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Nerber HN, Sorg JA. The small acid-soluble proteins of spore-forming organisms: Similarities and differences in function. Anaerobe 2024; 87:102844. [PMID: 38582142 DOI: 10.1016/j.anaerobe.2024.102844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
The small acid-soluble proteins are found in all endospore-forming organisms and are a major component of spores. Through their DNA binding capabilities, the SASPs shield the DNA from outside insults (e.g., UV and genotoxic chemicals). The absence of the major SASPs results in spores with reduced viability when exposed to UV light and, in at least one case, the inability to complete sporulation. While the SASPs have been characterized for decades, some evidence suggests that using newer technologies to revisit the roles of the SASPs could reveal novel functions in spore regulation.
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Affiliation(s)
- Hailee N Nerber
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station, TX, United States.
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2
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Setlow P, Christie G. New Thoughts on an Old Topic: Secrets of Bacterial Spore Resistance Slowly Being Revealed. Microbiol Mol Biol Rev 2023; 87:e0008022. [PMID: 36927044 PMCID: PMC10304885 DOI: 10.1128/mmbr.00080-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
The quest for bacterial survival is exemplified by spores formed by some Firmicutes members. They turn up everywhere one looks, and their ubiquity reflects adaptations to the stresses bacteria face. Spores are impactful in public health, food safety, and biowarfare. Heat resistance is the hallmark of spores and is countered principally by a mineralized gel-like protoplast, termed the spore core, with reduced water which minimizes macromolecular movement/denaturation/aggregation. Dry heat, however, introduces mutations into spore DNA. Spores have countermeasures to extreme conditions that are multifactorial, but the fact that spore DNA is in a crystalline-like nucleoid in the spore core, likely due to DNA saturation with small acid-soluble spore proteins (SASPs), suggests that reduced macromolecular motion is also critical in spore dry heat resistance. SASPs are also central in the radiation resistance characteristic of spores, where the contributions of four spore features-SASP; Ca2+, with pyridine-2,6-dicarboxylic acid (CaDPA); photoproduct lyase; and low water content-minimize DNA damage. Notably, the spore environment steers UV photochemistry toward a product that germinated spores can repair without significant mutagenesis. This resistance extends to chemicals and macromolecules that could damage spores. Macromolecules are excluded by the spore coat which impedes the passage of moieties of ≥10 kDa. Additionally, damaging chemicals may be degraded or neutralized by coat enzymes/proteins. However, the principal protective mechanism here is the inner membrane, a compressed structure lacking lipid fluidity and presenting a barrier to the diffusion of chemicals into the spore core; SASP saturation of DNA also protects against genotoxic chemicals. Spores are also resistant to other stresses, including high pressure and abrasion. Regardless, overarching mechanisms associated with resistance seem to revolve around reduced molecular motion, a fine balance between rigidity and flexibility, and perhaps efficient repair.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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3
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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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4
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Nyangaresi PO, Rathnayake T, Beck SE. Evaluation of disinfection efficacy of single UV-C, and UV-A followed by UV-C LED irradiation on Escherichia coli, B. spizizenii and MS2 bacteriophage, in water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160256. [PMID: 36402311 DOI: 10.1016/j.scitotenv.2022.160256] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/26/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Ultraviolet light-emitting diodes (UV LEDs) have shown ability to inactivate microorganisms and viruses in water. The unique characteristic of the UV-LEDs' diversity in wavelengths ranging from UV-C, UV-B, and UV-A, allows for wavelengths to be combined in different manners for polychromatic irradiation. Previous studies reported no synergy from simultaneous or sequential UV-C and UV-B as well as UV-C or UV-B followed by UV-A irradiation. However, synergy was reported for UV-A followed by UV-C or UV-B irradiation on various microorganisms. Nevertheless, no clear ground has been reached on whether to adopt single UV-C wavelengths or UV-A followed by UV-C LED, irradiation on inactivation of microorganisms and viruses in water. Therefore, this work evaluates the disinfection efficacy of single UV-C as well as UV-A followed by UV-C LED irradiation on Escherichia coli, Bacillus spizizenii spores and MS2 bacteriophage in water. The UV-C wavelengths were represented by 267 and 278 nm UV LEDs, and UV-A by 368 nm UV LEDs. In this study, E. coli was highly susceptible to UV radiation followed by B. spizizenii spores, and lastly MS2. Repair following UV inactivation was only observed in E. coli. The synergistic effect found in both E. coli, and B. spizizenii spores was attributed to the different inactivation mechanisms of the UV-C and UV-A wavelengths. In both single UV-C, and UV-A followed by UV-C LED irradiations, single 267 nm UV-C LED showed higher inactivation efficacy. Meanwhile, single 278 nm UV-C LED showed higher efficacy in terms of suppression of repair, and electrical energy consumption. Using single UV-C LEDs in a water disinfection system cuts down on related extra costs by avoiding combined wavelengths while still attaining better levels of microorganism inactivation, repair suppression and electrical energy consumption. These findings are applicable for the design and implementation of UV LED water disinfection systems.
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Affiliation(s)
- Paul Onkundi Nyangaresi
- Department of Civil Engineering, University of British Columbia, 2002-6250 Applied Science Lane, Vancouver, British Columbia V6T 1Z4, Canada.
