the gender-related prognostic value of MATH and relevant genomic pattern in CRC. Potential mechanisms are provided and it remains to be proven whether they are drivers of subclone formation and ITH. Taking MATH into consideration in clinical trial might contribute to better therapeutic strategies in CRC with researches added on in the future.
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Affiliation(s)
- Jieyun Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology
| | - Shican Yan
- Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, 12 Urumqi Road (M), Shanghai 200040, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Xiyu Liu
- Department of Oncology.,Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Lu Gan
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology
| | - Zhenhua Wu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology
| | - Yiwei Gong
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology
| | - Mingzhu Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology
| | - Xiaowei Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology
| | - Weijian Guo
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology
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31
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Yang L, Li L. Insights into the Activity Change of Spore Photoproduct Lyase Induced by Mutations at a Peripheral Glycine Residue. Front Chem 2017; 5:14. [PMID: 28401144 PMCID: PMC5368176 DOI: 10.3389/fchem.2017.00014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/28/2017] [Indexed: 12/19/2022] Open
Abstract
UV radiation triggers the formation of 5-thyminyl-5,6-dihydrothymine, i.e., the spore photoproduct (SP), in the genomic DNA of bacterial endospores. These SPs, if not repaired in time, may lead to genome instability and cell death. SP is mainly repaired by spore photoproduct lyase (SPL) during spore outgrowth via an unprecedented protein-harbored radical transfer pathway that is composed of at least a cysteine and two tyrosine residues. This mechanism is consistent with the recently solved SPL structure that shows all three residues are located in proximity and thus able to participate in the radical transfer process during the enzyme catalysis. In contrast, an earlier in vivo mutational study identified a glycine to arginine mutation at the position 168 on the B. subtilis SPL that is >15 Å away from the enzyme active site. This mutation appears to abolish the enzyme activity because endospores carrying this mutant were sensitive to UV light. To understand the molecular basis for this rendered enzyme activity, we constructed two SPL mutations G168A and G168R, examined their repair of dinucleotide SP TpT, and found that both mutants exhibit reduced enzyme activity. Comparing with the wildtype (WT) SPL enzyme, the G168A mutant slows down the SP TpT repair by 3~4-fold while the G168R mutant by ~ 80-fold. Both mutants exhibit a smaller apparent (DV) kinetic isotope effect (KIE) but a bigger competitive (DV/K) KIE than that by the WT SPL. Moreover, the G168R mutant also produces a large portion of the abortive repair product TpT-[Formula: see text]; the formation of which indicates that cysteine 141 is no longer well positioned as the H-donor to the thymine allylic radical intermediate. All these data imply that the mutation at the remote glycine 168 residue alters the enzyme 3D structure, subsequently reducing the SPL activity by changing the positions of the essential amino acids involved in the radical transfer process.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University IndianapolisIndianapolis, IN, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University IndianapolisIndianapolis, IN, USA
- Department of Dermatology, Indiana University School of MedicineIndianapolis, IN, USA
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32
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Yang L, Jian Y, Setlow P, Li L. Spore photoproduct within DNA is a surprisingly poor substrate for its designated repair enzyme-The spore photoproduct lyase. DNA Repair (Amst) 2017; 53:31-42. [PMID: 28320593 DOI: 10.1016/j.dnarep.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/23/2016] [Accepted: 11/15/2016] [Indexed: 12/15/2022]
Abstract
DNA repair enzymes typically recognize their substrate lesions with high affinity to ensure efficient lesion repair. In UV irradiated endospores, a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, termed the spore photoproduct (SP), is the dominant DNA photolesion, which is rapidly repaired during spore outgrowth mainly by spore photoproduct lyase (SPL) using an unprecedented protein-harbored radical transfer process. Surprisingly, our in vitro studies using SP-containing short oligonucleotides, pUC 18 plasmid DNA, and E. coli genomic DNA found that they are all poor substrates for SPL in general, exhibiting turnover numbers of 0.01-0.2min-1. The faster turnover numbers are reached under single turnover conditions, and SPL activity is low with oligonucleotide substrates at higher concentrations. Moreover, SP-containing oligonucleotides do not go past one turnover. In contrast, the dinucleotide SP TpT exhibits a turnover number of 0.3-0.4min-1, and the reaction may reach up to 10 turnovers. These observations distinguish SPL from other specialized DNA repair enzymes. To the best of our knowledge, SPL represents an unprecedented example of a major DNA repair enzyme that cannot effectively repair its substrate lesion within the normal DNA conformation adopted in growing cells. Factors such as other DNA binding proteins, helicases or an altered DNA conformation may cooperate with SPL to enable efficient SP repair in germinating spores. Therefore, both SP formation and SP repair are likely to be tightly controlled by the unique cellular environment in dormant and outgrowing spore-forming bacteria, and thus SP repair may be extremely slow in non-spore-forming organisms.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, United States
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States; Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
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33
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Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis. Nat Chem 2017. [PMID: 28644475 DOI: 10.1038/nchem.2714] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor. Unexpectedly, these D-amino acid residues proved to be essential for the activity of a peptide that induces the expression of LiaRS, a major component of the bacterial cell envelope stress-response system. Present in B. subtilis and in several members of the human microbiome, these epipeptides and radical SAM epimerases broaden the landscape of peptidyl structures accessible to living organisms.
