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Putnam CD, Kolodner RD. Insights into DNA cleavage by MutL homologs from analysis of conserved motifs in eukaryotic Mlh1. Bioessays 2023; 45:e2300031. [PMID: 37424007 PMCID: PMC10530380 DOI: 10.1002/bies.202300031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
MutL family proteins contain an N-terminal ATPase domain (NTD), an unstructured interdomain linker, and a C-terminal domain (CTD), which mediates constitutive dimerization between subunits and often contains an endonuclease active site. Most MutL homologs direct strand-specific DNA mismatch repair by cleaving the error-containing daughter DNA strand. The strand cleavage reaction is poorly understood; however, the structure of the endonuclease active site is consistent with a two- or three-metal ion cleavage mechanism. A motif required for this endonuclease activity is present in the unstructured linker of Mlh1 and is conserved in all eukaryotic Mlh1 proteins, except those from metamonads, which also lack the almost absolutely conserved Mlh1 C-terminal phenylalanine-glutamate-arginine-cysteine (FERC) sequence. We hypothesize that the cysteine in the FERC sequence is autoinhibitory, as it sequesters the active site. We further hypothesize that the evolutionary co-occurrence of the conserved linker motif with the FERC sequence indicates a functional interaction, possibly by linker motif-mediated displacement of the inhibitory cysteine. This role is consistent with available data for interactions between the linker motif with DNA and the CTDs in the vicinity of the active site.
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Affiliation(s)
- Christopher D. Putnam
- Ludwig Institute for Cancer Research San Diego Branch, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Departments of Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Moores Cancer Center, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
| | - Richard D. Kolodner
- Ludwig Institute for Cancer Research San Diego Branch, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Cellular and Molecular Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Moores Cancer Center, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Institute of Genomic Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
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Ragucci S, Landi N, Russo R, Valletta M, Pedone PV, Chambery A, Di Maro A. Ageritin from Pioppino Mushroom: The Prototype of Ribotoxin-Like Proteins, a Novel Family of Specific Ribonucleases in Edible Mushrooms. Toxins (Basel) 2021; 13:263. [PMID: 33917246 PMCID: PMC8068006 DOI: 10.3390/toxins13040263] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Ageritin is a specific ribonuclease, extracted from the edible mushroom Cyclocybe aegerita (synonym Agrocybe aegerita), which cleaves a single phosphodiester bond located within the universally conserved alpha-sarcin loop (SRL) of 23-28S rRNAs. This cleavage leads to the inhibition of protein biosynthesis, followed by cellular death through apoptosis. The structural and enzymatic properties show that Ageritin is the prototype of a novel specific ribonucleases family named 'ribotoxin-like proteins', recently found in fruiting bodies of other edible basidiomycetes mushrooms (e.g., Ostreatin from Pleurotus ostreatus, Edulitins from Boletus edulis, and Gambositin from Calocybe gambosa). Although the putative role of this toxin, present in high amount in fruiting body (>2.5 mg per 100 g) of C. aegerita, is unknown, its antifungal and insecticidal actions strongly support a role in defense mechanisms. Thus, in this review, we focus on structural, biological, antipathogenic, and enzymatic characteristics of this ribotoxin-like protein. We also highlight its biological relevance and potential biotechnological applications in agriculture as a bio-pesticide and in biomedicine as a therapeutic and diagnostic agent.
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Affiliation(s)
| | | | | | | | | | | | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100-Caserta, Italy; (S.R.); (N.L.); (R.R.); (M.V.); (P.V.P.); (A.C.)
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Valdelvira R, Bordanaba-Ruiseco L, Martín-Huestamendía C, Ruiz-Masó JA, Del Solar G. Acidic pH Decreases the Endonuclease Activity of Initiator RepB and Increases the Stability of the Covalent RepB-DNA Intermediate while Has Only a Limited Effect on the Replication of Plasmid pMV158 in Lactococcus lactis. Front Mol Biosci 2021; 8:634461. [PMID: 33889596 PMCID: PMC8056398 DOI: 10.3389/fmolb.2021.634461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/27/2021] [Indexed: 11/28/2022] Open
Abstract
Plasmid vectors constitute a valuable tool for homologous and heterologous gene expression, for characterization of promoter and regulatory regions, and for genetic manipulation and labeling of bacteria. During the last years, a series of vectors based on promiscuous replicons of the pMV158 family have been developed for their employment in a variety of Gram-positive bacteria and proved to be useful for all above applications in lactic acid bacteria. A proper use of the plasmid vectors requires detailed knowledge of their main replicative features under the changing growth conditions of the studied bacteria, such as the acidification of the culture medium by lactic acid production. Initiation of pMV158 rolling-circle replication is catalyzed by the plasmid-encoded RepB protein, which performs a sequence-specific cleavage on one of the parental DNA strands and, as demonstrated in this work, establishes a covalent bond with the 5′-P end generated in the DNA. This covalent adduct must last until the leading-strand termination stage, where a new cleavage on the regenerated nick site and a subsequent strand-transfer reaction result in rejoining of the ends of the cleaved parental strand, whereas hydrolysis of the newly-generated adduct would release the protein from a nicked double-stranded DNA plasmid form. We have analyzed here the effect of pH on the different in vitro reactions catalyzed by RepB and on the in vivo replication ability of plasmid pMV158. We show that acidic pH greatly impairs the catalytic activity of the protein and reduces hydrolysis of the covalent RepB-DNA adduct, as expected for the nucleophilic nature of these reactions. Conversely, the ability of pMV158 to replicate in vivo, as monitored by the copy number and segregational stability of the plasmid in Lactococcus lactis, remains almost intact at extracellular pHs ranging from 7.0 to 5.0, and a significant reduction (by ∼50%) in the plasmid copy number per chromosome equivalent is only observed at pH 4.5. Moreover, the RepB to pMV158 molar ratio is increased at pH 4.5, suggesting the existence of compensatory mechanisms that operate in vivo to allow pMV158 replication at pH values that severely disturb the catalytic activity of the initiator protein.