| | - Thusitha Rathnayake
- Department of Civil Engineering, University of British Columbia, 2002-6250 Applied Science Lane, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sara E Beck
- Department of Civil Engineering, University of British Columbia, 2002-6250 Applied Science Lane, Vancouver, British Columbia V6T 1Z4, Canada
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5
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Broderick JB, Broderick WE, Hoffman BM. Radical SAM enzymes: Nature's choice for radical reactions. FEBS Lett 2023; 597:92-101. [PMID: 36251330 PMCID: PMC9894703 DOI: 10.1002/1873-3468.14519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 02/04/2023]
Abstract
Enzymes that use a [4Fe-4S]1+ cluster plus S-adenosyl-l-methionine (SAM) to initiate radical reactions (radical SAM) form the largest enzyme superfamily, with over half a million members across the tree of life. This review summarizes recent work revealing the radical SAM reaction pathway, which ultimately liberates the 5'-deoxyadenosyl (5'-dAdo•) radical to perform extremely diverse, highly regio- and stereo-specific, transformations. Most surprising was the discovery of an organometallic intermediate Ω exhibiting an Fe-C5'-adenosyl bond. Ω liberates 5'-dAdo• through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12 , previously viewed as biology's paradigmatic radical generator. The 5'-dAdo• has been trapped and characterized in radical SAM enzymes via a recently discovered photoreactivity of the [4Fe-4S]+ /SAM complex, and has been confirmed as a catalytically active intermediate in enzyme catalysis. The regioselective SAM S-C bond cleavage to produce 5'-dAdo• originates in the Jahn-Teller effect. The simplicity of SAM as a radical precursor, and the exquisite control of 5'-dAdo• reactivity in radical SAM enzymes, may be why radical SAM enzymes pervade the tree of life, while B12 enzymes are only a few.
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Affiliation(s)
- Joan B. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - William E. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - Brian M. Hoffman
- Department of Chemistry, 2145 Sheridan Rd, Northwestern University, Evanston, IL. 60208
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Hendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran K. Clean room microbiome complexity impacts planetary protection bioburden. MICROBIOME 2021; 9:238. [PMID: 34861887 PMCID: PMC8643001 DOI: 10.1186/s40168-021-01159-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/13/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Spacecraft Assembly Facility (SAF) at the NASA's Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom. RESULTS Cleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate was Bacillus subtilis, and the most temporally abundant spore-former was Virgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter. CONCLUSION This study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of spacecraft-associated environments since it failed to detect several PP-relevant genera that were only recovered via molecular methods. This highlights the importance of a methodological paradigm shift to appropriately monitor bioburden in cleanrooms for not only the aeronautical industry but also for pharmaceutical, medical industries, etc., and the need to employ molecular sequencing to complement traditional culture-based assays. Video abstract.
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Affiliation(s)
- Ryan Hendrickson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Camilla Urbaniak
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Heidi S Aronson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Cameron Martino
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
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7
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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: 5] [Impact Index Per Article: 1.7] [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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8
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Nerber HN, Sorg JA. The small acid-soluble proteins of Clostridioides difficile are important for UV resistance and serve as a check point for sporulation. PLoS Pathog 2021; 17:e1009516. [PMID: 34496003 PMCID: PMC8452069 DOI: 10.1371/journal.ppat.1009516] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/20/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile is a nosocomial pathogen which causes severe diarrhea and colonic inflammation. C. difficile causes disease in susceptible patients when endospores germinate into the toxin-producing vegetative form. The action of these toxins results in diarrhea and the spread of spores into the hospital and healthcare environments. Thus, the destruction of spores is imperative to prevent disease transmission between patients. However, spores are resilient and survive extreme temperatures, chemical exposure, and UV treatment. This makes their elimination from the environment difficult and perpetuates their spread between patients. In the model spore-forming organism, Bacillus subtilis, the small acid-soluble proteins (SASPs) contribute to these resistances. The SASPs are a family of small proteins found in all endospore-forming organisms, C. difficile included. Although these proteins have high sequence similarity between organisms, the role(s) of the proteins differ. Here, we investigated the role of the main α/β SASPs, SspA and SspB, and two annotated putative SASPs, CDR20291_1130 and CDR20291_3080, in protecting C. difficile spores from environmental insults. We found that SspA is necessary for conferring spore UV resistance, SspB minorly contributes, and the annotated putative SASPs do not contribute to UV resistance. In addition, the SASPs minorly contribute to the resistance of nitrous acid. Surprisingly, the combined deletion of sspA and sspB prevented spore formation. Overall, our data indicate that UV resistance of C. difficile spores is dependent on SspA and that SspA and SspB regulate/serve as a checkpoint for spore formation, a previously unreported function of SASPs.
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Affiliation(s)
- Hailee N. Nerber
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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9
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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: 12] [Impact Index Per Article: 4.0] [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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10
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Tu Z, Setlow P, Brul S, Kramer G. Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate. Microorganisms 2021; 9:667. [PMID: 33807113 PMCID: PMC8005191 DOI: 10.3390/microorganisms9030667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
Bacterial endospores (spores) are among the most resistant living forms on earth. Spores of Bacillus subtilis A163 show extremely high resistance to wet heat compared to spores of laboratory strains. In this study, we found that spores of B. subtilis A163 were indeed very wet heat resistant and released dipicolinic acid (DPA) very slowly during heat treatment. We also determined the proteome of vegetative cells and spores of B. subtilis A163 and the differences in these proteomes from those of the laboratory strain PY79, spores of which are much less heat resistant. This proteomic characterization identified 2011 proteins in spores and 1901 proteins in vegetative cells of B. subtilis A163. Surprisingly, spore morphogenic protein SpoVM had no homologs in B. subtilis A163. Comparing protein expression between these two strains uncovered 108 proteins that were differentially present in spores and 93 proteins differentially present in cells. In addition, five of the seven proteins on an operon in strain A163, which is thought to be primarily responsible for this strain's spores high heat resistance, were also identified. These findings reveal proteomic differences of the two strains exhibiting different resistance to heat and form a basis for further mechanistic analysis of the high heat resistance of B. subtilis A163 spores.
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Affiliation(s)
- Zhiwei Tu
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06030-3303, USA;
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
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11
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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: 6] [Impact Index Per Article: 1.5] [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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12
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Francés-Monerris A, Hognon C, Douki T, Monari A. Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics*. Chemistry 2020; 26:14236-14241. [PMID: 32597544 DOI: 10.1002/chem.202002484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 11/07/2022]
Abstract
Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid-soluble proteins that drastically modify the structure and photoreactivity of the nucleic acid. Herein, multiscale molecular dynamics simulations, including extended classical molecular dynamics and quantum mechanics/molecular mechanics based dynamics, are used to elucidate the coupling of electronic and structural factors that lead to this photochemical outcome. In particular, the well-described impact of the peculiar DNA environment found in spores on the favored formation of the spore photoproduct, given the small free energy barrier found for this path, is rationalized. Meanwhile, the specific organization of spore DNA precludes the photochemical path that leads to cyclobutane pyrimidine dimer formation.