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34
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Berteau O, Benjdia A. DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From Biochemistry to Structural Investigations. Photochem Photobiol 2017; 93:67-77. [DOI: 10.1111/php.12702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Olivier Berteau
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Alhosna Benjdia
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
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35
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Yang L, Adhikari J, Gross ML, Li L. Kinetic Isotope Effects and Hydrogen/Deuterium Exchange Reveal Large Conformational Changes During the Catalysis of the Clostridium acetobutylicum Spore Photoproduct Lyase. Photochem Photobiol 2017; 93:331-342. [PMID: 27992649 PMCID: PMC5315627 DOI: 10.1111/php.12697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/29/2016] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6-dihydrothymine (i.e. the spore photoproduct (SP)) to two thymine residues in germinating endospores. Previous studies suggest that SPL from the bacterium Bacillus subtilis (Bs) harbors an unprecedented radical-transfer pathway starting with cysteine 141 proceeding through tyrosine 99. However, in SPL from the bacterium Clostridium acetobutylicum (Ca), the cysteine (at position 74) and the tyrosine are located on the opposite sides of a substrate-binding pocket that has to collapse to bring the two residues into proximity, enabling the C→Y radical passage as implied in SPL(Bs) . To test this hypothesis, we adopted hydrogen/deuterium exchange mass spectrometry (HDX-MS) to show that C74(Ca) is located at a highly flexible region. The repair of dinucleotide SP TpT by SPL(Ca) is eight-fold to 10-fold slower than that by SPL(Bs) ; the process also generates a large portion of the aborted product TpTSO2- . SPL(Ca) exhibits apparent (D V) kinetic isotope effects (KIEs) of ~6 and abnormally large competitive (D V/K) KIEs (~20), both of which are much larger than the KIEs observed for SPL(Bs) . All these observations indicate that SPL(Ca) possesses a flexible active site and readily undergoes conformational changes during catalysis.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Jagat Adhikari
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
- Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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36
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Heidinger L, Kneuttinger AC, Kashiwazaki G, Weber S, Carell T, Schleicher E. Direct observation of a deoxyadenosyl radical in an active enzyme environment. FEBS Lett 2016; 590:4489-4494. [PMID: 27878994 DOI: 10.1002/1873-3468.12498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/11/2022]
Abstract
5'-deoxyadenosyl radicals have been proposed as the first common intermediate in the molecular reaction mechanism of the family of radical S-adenosyl-l-methionine (SAM) enzymes. However, this radical species has not yet been directly observed in a catalytically active enzyme environment. In a reduced and SAM-containing C140A mutant of the spore photoproduct lyase from Geobacillus thermodenitrificans, a mutant with altered catalytic activity, we were able to identify an organic radical with pronounced hyperfine structure using electron paramagnetic resonance spectroscopy. Guided by quantum-chemical computations at the density functional theory level of theory, this radical could be tentatively assigned to a deoxyadenosyl radical, which provides first experimental evidence for this intermediate in the reaction mechanism of radical SAM enzymes.
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Affiliation(s)
- Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Andrea C Kneuttinger
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
| | - Gengo Kashiwazaki
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Thomas Carell
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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37
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Sulfatases and radical SAM enzymes: emerging themes in glycosaminoglycan metabolism and the human microbiota. Biochem Soc Trans 2016; 44:109-15. [PMID: 26862195 DOI: 10.1042/bst20150191] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Humans live in a permanent association with bacterial populations collectively called the microbiota. In the last 10 years, major advances in our knowledge of the microbiota have shed light on its critical roles in human physiology. The microbiota has also been shown to be a major factor in numerous pathologies including obesity or inflammatory disorders. Despite tremendous progresses, our understanding of the key functions of the human microbiota and the molecular basis of its interactions with the host remain still poorly understood. Among the factors involved in host colonization, two enzymes families, sulfatases and radical S-adenosyl-L-methionine enzymes, have recently emerged as key enzymes.
