1
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Friedhoff P, Li P, Gotthardt J. Protein-protein interactions in DNA mismatch repair. DNA Repair (Amst) 2015; 38:50-57. [PMID: 26725162 DOI: 10.1016/j.dnarep.2015.11.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 11/25/2022]
Abstract
The principal DNA mismatch repair proteins MutS and MutL are versatile enzymes that couple DNA mismatch or damage recognition to other cellular processes. Besides interaction with their DNA substrates this involves transient interactions with other proteins which is triggered by the DNA mismatch or damage and controlled by conformational changes. Both MutS and MutL proteins have ATPase activity, which adds another level to control their activity and interactions with DNA substrates and other proteins. Here we focus on the protein-protein interactions, protein interaction sites and the different levels of structural knowledge about the protein complexes formed with MutS and MutL during the mismatch repair reaction.
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Affiliation(s)
- Peter Friedhoff
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
| | - Pingping Li
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Julia Gotthardt
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
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2
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House AJ, Daye LR, Tarpley M, Addo K, Lamson DS, Parker MK, Bealer WE, Williams KP. Design and characterization of a photo-activatable hedgehog probe that mimics the natural lipidated form. Arch Biochem Biophys 2014; 567:66-74. [PMID: 25529135 DOI: 10.1016/j.abb.2014.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/08/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022]
Abstract
We have generated a photoactivatable form of sonic hedgehog protein by modifying the N-terminal cysteine with the heterobifunctional photocrosslinker 4-maleimidobenzophenone (Bzm). The Bzm modification on ShhN imparted a significant increase in activity as assessed in the C3H10T1/2 functional assay with potency comparable to that of the endogenous dual-lipidated form of ShhN (ShhNp). Reversed-phase HPLC analysis indicated that the increase in activity compared to unmodified ShhN may be due in part to the hydrophobic nature of the benzophenone group. In contrast to the fully processed ShhNp, Bzm-ShhN is monomeric as assessed by analytical SEC and does not require detergent to be soluble. Further, we demonstrated that the Bzm-ShhN was able to crosslink in vitro in the presence of a known binding partner, heparin. We suggest that Bzm-ShhN can serve as a relatively facile and preferred source of ShhNp for in vitro assays and as a probe to identify novel Hh protein interactions.
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Affiliation(s)
- Alan J House
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - Laura R Daye
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - Michael Tarpley
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - Kezia Addo
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - David S Lamson
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - Margie K Parker
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - Warren E Bealer
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - Kevin P Williams
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, USA.
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3
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Perevoztchikova SA, Romanova EA, Oretskaya TS, Friedhoff P, Kubareva EA. Modern aspects of the structural and functional organization of the DNA mismatch repair system. Acta Naturae 2013; 5:17-34. [PMID: 24303200 PMCID: PMC3848065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review is focused on the general aspects of the DNA mismatch repair (MMR) process. The key proteins of the DNA mismatch repair system are MutS and MutL. To date, their main structural and functional characteristics have been thoroughly studied. However, different opinions exist about the initial stages of the mismatch repair process with the participation of these proteins. This review aims to summarize the data on the relationship between the two MutS functions, ATPase and DNA-binding, and to systematize various models of coordination between the mismatch site and the strand discrimination site in DNA. To test these models, novel techniques for the trapping of short-living complexes that appear at different MMR stages are to be developed.