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Affiliation(s)
- Antonio Francés-Monerris
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Departament de Química Física, Universitat de València, 46100, Burjassot, Spain
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Université de Lorraine and CNRS, CRAN UMR 7039, 54000, Nancy, France
| | - Thierry Douki
- SyMMES, CEA, CNRS, IRIG, University Grenoble Alpes, 38000, Grenoble, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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13
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14
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Radical SAM enzymes: surprises along the path to understanding mechanism. J Biol Inorg Chem 2019; 24:769-776. [DOI: 10.1007/s00775-019-01706-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022]
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15
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Cortesão M, Fuchs FM, Commichau FM, Eichenberger P, Schuerger AC, Nicholson WL, Setlow P, Moeller R. Bacillus subtilis Spore Resistance to Simulated Mars Surface Conditions. Front Microbiol 2019; 10:333. [PMID: 30863384 PMCID: PMC6399134 DOI: 10.3389/fmicb.2019.00333] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
In a Mars exploration scenario, knowing if and how highly resistant Bacillus subtilis spores would survive on the Martian surface is crucial to design planetary protection measures and avoid false positives in life-detection experiments. Therefore, in this study a systematic screening was performed to determine whether B. subtilis spores could survive an average day on Mars. For that, spores from two comprehensive sets of isogenic B. subtilis mutant strains, defective in DNA protection or repair genes, were exposed to 24 h of simulated Martian atmospheric environment with or without 8 h of Martian UV radiation [M(+)UV and M(-)UV, respectively]. When exposed to M(+)UV, spore survival was dependent on: (1) core dehydration maintenance, (2) protection of DNA by α/β-type small acid soluble proteins (SASP), and (3) removal and repair of the major UV photoproduct (SP) in spore DNA. In turn, when exposed to M(-)UV, spore survival was mainly dependent on protection by the multilayered spore coat, and DNA double-strand breaks represent the main lesion accumulated. Bacillus subtilis spores were able to survive for at least a limited time in a simulated Martian environment, both with or without solar UV radiation. Moreover, M(-)UV-treated spores exhibited survival rates significantly higher than the M(+)UV-treated spores. This suggests that on a real Martian surface, radiation shielding of spores (e.g., by dust, rocks, or spacecraft surface irregularities) might significantly extend survival rates. Mutagenesis were strongly dependent on the functionality of all structural components with small acid-soluble spore proteins, coat layers and dipicolinic acid as key protectants and efficiency DNA damage removal by AP endonucleases (ExoA and Nfo), non-homologous end joining (NHEJ), mismatch repair (MMR) and error-prone translesion synthesis (TLS). Thus, future efforts should focus on: (1) determining the DNA damage in wild-type spores exposed to M(+/-)UV and (2) assessing spore survival and viability with shielding of spores via Mars regolith and other relevant materials.
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Affiliation(s)
- Marta Cortesão
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Felix M Fuchs
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Patrick Eichenberger
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - Andrew C Schuerger
- Department of Plant Pathology, Space Life Sciences Laboratory, University of Florida, Merritt Island, FL, United States
| | - Wayne L Nicholson
- Department of Microbiology and Cell Science, Space Life Sciences Laboratory, University of Florida, Merritt Island, FL, United States
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, United States
| | - Ralf Moeller
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
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16
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Broderick WE, Hoffman BM, Broderick JB. Mechanism of Radical Initiation in the Radical S-Adenosyl-l-methionine Superfamily. Acc Chem Res 2018; 51:2611-2619. [PMID: 30346729 PMCID: PMC6324848 DOI: 10.1021/acs.accounts.8b00356] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The seeds for recognition of the vast superfamily of radical S-adenosyl-l-methionine (SAM) enzymes were sown in the 1960s, when Joachim Knappe found that the dissimilation of pyruvate was dependent on SAM and Fe(II), and Barker and co-workers made similar observations for lysine 2,3-aminomutase. These intriguing observations, coupled with the evidence that SAM and Fe were cofactors in radical catalysis by these enzyme systems, drew us in the 1990s to explore how Fe(II) and SAM initiate radical reactions. Our early work focused on the same enzyme Knappe had originally characterized: the pyruvate formate-lyase activating enzyme (PFL-AE). Our discovery of an iron-sulfur cluster in this enzyme, together with similar findings for other SAM-dependent enzymes at the time, led to the recognition of an emerging class of enzymes that use iron-sulfur clusters to cleave SAM, liberating the 5'-deoxyadenosyl radical (5'-dAdo•) that initiates radical reactions. A major bioinformatics study by Heidi Sofia and co-workers identified the enzyme superfamily denoted Radical SAM, now known to span all kingdoms of life with more than 100,000 unique sequences encoding enzymes that catalyze remarkably diverse reactions. Despite the limited sequence similarity and vastly divergent reactions catalyzed, the radical SAM enzymes appear to employ a common mechanism for initiation of radical chemistry, a mechanism we have helped to clarify over the last 25 years. A reduced [4Fe-4S]+ cluster provides the electron needed for the reductive cleavage of SAM. The resulting [4Fe-4S]2+ cluster can be rereduced either by an external reductant, with SAM acting as a cosubstrate, or by an electron provided during the reformation of SAM in cases where SAM is used as a cofactor. The amino and carboxylate groups of SAM bind to the unique iron of the catalytic [4Fe-4S] cluster, placing the sulfonium of SAM in close proximity to the cluster. Surprising recent results have shown that the initiating enzymatic cleavage of SAM generates an organometallic intermediate prior to liberation of 5'-dAdo•, which initiates radical chemistry on the substrate. This organometallic intermediate, denoted Ω, has a 5'-deoxyadenosyl moiety directly bound to the unique iron of the [4Fe-4S] cluster via the 5'-C, giving a structure that is directly analogous to the Co-(5'-C) bond of the organometallic cofactor adenosylcobalamin. Our observation that this intermediate Ω is formed throughout the superfamily suggests that this is a key intermediate in initiating radical SAM reactions, and that organometallic chemistry is much more broadly relevant in biology than previously thought.