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38
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Hayes EC, Jian Y, Li L, Stoll S. EPR Study of UV-Irradiated Thymidine Microcrystals Supports Radical Intermediates in Spore Photoproduct Formation. J Phys Chem B 2016; 120:10923-10931. [DOI: 10.1021/acs.jpcb.6b06587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ellen C. Hayes
- Department
of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195, United States
| | - Yajun Jian
- Department
of Chemistry and Chemical Biology, 402 N. Blackford Street, LD 326, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Lei Li
- Department
of Chemistry and Chemical Biology, 402 N. Blackford Street, LD 326, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Stefan Stoll
- Department
of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195, United States
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39
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Setlow P, Li L. Photochemistry and Photobiology of the Spore Photoproduct: A 50-Year Journey. Photochem Photobiol 2015; 91:1263-90. [PMID: 26265564 PMCID: PMC4631623 DOI: 10.1111/php.12506] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/21/2015] [Indexed: 02/06/2023]
Abstract
Fifty years ago, a new thymine dimer was discovered as the dominant DNA photolesion in UV-irradiated bacterial spores [Donnellan, J. E. & Setlow R. B. (1965) Science, 149, 308-310], which was later named the spore photoproduct (SP). Formation of SP is due to the unique environment in the spore core that features low hydration levels favoring an A-DNA conformation, high levels of calcium dipicolinate that acts as a photosensitizer, and DNA saturation with small, acid-soluble proteins that alters DNA structure and reduces side reactions. In vitro studies reveal that any of these factors alone can promote SP formation; however, SP formation is usually accompanied by the production of other DNA photolesions. Therefore, the nearly exclusive SP formation in spores is due to the combined effects of these three factors. Spore photoproduct photoreaction is proved to occur via a unique H-atom transfer mechanism between the two involved thymine residues. Successful incorporation of SP into an oligonucleotide has been achieved via organic synthesis, which enables structural studies that reveal minor conformational changes in the SP-containing DNA. Here, we review the progress on SP photochemistry and photobiology in the past 50 years, which indicates a very rich SP photobiology that may exist beyond endospores.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
- Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana 46202
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40
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Benjdia A, Pierre S, Gherasim C, Guillot A, Carmona M, Amara P, Banerjee R, Berteau O. The thiostrepton A tryptophan methyltransferase TsrM catalyses a cob(II)alamin-dependent methyl transfer reaction. Nat Commun 2015; 6:8377. [PMID: 26456915 PMCID: PMC4632189 DOI: 10.1038/ncomms9377] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 08/17/2015] [Indexed: 11/09/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a novel class of natural products including several antibiotics and bacterial toxins. In countless RiPP biosynthetic pathways, cobalamin-dependent radical SAM (B12/rSAM) enzymes play a pivotal role. In the biosynthetic pathway of the antibiotic and anti-cancer agent thiostrepton A, TsrM, a B12/rSAM enzyme, catalyses the transfer of a methyl group to an electrophilic carbon atom of tryptophan. Here we show that methylcob(III)alamin is the probable physiological enzyme cofactor, and cob(II)alamin rather than cob(I)alamin is a key reaction intermediate. Furthermore, we establish that TsrM and a triple-alanine mutant alkylate cob(II)alamin efficiently leading to the synthesis of MeCbl. Exploiting TsrM substrate ambiguity, we demonstrate that TsrM does not catalyse substrate H-atom abstraction like most radical SAM enzymes. Based on these data, we propose an unprecedented radical-based C-methylation mechanism, which further expands the chemical versatility of rSAM enzymes.
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Affiliation(s)
- Alhosna Benjdia
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Stéphane Pierre
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Carmen Gherasim
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA
| | - Alain Guillot
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Manon Carmona
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Patricia Amara
- Metalloproteins Unit, Institut de Biologie Structurale, UMR5075, CEA, CNRS, Univ. Grenoble-Alpes. 71, Avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA
| | - Olivier Berteau
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
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41
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Shibata N, Toraya T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J Biochem 2015; 158:271-92. [PMID: 26261050 DOI: 10.1093/jb/mvv078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023] Open
Abstract
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named 'radical enzymes'. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan and
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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Benjdia A, Heil K, Winkler A, Carell T, Schlichting I. Rescuing DNA repair activity by rewiring the H-atom transfer pathway in the radical SAM enzyme, spore photoproduct lyase. Chem Commun (Camb) 2015; 50:14201-4. [PMID: 25285338 DOI: 10.1039/c4cc05158k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radical SAM enzyme, spore photoproduct lyase, requires an H-atom transfer (HAT) pathway to catalyze DNA repair. By rational engineering, we demonstrate that it is possible to rewire its HAT pathway, a first step toward the development of novel catalysts based on the radical SAM enzyme scaffold.