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Affiliation(s)
- Rafael Valdelvira
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Lorena Bordanaba-Ruiseco
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Cristina Martín-Huestamendía
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Angel Ruiz-Masó
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gloria Del Solar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Correa EME, De Tullio L, Vélez PS, Martina MA, Argaraña CE, Barra JL. Analysis of DNA structure and sequence requirements for Pseudomonas aeruginosa MutL endonuclease activity. J Biochem 2013; 154:505-11. [PMID: 23969026 DOI: 10.1093/jb/mvt080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hallmark of the mismatch repair system in bacterial and eukaryotic organisms devoid of MutH is the presence of a MutL homologue with endonuclease activity. The aim of this study was to analyse whether different DNA structures affect Pseudomonas aeruginosa MutL (PaMutL) endonuclease activity and to determine if a specific nucleotide sequence is required for this activity. Our results showed that PaMutL was able to nick covalently closed circular plasmids but not linear DNA at high ionic strengths, while the activity on linear DNA was only found below 60 mM salt. In addition, single strand DNA, ss/ds DNA boundaries and negatively supercoiling degree were not required for PaMutL nicking activity. Finally, the analysis of the incision sites revealed that PaMutL, as well as Bacillus thuringiensis MutL homologue, did not show DNA sequence specificity.
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Affiliation(s)
- Elisa M E Correa
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina and Centro de Excelencia en Productos, Procesos e Innovación Tecnológica de la Provincia de Córdoba (CEPROCOR), Pabellón CEPROCOR (X5164), Santa María de Punilla, Córdoba, Argentina
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Shimada A, Kawasoe Y, Hata Y, Takahashi TS, Masui R, Kuramitsu S, Fukui K. MutS stimulates the endonuclease activity of MutL in an ATP-hydrolysis-dependent manner. FEBS J 2013; 280:3467-79. [PMID: 23679952 DOI: 10.1111/febs.12344] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/02/2013] [Accepted: 05/07/2013] [Indexed: 11/30/2022]
Abstract
In the initial steps of DNA mismatch repair, MutS recognizes a mismatched base and recruits the latent endonuclease MutL onto the mismatch-containing DNA in concert with other proteins. MutL then cleaves the error-containing strand to introduce an entry point for the downstream excision reaction. Because MutL has no intrinsic ability to recognize a mismatch and discriminate between newly synthesized and template strands, the endonuclease activity of MutL is strictly regulated by ATP-binding in order to avoid nonspecific degradation of the genomic DNA. However, the activation mechanism for its endonuclease activity remains unclear. In this study, we found that the coexistence of a mismatch, ATP and MutS unlocks the ATP-binding-dependent suppression of MutL endonuclease activity. Interestingly, ATPase-deficient mutants of MutS were unable to activate MutL. Furthermore, wild-type MutS activated ATPase-deficient mutants of MutL less efficiently than wild-type MutL. We concluded that ATP hydrolysis by MutS and MutL is involved in the mismatch-dependent activation of MutL endonuclease activity.
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Affiliation(s)
- Atsuhiro Shimada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Suita, Osaka, Japan
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Rigden DJ, Setlow P, Setlow B, Bagyan I, Stein RA, Jedrzejas MJ. PrfA protein of Bacillus species: prediction and demonstration of endonuclease activity on DNA. Protein Sci 2002; 11:2370-81. [PMID: 12237459 PMCID: PMC2373696 DOI: 10.1110/ps.0216802] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The prfA gene product of Gram-positive bacteria is unusual in being implicated in several cellular processes; cell wall synthesis, chromosome segregation, and DNA recombination and repair. However, no homology of PrfA with other proteins has been evident. Here we report a structural relationship between PrfA and the restriction enzyme PvuII, and thereby produce models that predict that PrfA binds DNA. Indeed, wild-type Bacillus stearothermophilus PrfA, but not a catalytic site mutant, nicked one strand of supercoiled plasmid templates leaving 5'-phosphate and 3'-hydroxyl termini. This activity, much lower on linear or relaxed circular double-stranded DNA or on single-stranded DNA, is consistent with a role for this protein in chromosome segregation, DNA recombination, or DNA repair.
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Affiliation(s)
- Daniel J Rigden
- National Centre of Genetic Resources and Biotechnology, Cenargen/Embrapa, Brasília, Brazil, D.F. 70770-900.
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