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Affiliation(s)
- William E. 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
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States,Corresponding Author, .
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17
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Byer A, Yang H, McDaniel EC, Kathiresan V, Impano S, Pagnier A, Watts H, Denler C, Vagstad AL, Piel J, Duschene KS, Shepard EM, Shields TP, Scott LG, Lilla EA, Yokoyama K, Broderick WE, Hoffman BM, Broderick JB. Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis. J Am Chem Soc 2018; 140:8634-8638. [PMID: 29954180 PMCID: PMC6053644 DOI: 10.1021/jacs.8b04061] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an intermediate under a variety of mixing order conditions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double resonance spectroscopy establish that Ω involves an Fe-C5' bond between 5'-dAdo· and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (coenzyme B12) cofactor used to initiate radical reactions via a 5'-dAdo· intermediate. Liberation of a reactive 5'-dAdo· intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However, coenzyme B12 is involved in enzymes catalyzing only a small number (∼12) of distinct reactions, whereas the RS superfamily has more than 100 000 distinct sequences and over 80 reaction types characterized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.
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Affiliation(s)
- Amanda
S. Byer
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Hao Yang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Elizabeth C. McDaniel
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Venkatesan Kathiresan
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Stella Impano
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Adrien Pagnier
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Hope Watts
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Carly Denler
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Anna L. Vagstad
- Institute
of Microbiology, Eidgenössische Technische
Hochschule Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Jörn Piel
- Institute
of Microbiology, Eidgenössische Technische
Hochschule Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Kaitlin S. Duschene
- 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
| | - Thomas P. Shields
- Cassia,
LLC, 3030 Bunker Hill
Street, Ste. 214, San Diego, California 92109, United States
| | - Lincoln G. Scott
- Cassia,
LLC, 3030 Bunker Hill
Street, Ste. 214, San Diego, California 92109, United States
| | - Edward A. Lilla
- Department
of Biochemistry, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Kenichi Yokoyama
- Department
of Biochemistry, Duke University Medical
Center, Durham, North Carolina 27710, 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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18
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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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19
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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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20
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Douki T, von Koschembahr A, Cadet J. Insight in DNA Repair of UV-induced Pyrimidine Dimers by Chromatographic Methods. Photochem Photobiol 2017; 93:207-215. [PMID: 27935042 DOI: 10.1111/php.12685] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/21/2016] [Indexed: 01/15/2023]
Abstract
UV-induced formation of pyrimidine dimers in DNA is a major deleterious event in both eukaryotic and prokaryotic cells. Accumulation of cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts can lead to cell death or be at the origin of mutations. In skin, UV induction of DNA damage is a major initiating event in tumorigenesis. To counteract these deleterious effects, all cell types possess DNA repair machinery, such as nucleotide excision repair and, in some cell types, direct reversion. Different analytical approaches were used to assess the efficiency of repair and decipher the enzymatic mechanisms. We presently review the information provided by chromatographic methods, which are complementary to biochemical assays, such as immunological detection and electrophoresis-based techniques. Chromatographic assays are interesting in their ability to provide quantitative data on a wide range of damage and are also valuable tools for the identification of repair intermediates.
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Affiliation(s)
- Thierry Douki
- Univ. Grenoble Alpes, INAC, LCIB, LAN, Grenoble, France.,CEA, INAC, SyMMES, LAN, Grenoble, France
| | - Anne von Koschembahr
- Univ. Grenoble Alpes, INAC, LCIB, LAN, Grenoble, France.,CEA, INAC, SyMMES, LAN, Grenoble, France
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
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21
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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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22
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Giroux X, MacNeill SA. A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner. Mol Microbiol 2015; 99:1-14. [PMID: 26337406 DOI: 10.1111/mmi.13210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2015] [Indexed: 01/11/2023]
Abstract
The sliding clamp proliferating cell nuclear antigen (PCNA) plays a vital role in a number of DNA repair pathways in eukaryotes and archaea by acting as a stable platform onto which other essential protein factors assemble. Many of these proteins interact with PCNA via a short peptide sequence known as a PIP (PCNA interacting protein) motif. Here we describe the identification and functional analysis of a novel PCNA interacting protein NreA that is conserved in the archaea and that has a PIP motif at its C-terminus. Using the genetically tractable euryarchaeon Haloferax volcanii as a model system, we show that the NreA protein is not required for cell viability but that loss of NreA (or replacement of the wild-type protein with a truncated version lacking the C-terminal PIP motif) results in an increased sensitivity to the DNA damaging agent mitomycin C (MMC) that correlates with delayed repair of MMC-induced chromosomal DNA damage monitored by pulsed-field gel electrophoresis. Genetic epistasis analysis in Hfx. volcanii suggests that NreA works together with the UvrABC proteins in repairing DNA damage resulting from exposure to MMC. The wide distribution of NreA family members implies an important role for the protein in DNA damage repair in all archaeal lineages.