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Affiliation(s)
- Alhosna Benjdia
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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43
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Horitani M, Byer AS, Shisler KA, Chandra T, Broderick JB, Hoffman BM. Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5'-dAdo• "Free Radical" Is Never Free. J Am Chem Soc 2015; 137:7111-21. [PMID: 25923449 PMCID: PMC4612528 DOI: 10.1021/jacs.5b00498] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysine 2,3-aminomutase (LAM) is a radical S-adenosyl-L-methionine (SAM) enzyme and, like other members of this superfamily, LAM utilizes radical-generating machinery comprising SAM anchored to the unique Fe of a [4Fe-4S] cluster via a classical five-membered N,O chelate ring. Catalysis is initiated by reductive cleavage of the SAM S-C5' bond, which creates the highly reactive 5'-deoxyadenosyl radical (5'-dAdo•), the same radical generated by homolytic Co-C bond cleavage in B12 radical enzymes. The SAM surrogate S-3',4'-anhydroadenosyl-L-methionine (anSAM) can replace SAM as a cofactor in the isomerization of L-α-lysine to L-β-lysine by LAM, via the stable allylic anhydroadenosyl radical (anAdo•). Here electron nuclear double resonance (ENDOR) spectroscopy of the anAdo• radical in the presence of (13)C, (2)H, and (15)N-labeled lysine completes the picture of how the active site of LAM from Clostridium subterminale SB4 "tames" the 5'-dAdo• radical, preventing it from carrying out harmful side reactions: this "free radical" in LAM is never free. The low steric demands of the radical-generating [4Fe-4S]/SAM construct allow the substrate target to bind adjacent to the S-C5' bond, thereby enabling the 5'-dAdo• radical created by cleavage of this bond to react with its partners by undergoing small motions, ∼0.6 Å toward the target and ∼1.5 Å overall, that are controlled by tight van der Waals contact with its partners. We suggest that the accessibility to substrate and ready control of the reactive C5' radical, with "van der Waals control" of small motions throughout the catalytic cycle, is common within the radical SAM enzyme superfamily and is a major reason why these enzymes are the preferred means of initiating radical reactions in nature.
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Affiliation(s)
- Masaki Horitani
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amanda S. Byer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Krista A. Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Tilak Chandra
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Department of Chemistry and 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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44
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Benjdia A, Heil K, Winkler A, Carell T, Schlichting I. Structural Perspectives on the Mechanism of the Radical SAM Enzyme, Spore Photoproduct Lyase. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.895.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alhosna Benjdia
- MICALIS ChemSyBio INRAJouy‐en‐JosasFrance
- Biomolecular Mechanisms Max‐Planck Institute for Medical Research HeidelbergGermany
| | - Korbinian Heil
- Center for Integrated Protein Science Ludwig‐Maximilians‐Universitat Munchen MunchenGermany
| | - Andreas Winkler
- Biomolecular Mechanisms Max‐Planck Institute for Medical Research HeidelbergGermany
| | - Thomas Carell
- Center for Integrated Protein Science Ludwig‐Maximilians‐Universitat Munchen MunchenGermany
| | - Ilme Schlichting
- Biomolecular Mechanisms Max‐Planck Institute for Medical Research HeidelbergGermany
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45
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Karentz D. Beyond xeroderma pigmentosum: DNA damage and repair in an ecological context. A tribute to James E. Cleaver. Photochem Photobiol 2014; 91:460-74. [PMID: 25395165 DOI: 10.1111/php.12388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/29/2014] [Indexed: 12/12/2022]
Abstract
The ability to repair DNA is a ubiquitous characteristic of life on Earth and all organisms possess similar mechanisms for dealing with DNA damage, an indication of a very early evolutionary origin for repair processes. James E. Cleaver's career (initiated in the early 1960s) has been devoted to the study of mammalian ultraviolet radiation (UVR) photobiology, specifically the molecular genetics of xeroderma pigmentosum and other human diseases caused by defects in DNA damage recognition and repair. This work by Jim and others has influenced the study of DNA damage and repair in a variety of taxa. Today, the field of DNA repair is enhancing our understanding of not only how to treat and prevent human disease, but is providing insights on the evolutionary history of life on Earth and how natural populations are coping with UVR-induced DNA damage from anthropogenic changes in the environment such as ozone depletion.