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Affiliation(s)
- S. A. Perevoztchikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bld. 40, Moscow, Russia, 119991
| | - E. A. Romanova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bld. 40, Moscow, Russia, 119991
| | - T. S. Oretskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bld. 40, Moscow, Russia, 119991
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 1, bld. 3, Moscow, Russia, 119991
| | - P. Friedhoff
- Institute of Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - E. A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bld. 40, Moscow, Russia, 119991
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4
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Vecchiarelli AG, Funnell BE. Probing the N-terminus of ParB using cysteine-scanning mutagenesis and thiol modification. Plasmid 2013; 70:86-93. [PMID: 23428603 DOI: 10.1016/j.plasmid.2013.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/07/2013] [Accepted: 02/10/2013] [Indexed: 11/18/2022]
Abstract
Plasmid partition systems require site-specific DNA binding proteins to recognize the plasmid partition site, or centromere. When bound to the centromere, these proteins, typically called ParB, interact with the ParA ATPases, which in turn promote the proper positioning of plasmids prior to cell division. P1 ParB is a typical member of a major class of ParB-like proteins that are dimeric helix-turn-helix DNA binding proteins. The N-terminus of ParB contains the region that interacts with ParA and with itself, but it has been difficult to study because this region of the protein is flexible in solution. Here we describe the use of cysteine-scanning mutagenesis and thiol modification of the N-terminus of ParB to create tools to probe the interactions of ParB with itself, with ParA and with DNA. We introduce twelve single-cysteine substitutions across the N-terminus of ParB and show that most do not compromise the function of ParB and that none completely inactivate the protein in vivo. We test three of these ParB variants in vitro and show that they do not alter ParB function, measured by its ability to stimulate ParA ATPase activity and its site-specific DNA binding activity. We discuss that this approach will be generally applicable to the ParB-like proteins in this class of partition systems because of their natural low content of cysteines, and because our evidence suggests that many residues in the N-terminus are amenable to substitution by cysteine.
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Affiliation(s)
- Anthony G Vecchiarelli
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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5
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Cristóvão M, Sisamakis E, Hingorani MM, Marx AD, Jung CP, Rothwell PJ, Seidel CAM, Friedhoff P. Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA. Nucleic Acids Res 2012; 40:5448-64. [PMID: 22367846 PMCID: PMC3384296 DOI: 10.1093/nar/gks138] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mismatch repair (MMR) corrects replication errors such as mismatched bases and loops in DNA. The evolutionarily conserved dimeric MMR protein MutS recognizes mismatches by stacking a phenylalanine of one subunit against one base of the mismatched pair. In all crystal structures of G:T mismatch-bound MutS, phenylalanine is stacked against thymine. To explore whether these structures reflect directional mismatch recognition by MutS, we monitored the orientation of Escherichia coli MutS binding to mismatches by FRET and anisotropy with steady state, pre-steady state and single-molecule multiparameter fluorescence measurements in a solution. The results confirm that specifically bound MutS bends DNA at the mismatch. We found additional MutS–mismatch complexes with distinct conformations that may have functional relevance in MMR. The analysis of individual binding events reveal significant bias in MutS orientation on asymmetric mismatches (G:T versus T:G, A:C versus C:A), but not on symmetric mismatches (G:G). When MutS is blocked from binding a mismatch in the preferred orientation by positioning asymmetric mismatches near the ends of linear DNA substrates, its ability to authorize subsequent steps of MMR, such as MutH endonuclease activation, is almost abolished. These findings shed light on prerequisites for MutS interactions with other MMR proteins for repairing the appropriate DNA strand.
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Affiliation(s)
- Michele Cristóvão
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Evangelos Sisamakis
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Manju M. Hingorani
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Andreas D. Marx
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Caroline P. Jung
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Paul J. Rothwell
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
| | - Claus A. M. Seidel
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
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6
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Xiao Y, Jung C, Marx AD, Winkler I, Wyman C, Lebbink JHG, Friedhoff P, Cristovao M. Generation of DNA nanocircles containing mismatched bases. Biotechniques 2012; 51:259-62, 264-5. [PMID: 21988692 DOI: 10.2144/000113749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 08/25/2011] [Indexed: 11/23/2022] Open
Abstract
The DNA mismatch repair (MMR) system recognizes and repairs errors that escaped the proofreading function of DNA polymerases. To study molecular details of the MMR mechanism, in vitro biochemical assays require specific DNA substrates carrying mismatches and strand discrimination signals. Current approaches used to generate MMR substrates are time-consuming and/or not very flexible with respect to sequence context. Here we report an approach to generate small circular DNA containing a mismatch (nanocircles). Our method is based on the nicking of PCR products resulting in single-stranded 3' overhangs, which form DNA circles after annealing and ligation. Depending on the DNA template, one can generate mismatched circles containing a single hemimethylated GATC site (for use with the bacterial system) and/or nicking sites to generate DNA circles nicked in the top or bottom strand (for assays with the bacterial or eukaryotic MMR system). The size of the circles varied (323 to 1100 bp), their sequence was determined by the template DNA, and purification of the circles was achieved by ExoI/ExoIII digestion and/or gel extraction. The quality of the nanocircles was assessed by scanning-force microscopy and their suitability for in vitro repair initiation was examined using recombinant Escherichia coli MMR proteins.