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Affiliation(s)
- Xavier Giroux
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
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23
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Checinska A, Paszczynski A, Burbank M. Bacillusand Other Spore-Forming Genera: Variations in Responses and Mechanisms for Survival. Annu Rev Food Sci Technol 2015; 6:351-69. [DOI: 10.1146/annurev-food-030713-092332] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aleksandra Checinska
- School of Food Science, University of Idaho, Moscow, Idaho 83844-1052 and Washington State University, Pullman, Washington 99164-6376; ,
- Present address: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109;
| | - Andrzej Paszczynski
- School of Food Science, University of Idaho, Moscow, Idaho 83844-1052 and Washington State University, Pullman, Washington 99164-6376; ,
| | - Malcolm Burbank
- School of Food Science, University of Idaho, Moscow, Idaho 83844-1052 and Washington State University, Pullman, Washington 99164-6376; ,
- Present address: BioCement Technologies Inc., Seattle, Washington 98101
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24
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Paul VD, Lill R. Biogenesis of cytosolic and nuclear iron-sulfur proteins and their role in genome stability. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1528-39. [PMID: 25583461 DOI: 10.1016/j.bbamcr.2014.12.018] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/08/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023]
Abstract
Iron-sulfur (Fe-S) clusters are versatile protein cofactors that require numerous components for their synthesis and insertion into apoproteins. In eukaryotes, maturation of cytosolic and nuclear Fe-S proteins is accomplished by cooperation of the mitochondrial iron-sulfur cluster (ISC) assembly and export machineries, and the cytosolic iron-sulfur protein assembly (CIA) system. Currently, nine CIA proteins are known to specifically assist the two major steps of the biogenesis reaction. They are essential for cell viability and conserved from yeast to man. The essential character of this biosynthetic process is explained by the involvement of Fe-S proteins in central processes of life, e.g., protein translation and numerous steps of nuclear DNA metabolism such as DNA replication and repair. Malfunctioning of these latter Fe-S enzymes leads to genome instability, a hallmark of cancer. This review is focused on the maturation and biological function of cytosolic and nuclear Fe-S proteins, a topic of central interest for both basic and medical research. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Viktoria Désirée Paul
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Straße 6, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Straße 6, 35032 Marburg, Germany; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Str., 35043 Marburg, Germany.
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25
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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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26
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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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27
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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: 573] [Impact Index Per Article: 57.3] [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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28
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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Biogenesis of [Fe–S] cluster in Firmicutes: an unexploited field of investigation. Antonie Van Leeuwenhoek 2013; 104:283-300. [DOI: 10.1007/s10482-013-9966-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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Yang L, Li L. The enzyme-mediated direct reversal of a dithymine photoproduct in germinating endospores. Int J Mol Sci 2013; 14:13137-53. [PMID: 23799365 PMCID: PMC3742179 DOI: 10.3390/ijms140713137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 11/16/2022] Open
Abstract
Spore photoproduct lyase (SPL) repairs a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct, or SP, in germinating endospores. SP is the exclusive DNA photo-damaging product found in endospores; its generation and swift repair by SPL are responsible for the spores’ extremely high UV resistance. Early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair SP in the absence of light. Recently, it has been established that SPL belongs to the radical S-adenosylmethionine (SAM) superfamily. The enzymes in this superfamily utilize a tri-cysteine CXXXCXXC motif to bind a [4Fe-4S] cluster. The cluster provides an electron to the S-adenosylmethionine (SAM) to reductively cleave its C5′-S bond, generating a reactive 5′-deoxyadenosyl (5′-dA) radical. This 5′-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. The H atom donor is suggested to be a conserved cysteine141 in B. subtilis SPL; the resulting thiyl radical likely interacts with a neighboring tyrosine99 before oxidizing the 5′-dA to 5′-dA radical and, subsequently, regenerating SAM. These findings suggest SPL to be the first enzyme in the large radical SAM superfamily (>44,000 members) to utilize a radical transfer pathway for catalysis; its study should shed light on the mechanistic understanding of the SAM regeneration process in other members of the superfamily.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA; E-Mail:
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA; E-Mail:
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-317-278-2202; Fax: +1-317-274-4701
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31
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Abstract
5-(α-Thyminyl)-5,6-dihydrothymine, also called spore photoproduct or SP, is commonly found in the genomic DNA of UV-irradiated bacterial endospores. Despite the fact that SP was discovered nearly 50 years ago, its biochemical impact is still largely unclear due to the difficulty of preparing SP-containing oligonucleotide in high purity. Here, we report the first synthesis of the phosphoramidite derivative of dinucleotide SP TpT, which enables successful incorporation of SP TpT into oligodeoxyribonucleotides with high efficiency via standard solid-phase synthesis. This result provides the scientific community a reliable means to prepare SP-containing oligonucleotides, laying the foundation for future SP biochemical studies. Thermal denaturation studies of the SP-containing oligonucleotide found that SP destabilizes the duplex by 10-20 kJ/mol, suggesting that its presence in the spore-genomic DNA may alter the DNA local conformation.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Indianapolis, Indiana 46202
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32
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Li L. Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL). BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1264-77. [PMID: 22197590 PMCID: PMC3314140 DOI: 10.1016/j.bbapap.2011.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 11/28/2011] [Indexed: 02/06/2023]
Abstract
Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Lei Li
- Department of Chemistry, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA.