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Affiliation(s)
- Deneb Karentz
- Department of Biology, University of San Francisco, San Francisco, CA
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Abstract
Spore photoproduct lyase (SPL) repairs 5-thyminyl-5,6-dihydrothymine, a thymine dimer that is also called the spore photoproduct (SP), in germinating endospores. SPL is a radical S-adenosylmethionine (SAM) enzyme, utilizing the 5'-deoxyadenosyl radical generated by SAM reductive cleavage reaction to revert SP to two thymine residues. Here we review the current progress in SPL mechanistic studies. Protein radicals are known to be involved in SPL catalysis; however, how these radicals are quenched to close the catalytic cycle is under debate.
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Affiliation(s)
- Linlin Yang
- From the Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202 and
| | - Lei Li
- From the Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202 and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), Indianapolis, Indiana 46202
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47
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Wang J, Woldring RP, Román-Meléndez GD, McClain AM, Alzua BR, Marsh ENG. Recent advances in radical SAM enzymology: new structures and mechanisms. ACS Chem Biol 2014; 9:1929-38. [PMID: 25009947 PMCID: PMC4168785 DOI: 10.1021/cb5004674] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The radical S-adenosylmethionine
(SAM) superfamily of enzymes catalyzes
an amazingly diverse variety of reactions ranging from simple hydrogen
abstraction to complicated multistep rearrangements and insertions.
The reactions they catalyze are important for a broad range of biological
functions, including cofactor and natural product biosynthesis, DNA
repair, and tRNA modification. Generally conserved features of the
radical SAM superfamily include a CX3CX2C motif
that binds an [Fe4S4] cluster essential for
the reductive cleavage of SAM. Here, we review recent advances in
our understanding of the structure and mechanisms of these enzymes
that, in some cases, have overturned widely accepted mechanisms.
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Affiliation(s)
- Jiarui Wang
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rory P. Woldring
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alan M. McClain
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brian R. Alzua
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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48
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Ghose S, Hilmer JK, Bothner B, Broderick JB. Solution phase dynamics of the DNA repair enzyme spore photoproduct lyase as probed by H/D exchange. FEBS Lett 2014; 588:3023-9. [PMID: 24950428 DOI: 10.1016/j.febslet.2014.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 11/16/2022]
Abstract
Spore photoproduct lyase (SPL) catalyzes the repair of the UV lesion spore photoproduct (SP) in a reaction dependent on S-adenosyl-L-methionine (SAM). We have utilized H/D exchange to show that in the presence of SAM, a significant reduction in H/D exchange is observed upon binding SPTpT or undamaged oligonucleotide, indicating a shift of 20 or 10 amide protons, respectively, from a rapidly-exchangable state to a fully-protected conformation. In the absence of SAM, neither the oligonucleotide nor the SPTpT produce a significant perturbation in H/D exchange, indicating SAM is a requisite binding partner. Performing the same experiments in aerobic conditions reduced the magnitude of ligand-induced structural changes, consistent with the importance of the oxygen-sensitive iron-sulfur cluster for SAM and substrate binding.
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Affiliation(s)
- Shourjo Ghose
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jonathan K Hilmer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States.
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49
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Ames DM, Lin G, Jian Y, Cadet J, Li L. Unusually large deuterium discrimination during spore photoproduct formation. J Org Chem 2014; 79:4843-51. [PMID: 24820206 PMCID: PMC4049236 DOI: 10.1021/jo500775b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The deuterium-labeling strategy has been widely used and proved highly effective in mechanistic investigation of chemical and biochemical reactions. However, it is often hampered by the incomplete label transfer, which subsequently obscures the mechanistic conclusion. During the study of photoinduced generation of 5-thyminyl-5,6-dihydrothymine, which is commonly called the spore photoproduct (SP), the Cadet laboratory found an incomplete (~67%) deuterium transfer in SP formation, which contrasts to the exclusive transfer observed by the Li laboratory. Here, we investigated this discrepancy by re-examining the SP formation using d3-thymidine. We spiked the d3-thymidine with varying amounts of unlabeled thymidine before the SP photochemistry is performed. Strikingly, our data show that the reaction is highly sensitive to the trace protiated thymidine in the starting material. As many as 17-fold enrichment is detected in the formed SP, which may explain the previously observed one-third protium incorporation. Although commercially available deuterated reagents are generally satisfactory as mechanistic probes, our results argue that attention is still needed to the possible interference from the trace protiated impurity, especially when the reaction yield is low and large isotopic discrimination is involved.
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Affiliation(s)
- David M Ames
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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50
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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