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Affiliation(s)
- Yu Xiao
- Institute of Biochemistry, Justus-Liebig University, Giessen, Germany
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7
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Winkler I, Marx AD, Lariviere D, Heinze RJ, Cristovao M, Reumer A, Curth U, Sixma TK, Friedhoff P. Chemical trapping of the dynamic MutS-MutL complex formed in DNA mismatch repair in Escherichia coli. J Biol Chem 2011; 286:17326-37. [PMID: 21454657 DOI: 10.1074/jbc.m110.187641] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ternary complex comprising MutS, MutL, and DNA is a key intermediate in DNA mismatch repair. We used chemical cross-linking and fluorescence resonance energy transfer (FRET) to study the interaction between MutS and MutL and to shed light onto the structure of this complex. Via chemical cross-linking, we could stabilize this dynamic complex and identify the structural features of key events in DNA mismatch repair. We could show that in the complex between MutS and MutL the mismatch-binding and connector domains of MutS are in proximity to the N-terminal ATPase domain of MutL. The DNA- and nucleotide-dependent complex formation could be monitored by FRET using single cysteine variants labeled in the connector domain of MutS and the transducer domain of MutL, respectively. In addition, we could trap MutS after an ATP-induced conformational change by an intramolecular cross-link between Cys-93 of the mismatch-binding domain and Cys-239 of the connector domain.
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Affiliation(s)
- Ines Winkler
- Institute for Biochemistry, FB 08, Justus Liebig University, D-35392 Giessen, Germany
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8
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Ahrends R, Pieper S, Neumann B, Scheler C, Linscheid MW. Metal-Coded Affinity Tag Labeling: A Demonstration of Analytical Robustness and Suitability for Biological Applications. Anal Chem 2009; 81:2176-84. [DOI: 10.1021/ac802310c] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Robert Ahrends
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Stefan Pieper
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Boris Neumann
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Christian Scheler
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Michael W. Linscheid
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
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9
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Gong J, Liu WQ, Liu GR, Chen F, Li JQ, Xu GM, Wang L, Johnston RN, Eisenstark A, Liu SL. Spontaneous conversion between mutL and 6 bpΔmutL in Salmonella typhimurium LT7: Association with genome diversification and possible roles in bacterial adaptation. Genomics 2007; 90:542-9. [PMID: 17689047 DOI: 10.1016/j.ygeno.2007.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 06/02/2007] [Accepted: 06/26/2007] [Indexed: 10/23/2022]
Abstract
Previously, we reported the phenomenon of genome diversification in Salmonella typhimurium LT7, i.e., individual strains derived from LT7 kept changing the genome structure by inversions, translocations, duplications, and mutations. To elucidate the genetic basis, we sequenced selected genes of the mismatch repair (MMR) system for correlations between MMR defects and genome diversification. We chose S. typhimurium LT7 mutants 8111F2 and 9052D1 for mut gene sequence analyses and found that both mutants had a deletion of one of three tandem 6-bp repeats, GCTGGC GCTGGC GCTGGC, within mutL, which was designated 6 bpDeltamutL. mutS and mutH genes were unchanged in the mutants analyzed. Some sublines of 8111F2 and 9052D1 spontaneously stopped the genome diversification process at certain stages during single-colony restreaking passages, and in these strains the 6 bpDeltamutL genotype also became wild-type mutL. We conclude that conversion between mutL and 6 bpDeltamutL occurs spontaneously and that transient defects of mutL facilitate genome diversification without leading to the accumulation of multiple detrimental genetic changes. Spontaneous conversion between mutL and 6 bpDeltamutL may be an important mechanism used by bacteria to regulate genetic stability in adaptation to changing environments.