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33
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Yang L, Lin G, Nelson RS, Jian Y, Telser J, Li L. Mechanistic studies of the spore photoproduct lyase via a single cysteine mutation. Biochemistry 2012; 51:7173-88. [PMID: 22906093 PMCID: PMC3448869 DOI: 10.1021/bi3010945] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
5-Thyminyl-5,6-dihydrothymine (also called spore photoproduct or SP) is the exclusive DNA photodamage product in bacterial endospores. It is repaired by a radical SAM (S-adenosylmethionine) enzyme, the spore photoproduct lyase (SPL), at the bacterial early germination phase. Our previous studies proved that SPL utilizes the 5'-dA• generated by the SAM cleavage reaction to abstract the H(6proR) atom to initiate the SP repair process. The resulting thymine allylic radical was suggested to take an H atom from an unknown protein source, most likely cysteine 141. Here we show that C141 can be readily alkylated in the native SPL by an iodoacetamide treatment, suggesting that it is accessible to the TpT radical. SP repair by the SPL C141A mutant yields TpTSO(2)(-) and TpT simultaneously from the very beginning of the reaction; no lag phase is observed for TpTSO(2)(-) formation. Should any other protein residue serve as the H donor, its presence would result in TpT being the major product at least for the first enzyme turnover. These observations provide strong evidence to support C141 as the direct H atom donor. Moreover, because of the lack of this intrinsic H donor, the C141A mutant produces TpT via an unprecedented thymine cation radical reduction (proton-coupled electron transfer) process, contrasting to the H atom transfer mechanism in the wild-type (WT) SPL reaction. The C141A mutant repairs SP at a rate that is ~3-fold slower than that of the WT enzyme. Formation of TpTSO(2)(-) and TpT exhibits a V(max) deuterium kinetic isotope effect (KIE) of 1.7 ± 0.2, which is smaller than the (D)V(max) KIE of 2.8 ± 0.3 determined for the WT SPL reaction. These findings suggest that removing the intrinsic H atom donor disturbs the rate-limiting process during enzyme catalysis. As expected, the prereduced C141A mutant supports only ~0.4 turnover, which is in sharp contrast to the >5 turnovers exhibited by the WT SPL reaction, suggesting that the enzyme catalytic cycle (SAM regeneration) is disrupted by this single mutation.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Renae S. Nelson
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Joshua Telser
- Department of Biological, Chemical, and Physical Sciences, Roosevelt University, Chicago, Illinois 60605
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Indianapolis, Indiana 46202
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34
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Alternative excision repair of ultraviolet B- and C-induced DNA damage in dormant and developing spores of Bacillus subtilis. J Bacteriol 2012; 194:6096-104. [PMID: 22961846 DOI: 10.1128/jb.01340-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The nucleotide excision repair (NER) and spore photoproduct lyase DNA repair pathways are major determinants of Bacillus subtilis spore resistance to UV radiation. We report here that a putative ultraviolet (UV) damage endonuclease encoded by ywjD confers protection to developing and dormant spores of B. subtilis against UV DNA damage. In agreement with its predicted function, a His(6)-YwjD recombinant protein catalyzed the specific incision of UV-irradiated DNA in vitro. The maximum expression of a reporter gene fusion to the ywjD opening reading frame occurred late in sporulation, and this maximal expression was dependent on the forespore-specific RNA polymerase sigma factor, σ(G). Although the absence of YwjD and/or UvrA, an essential protein of the NER pathway, sensitized developing spores to UV-C, this effect was lower when these cells were treated with UV-B. In contrast, UV-B but not UV-C radiation dramatically decreased the survival of dormant spores deficient in both YwjD and UvrA. The distinct range of lesions generated by UV-C and UV-B and the different DNA photochemistry in developing and dormant spores may cause these differences. We postulate that in addition to the UvrABC repair system, developing and dormant spores of B. subtilis also rely on an alternative excision repair pathway involving YwjD to deal with the deleterious effects of various UV photoproducts.
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35
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Hiscox MJ, Driesener RC, Roach PL. Enzyme catalyzed formation of radicals from S-adenosylmethionine and inhibition of enzyme activity by the cleavage products. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1165-77. [PMID: 22504666 DOI: 10.1016/j.bbapap.2012.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 03/06/2012] [Accepted: 03/27/2012] [Indexed: 01/06/2023]
Abstract
A large superfamily of enzymes have been identified that make use of radical intermediates derived by reductive cleavage of S-adenosylmethionine. The primary nature of the radical intermediates makes them highly reactive and potent oxidants. They are used to initiate biotransformations by hydrogen atom abstraction, a process that allows a particularly diverse range of substrates to be functionalized, including substrates with relatively inert chemical structures. In the first part of this review, we discuss the evidence supporting the mechanism of radical formation from S-adenosylmethionine. In the second part of the review, we examine the potential of reaction products arising from S-adenosylmethionine to cause product inhibition. The effects of this product inhibition on kinetic studies of 'radical S-adenosylmethionine' enzymes are discussed and strategies to overcome these issues are reviewed. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Martyn J Hiscox
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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36
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Challand MR, Driesener RC, Roach PL. Radical S-adenosylmethionine enzymes: mechanism, control and function. Nat Prod Rep 2011; 28:1696-721. [PMID: 21779595 DOI: 10.1039/c1np00036e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Martin R Challand
- School of Cellular and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS81TD, USA
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37
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Desnous C, Guillaume D, Clivio P. Spore Photoproduct: A Key to Bacterial Eternal Life. Chem Rev 2009; 110:1213-32. [DOI: 10.1021/cr0781972] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Céline Desnous
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
| | - Dominique Guillaume
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
| | - Pascale Clivio
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
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38
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Szu PH, Ruszczycky MW, Choi SH, Yan F, Liu HW. Characterization and mechanistic studies of DesII: a radical S-adenosyl-L-methionine enzyme involved in the biosynthesis of TDP-D-desosamine. J Am Chem Soc 2009; 131:14030-42. [PMID: 19746907 PMCID: PMC2780582 DOI: 10.1021/ja903354k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
D-desosamine (1) is a 3-(N,N-dimethylamino)-3,4,6-trideoxyhexose found in a number of macrolide antibiotics including methymycin (2), neomethymycin (3), pikromycin (4), and narbomycin (5) produced by Streptomyces venezuelae . It plays an essential role in conferring biological activities to its parent aglycones. Previous genetic and biochemical studies of the biosynthesis of desosamine in S. venezuelae showed that the conversion of TDP-4-amino-4,6-dideoxy-D-glucose (8) to TDP-3-keto-4,6-dideoxy-D-glucose (9) is catalyzed by DesII, which is a member of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily. Here, we report the purification and reconstitution of His(6)-tagged DesII, characterization of its [4Fe-4S] cluster using UV-vis and EPR spectroscopies, and the capability of flavodoxin, flavodoxin reductase, and NADPH to reduce the [4Fe-4S](2+) cluster. Also included are a steady-state kinetic analysis of DesII-catalyzed reaction and an investigation of the substrate flexibility of DesII. Studies of deuterium incorporation into SAM using TDP-[3-(2)H]-4-amino-4,6-dideoxy-D-glucose as the substrate provides strong evidence for direct hydrogen atom transfer to a 5'-deoxyadenosyl radical in the catalytic cycle. The fact that hydrogen atom abstraction occurs at C-3 also sheds light on the mechanism of this intriguing deamination reaction.
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Affiliation(s)
- Ping-Hui Szu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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39
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Chandra T, Silver SC, Zilinskas E, Shepard EM, Broderick WE, Broderick JB. Spore photoproduct lyase catalyzes specific repair of the 5R but not the 5S spore photoproduct. J Am Chem Soc 2009; 131:2420-1. [PMID: 19178276 DOI: 10.1021/ja807375c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial spores are remarkable in their resistance to chemical and physical stresses, including exposure to UV radiation. The unusual UV resistance of bacterial spores is a result of the unique photochemistry of spore DNA, which results in accumulation of 5-thyminyl-5,6-dihydrothymine (spore photoproduct, or SP), coupled with the efficient repair of accumulated damage by the enzyme spore photoproduct lyase (SPL). SPL is a member of the radical AdoMet superfamily of enzymes, and utilizes an iron-sulfur cluster and S-adenosylmethionine to repair SP by a direct reversal mechanism initiated by H atom abstraction from C-6 of the thymine dimer. While two distinct diastereomers of SP (5R or 5S) could in principle be formed upon UV irradiation of bacterial spores, only the 5R configuration is possible for SP formed from adjacent thymines in double helical DNA, due to the constraints imposed by the DNA structure; the 5S configuration is possible in less well-defined DNA structures or as an interstrand cross-link. We report here results from HPLC and MS analysis of in vitro enzymatic assays on stereochemically defined SP substrates demonstrating that SPL specifically repairs only the 5R isomer of SP. The observation that 5R-SP, but not 5S-SP, is a substrate for SPL is consistent with the expectation that 5R is the SP isomer produced in vivo upon UV irradiation of bacterial spore DNA.
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Affiliation(s)
- Tilak Chandra
- Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, USA
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40
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Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 2009; 5:e1000362. [PMID: 19197347 PMCID: PMC2628731 DOI: 10.1371/journal.pgen.1000362] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 12/31/2008] [Indexed: 11/19/2022] Open
Abstract
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment--some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20 degrees C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere--anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.
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Chandor-Proust A, Berteau O, Douki T, Gasparutto D, Ollagnier-de-Choudens S, Fontecave M, Atta M. DNA repair and free radicals, new insights into the mechanism of spore photoproduct lyase revealed by single amino acid substitution. J Biol Chem 2008; 283:36361-8. [PMID: 18957420 DOI: 10.1074/jbc.m806503200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major DNA photoproduct in UV-irradiated Bacillus subtilis spores is the thymine dimer named spore photoproduct (SP, 5-(alpha-thyminyl)-5,6-dihydrothymine). The SP lesion has been found to be efficiently repaired by SP lyase (SPL) a very specific enzyme that reverses the SP to two intact thymines, at the origin of the great resistance of the spores to UV irradiation. SPL belongs to a superfamily of [4Fe-4S] iron-sulfur enzymes, called "Radical-SAM." Here, we show that the single substitution of cysteine 141 into alanine, a residue fully conserved in Bacillus species and previously shown to be essential for spore DNA repair in vivo, has a major impact on the outcome of the SPL-dependent repair reaction in vitro. Indeed the modified enzyme catalyzes the almost quantitative conversion of the SP lesion into one thymine and one thymine sulfinic acid derivative. This compound results from the trapping of the allyl-type radical intermediate by dithionite, used as reducing agent in the reaction mixture. Implications of the data reported here regarding the repair mechanism and the role of Cys-141 are discussed.
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Affiliation(s)
- Alexia Chandor-Proust
- Commissariat à l'Energie Atomique (CEA), Institut de Recherches en Technologie et Sciences pour le Vivant, Laboratoire de Chimie et Biologie des Métaux, Grenoble 38054, France
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42
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Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme. Proc Natl Acad Sci U S A 2008; 105:16137-41. [PMID: 18852451 DOI: 10.1073/pnas.0806640105] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.
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43
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Abstract
The radical S-adenosylmethionine (SAM) superfamily currently comprises more than 2800 proteins with the amino acid sequence motif CxxxCxxC unaccompanied by a fourth conserved cysteine. The charcteristic three-cysteine motif nucleates a [4Fe-4S] cluster, which binds SAM as a ligand to the unique Fe not ligated to a cysteine residue. The members participate in more than 40 distinct biochemical transformations, and most members have not been biochemically characterized. A handful of the members of this superfamily have been purified and at least partially characterized. Significant mechanistic and structural information is available for lysine 2,3-aminomutase, pyruvate formate-lyase, coproporphyrinogen III oxidase, and MoaA required for molybdopterin biosynthesis. Biochemical information is available for spore photoproduct lyase, anaerobic ribonucleotide reductase activation subunit, lipoyl synthase, and MiaB involved in methylthiolation of isopentenyladenine-37 in tRNA. The radical SAM enzymes biochemically characterized to date have in common the cleavage of the [4Fe-4S](1 +) -SAM complex to [4Fe-4S](2 +)-Met and the 5' -deoxyadenosyl radical, which abstracts a hydrogen atom from the substrate to initiate a radical mechanism.
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Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Madison, Wisconin-Madison, Wisconsin 53726, USA.
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44
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Bürckstümmer E, Carell T. Synthesis and properties of DNA containing a spore photoproduct analog. Chem Commun (Camb) 2008:4037-9. [DOI: 10.1039/b810008j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, Ishitani R, Nureki O. Crystal Structure of the Radical SAM Enzyme Catalyzing Tricyclic Modified Base Formation in tRNA. J Mol Biol 2007; 372:1204-14. [PMID: 17727881 DOI: 10.1016/j.jmb.2007.07.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 07/03/2007] [Accepted: 07/09/2007] [Indexed: 11/26/2022]
Abstract
Wyosine and its derivatives, such as wybutosine, found in eukaryotic and archaeal tRNAs, are tricyclic hypermodified nucleosides. In eukaryotes, wybutosine exists exclusively in position 37, 3'-adjacent to the anticodon, of tRNA(Phe), where it ensures correct translation by stabilizing the codon-anticodon base-pairing during the ribosomal decoding process. Recent studies revealed that the wyosine biosynthetic pathway consists of multistep enzymatic reactions starting from a guanosine residue. Among these steps, TYW1 catalyzes the second step to form the tricyclic ring structure, by cyclizing N(1)-methylguanosine. In this study, we solved the crystal structure of TYW1 from Methanocaldococcus jannaschii at 2.4 A resolution. TYW1 assumes an incomplete TIM barrel with (alpha/beta)(6) topology, which closely resembles the reported structures of radical SAM enzymes. Hence, TYW1 was considered to catalyze the cyclization reaction by utilizing the radical intermediate. Comparison with other radical SAM enzymes allowed us to build a model structure complexed with S-adenosylmethionine and two [4Fe-4S] clusters. Mutational analyses in yeast supported the validity of this complex model structure, which provides a structural insight into the radical reaction involving two [4Fe-4S] clusters to create a complex tricyclic base.