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Affiliation(s)
- Jun Gong
- Department of Microbiology, Peking University Health Science Center, Beijing 100083, China
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10
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Plotz G, Welsch C, Giron-Monzon L, Friedhoff P, Albrecht M, Piiper A, Biondi RM, Lengauer T, Zeuzem S, Raedle J. Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair. Nucleic Acids Res 2006; 34:6574-86. [PMID: 17135187 PMCID: PMC1747184 DOI: 10.1093/nar/gkl944] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
MutLα, a heterodimer of MLH1 and PMS2, plays a central role in human DNA mismatch repair. It interacts ATP-dependently with the mismatch detector MutSα and assembles and controls further repair enzymes. We tested if the interaction of MutLα with DNA-bound MutSα is impaired by cancer-associated mutations in MLH1, and identified one mutation (Ala128Pro) which abolished interaction as well as mismatch repair activity. Further examinations revealed three more residues whose mutation interfered with interaction. Homology modelling of MLH1 showed that all residues clustered in a small accessible surface patch, suggesting that the major interaction interface of MutLα for MutSα is located on the edge of an extensive β-sheet that backs the MLH1 ATP binding pocket. Bioinformatic analysis confirmed that this patch corresponds to a conserved potential protein–protein interaction interface which is present in both human MLH1 and its E.coli homologue MutL. MutL could be site-specifically crosslinked to MutS from this patch, confirming that the bacterial MutL–MutS complex is established by the corresponding interface in MutL. This is the first study that identifies the conserved major MutLα–MutSα interaction interface in MLH1 and demonstrates that mutations in this interface can affect interaction and mismatch repair, and thereby can also contribute to cancer development.
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Affiliation(s)
- Guido Plotz
- Klinik für Innere Medizin II, Gebäude 41Kirrberger Straße, Universität des Saarlandes, D-66421 Homburg/Saar, Germany
- To whom correspondence should be addressed. Tel: +49 6841 16 23253; Fax: +49 6841 16 23570;
| | - Christoph Welsch
- Klinik für Innere Medizin II, Gebäude 41Kirrberger Straße, Universität des Saarlandes, D-66421 Homburg/Saar, Germany
- Max Planck Institut für Informatik, Stuhlsatzenhausweg 85D-66123 Saarbrücken, Germany
| | - Luis Giron-Monzon
- Institut für Biochemie (FB 08), Justus-Liebig-Universität GiessenD-35392 Giessen, Germany
| | - Peter Friedhoff
- Institut für Biochemie (FB 08), Justus-Liebig-Universität GiessenD-35392 Giessen, Germany
| | - Mario Albrecht
- Max Planck Institut für Informatik, Stuhlsatzenhausweg 85D-66123 Saarbrücken, Germany
| | - Albrecht Piiper
- Klinik für Innere Medizin II, Gebäude 41Kirrberger Straße, Universität des Saarlandes, D-66421 Homburg/Saar, Germany
| | - Ricardo M. Biondi
- Klinik für Innere Medizin II, Gebäude 41Kirrberger Straße, Universität des Saarlandes, D-66421 Homburg/Saar, Germany
| | - Thomas Lengauer
- Max Planck Institut für Informatik, Stuhlsatzenhausweg 85D-66123 Saarbrücken, Germany
| | - Stefan Zeuzem
- Klinik für Innere Medizin II, Gebäude 41Kirrberger Straße, Universität des Saarlandes, D-66421 Homburg/Saar, Germany
| | - Jochen Raedle
- Klinik für Innere Medizin II, Gebäude 41Kirrberger Straße, Universität des Saarlandes, D-66421 Homburg/Saar, Germany
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11
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Manelyte L, Urbanke C, Giron-Monzon L, Friedhoff P. Structural and functional analysis of the MutS C-terminal tetramerization domain. Nucleic Acids Res 2006; 34:5270-9. [PMID: 17012287 PMCID: PMC1636413 DOI: 10.1093/nar/gkl489] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Escherichia coli DNA mismatch repair (MMR) protein MutS is essential for the correction of DNA replication errors. In vitro, MutS exists in a dimer/tetramer equilibrium that is converted into a monomer/dimer equilibrium upon deletion of the C-terminal 53 amino acids. In vivo and in vitro data have shown that this C-terminal domain (CTD, residues 801–853) is critical for tetramerization and the function of MutS in MMR and anti-recombination. We report the expression, purification and analysis of the E.coli MutS-CTD. Secondary structure prediction and circular dichroism suggest that the CTD is folded, with an α-helical content of 30%. Based on sedimentation equilibrium and velocity analyses, MutS-CTD forms a tetramer of asymmetric shape. A single point mutation (D835R) abolishes tetramerization but not dimerization of both MutS-CTD and full-length MutS. Interestingly, the in vivo and in vitro MMR activity of MutSCF/D835R is diminished to a similar extent as a truncated MutS variant (MutS800, residues 1–800), which lacks the CTD. Moreover, the dimer-forming MutSCF/D835R has comparable DNA binding affinity with the tetramer-forming MutS, but is impaired in mismatch-dependent activation of MutH. Our data support the hypothesis that tetramerization of MutS is important but not essential for MutS function in MMR.