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Affiliation(s)
- Yoko Suzuki
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan
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46
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Chandor A, Douki T, Gasparutto D, Gambarelli S, Sanakis Y, Nicolet Y, Ollagnier-de-Choudens S, Atta M, Fontecave M. Characterization of the DNA repair spore photoproduct lyase enzyme from Clostridium acetobutylicum: A radical-SAM enzyme. CR CHIM 2007. [DOI: 10.1016/j.crci.2007.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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47
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Boal AK, Yavin E, Barton JK. DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport? J Inorg Biochem 2007; 101:1913-21. [PMID: 17599416 PMCID: PMC2094209 DOI: 10.1016/j.jinorgbio.2007.05.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 04/30/2007] [Accepted: 05/03/2007] [Indexed: 02/08/2023]
Abstract
The [4Fe-4S] cluster is ubiquitous to a class of base excision repair enzymes in organisms ranging from bacteria to man and was first considered as a structural element, owing to its redox stability under physiological conditions. When studied bound to DNA, two of these repair proteins (MutY and Endonuclease III from Escherichia coli) display DNA-dependent reversible electron transfer with characteristics typical of high potential iron proteins. These results have inspired a reexamination of the role of the [4Fe-4S] cluster in this class of enzymes. Might the [4Fe-4S] cluster be used as a redox cofactor to search for damaged sites using DNA-mediated charge transport, a process well known to be highly sensitive to lesions and mismatched bases? Described here are experiments demonstrating the utility of DNA-mediated charge transport in characterizing these DNA-binding metalloproteins, as well as efforts to elucidate this new function for DNA as an electronic signaling medium among the proteins.
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Friedel MG, Berteau O, Pieck JC, Atta M, Ollagnier-de-Choudens S, Fontecave M, Carell T. The spore photoproduct lyase repairs the 5S- and not the 5R-configured spore photoproduct DNA lesion. Chem Commun (Camb) 2007:445-7. [PMID: 16493831 DOI: 10.1039/b514103f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spore photoproduct lyase is a Fe-S/AdoMet DNA repair enzyme, which directly repairs spore lesions, induced by UV irradiation of spores, using an unknown radical mechanism. The air sensitive radical SAM enzyme was for the first time challenged with synthetically pure substrates. It was found that the enzyme recognizes a synthetic 5S-configured spore lesion without the central phosphodiester bond. The 5R-configured lesion is in contrast to current belief not a substrate.
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Affiliation(s)
- Marcus G Friedel
- Department of Chemistry and Biochemistry, LMU Munich, Butenandtstr. 5-13, D-81377, Munich, Germany
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49
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Wang SC, Frey PA. S-adenosylmethionine as an oxidant: the radical SAM superfamily. Trends Biochem Sci 2007; 32:101-10. [PMID: 17291766 DOI: 10.1016/j.tibs.2007.01.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 01/09/2007] [Accepted: 01/30/2007] [Indexed: 10/23/2022]
Abstract
A recently discovered superfamily of enzymes function using chemically novel mechanisms, in which S-adenosylmethionine (SAM) serves as an oxidizing agent in DNA repair and the biosynthesis of vitamins, coenzymes and antibiotics. Members of this superfamily, the radical SAM enzymes, are related by the cysteine motif CxxxCxxC, which nucleates the [4Fe-4S] cluster found in each. A common thread in the novel chemistry of these proteins is the use of a strong reducing agent--a low-potential [4Fe-4S](1+) cluster--to generate a powerful oxidizing agent, the 5'-deoxyadenosyl radical, from SAM. Recent results are beginning to determine the unique biochemistry for some of the radical SAM enzymes, for example, lysine 2,3 aminomutase, pyruvate formate lyase activase and biotin synthase.
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Affiliation(s)
- Susan C Wang
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, WI 53726, USA
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50
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Pieck JC, Hennecke U, Pierik AJ, Friedel MG, Carell T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates. J Biol Chem 2006; 281:36317-26. [PMID: 16968710 DOI: 10.1074/jbc.m607053200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Geobacillus stearothermophilus splG gene encodes a thermophilic spore photoproduct lyase (SplG) that belongs to the family of radical S-adenosylmethionine (AdoMet) enzymes. The aerobically purified apo-SplG forms a homodimer, which contains one [4Fe-4S] cluster per monomer unit after reconstitution to the holoform. Formation of the [4Fe-4S] cluster was proven by quantification of the amount of iron and sulfur per homodimer and by UV and EPR spectroscopy. The UV spectrum features a characteristic absorbance at 420 nm typical for [4Fe-4S] clusters, and the EPR data were found to be identical to those of other proteins containing an [4Fe-4S]+ center. Probing of the activity of the holo-SplG with oligonucleotides containing one spore photoproduct lesion at a defined site proved that the enzyme is able to turn over substrate. In addition to repair, we observed cleavage of AdoMet to generate 5'-deoxyadenosine. In the presence of aza-AdoMet the SplG is completely inhibited, which provides direct support for the repair mechanism.
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Affiliation(s)
- J Carsten Pieck
- Department of Chemistry and Biochemistry, Ludwig Maximilians University Munich, D-81377 Munich, Germany
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