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Affiliation(s)
| | - Claus Urbanke
- Medizinische Hochschule, StrukturanalyseCarl Neuberg Strasse 1, D-30625 Hannover, Germany
| | | | - Peter Friedhoff
- To whom correspondence should be addressed: Tel: +49 641 99 35407; Fax: +49 641 99 35409;
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12
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Ahrends R, Kosinski J, Kirsch D, Manelyte L, Giron-Monzon L, Hummerich L, Schulz O, Spengler B, Friedhoff P. Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry. Nucleic Acids Res 2006; 34:3169-80. [PMID: 16772401 PMCID: PMC1483222 DOI: 10.1093/nar/gkl407] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To investigate protein–protein interaction sites in the DNA mismatch repair system we developed a crosslinking/mass spectrometry technique employing a commercially available trifunctional crosslinker with a thiol-specific methanethiosulfonate group, a photoactivatable benzophenone moiety and a biotin affinity tag. The XACM approach combines photocrosslinking (X), in-solution digestion of the crosslinked mixtures, affinity purification via the biotin handle (A), chemical coding of the crosslinked products (C) followed by MALDI-TOF mass spectrometry (M). We illustrate the feasibility of the method using a single-cysteine variant of the homodimeric DNA mismatch repair protein MutL. Moreover, we successfully applied this method to identify the photocrosslink formed between the single-cysteine MutH variant A223C, labeled with the trifunctional crosslinker in the C-terminal helix and its activator protein MutL. The identified crosslinked MutL-peptide maps to a conserved surface patch of the MutL C-terminal dimerization domain. These observations are substantiated by additional mutational and chemical crosslinking studies. Our results shed light on the potential structures of the MutL holoenzyme and the MutH–MutL–DNA complex.
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Affiliation(s)
- Robert Ahrends
- Institut für Biochemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
- Institut für Chemie, Humboldt-Universität zu BerlinBrook-Taylor-Strasse 2, 12489 Berlin
| | - Jan Kosinski
- Institut für Biochemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology4 Ks. Trojdena, 02-109 Warsaw, Poland
| | - Dieter Kirsch
- Institut für Anorganische und Analytische Chemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
| | - Laura Manelyte
- Institut für Biochemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
| | - Luis Giron-Monzon
- Institut für Biochemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
| | - Lars Hummerich
- Institut für Biochemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
| | - Oliver Schulz
- Institut für Anorganische und Analytische Chemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
| | - Bernhard Spengler
- Institut für Anorganische und Analytische Chemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
| | - Peter Friedhoff
- Institut für Biochemie (FB 08), Justus-Liebig-UniversitätD-35392 Giessen, Germany
- To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
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Joseph N, Duppatla V, Rao DN. Prokaryotic DNA Mismatch Repair. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2006; 81:1-49. [PMID: 16891168 DOI: 10.1016/s0079-6603(06)81001-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nimesh Joseph
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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14
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Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W. MutH Complexed with Hemi- and Unmethylated DNAs: Coupling Base Recognition and DNA Cleavage. Mol Cell 2005; 20:155-66. [PMID: 16209953 DOI: 10.1016/j.molcel.2005.08.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 06/29/2005] [Accepted: 08/17/2005] [Indexed: 11/24/2022]
Abstract
MutH initiates mismatch repair by nicking the transiently unmethylated daughter strand 5' to a GATC sequence. Here, we report crystal structures of MutH complexed with hemimethylated and unmethylated GATC substrates. Both structures contain two Ca2+ ions jointly coordinated by a conserved aspartate and the scissile phosphate, as observed in the restriction endonucleases BamHI and BglI. In the hemimethylated complexes, the active site is more compact and DNA cleavage is more efficient. The Lys residue in the conserved DEK motif coordinates the nucleophilic water in conjunction with the phosphate 3' to the scissile bond; the same Lys is also hydrogen bonded with a carbonyl oxygen in the DNA binding module. We propose that this Lys, which is conserved in many restriction endonucleases and is replaced by Glu or Gln in BamHI and BglII, is a sensor for DNA binding and the linchpin that couples base recognition and DNA cleavage.
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Affiliation(s)
- Jae Young Lee
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P. Analysis of the quaternary structure of the MutL C-terminal domain. J Mol Biol 2005; 351:895-909. [PMID: 16024043 DOI: 10.1016/j.jmb.2005.06.044] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Revised: 06/14/2005] [Accepted: 06/17/2005] [Indexed: 11/29/2022]
Abstract
The dimeric DNA mismatch repair protein MutL has a key function in communicating mismatch recognition by MutS to downstream repair processes. Dimerization of MutL is mediated by the C-terminal domain, while activity of the protein is modulated by the ATP-dependent dimerization of the highly conserved N-terminal domain. Recently, a crystal structure analysis of the Escherichia coli MutL C-terminal dimerization domain has been reported and a model for the biological dimer was proposed. In this model, dimerization is mediated by the internal (In) subdomain comprising residues 475-569. Here, we report a computational analysis of all protein interfaces observed in the crystal structure and suggest that the biological dimer interface is formed by a hydrophobic surface patch of the external (Ex) subdomain (residues 432-474 and 570-615). Moreover, sequence analysis revealed that this surface patch is conserved among the MutL proteins. To test this hypothesis, single and double-cysteine variants of MutL were generated and tested for their ability to be cross-linked with chemical cross-linkers of various size. Finally, deletion of the C-terminal residues 605-615 abolished homodimerization. The biochemical data are fully compatible with a revised model for the biological dimer, which has important implications for understanding the heterodimerization of eukaryotic MutL homologues, modeling the MutL holoenzyme and predicting protein-protein interaction sites.
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Affiliation(s)
- Jan Kosinski
- Institut für Biochemie FB 08, Justus-Liebig Universität, Giessen D-35392, Germany
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16
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Joseph N, Sawarkar R, Rao DN. DNA mismatch correction in Haemophilus influenzae: characterization of MutL, MutH and their interaction. DNA Repair (Amst) 2004; 3:1561-77. [PMID: 15474418 DOI: 10.1016/j.dnarep.2004.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Indexed: 11/22/2022]
Abstract
Haemophilus influenzae DNA mismatch repair proteins, MutS, MutL and MutH, are functionally characterized in this study. Introduction of mutS, mutL and mutH genes of H. influenzae resulted in complementation of the mismatch repair activity of the respective mutant strains of Escherichia coli to varying levels. DNA binding studies using H. influenzae MutH have shown that the protein is capable of binding to any DNA sequence non-specifically in a co-operative and metal independent manner. Presence of MutL and ATP in the binding reaction resulted in the formation of a more specific complex, which indicates that MutH is conferred specificity for binding hemi-methylated DNA through structural alterations mediated by its interaction with MutL. To study the role of conserved amino acids Ile213 and Leu214 in the helix at the C-terminus of MutH, they were mutated to alanine. The mutant proteins showed considerably reduced DNA binding and nicking, as well as MutL-mediated activation. MutH failed to nick HU bound DNA whereas MboI and Sau3AI, which have the same recognition sequence as MutH, efficiently cleaved the substrate. MutS ATPase activity was found to be reduced two-fold in presence of covalently closed circular duplex containing a mismatched base pair whereas, the activity was regained upon linearization of the circular duplex. This observation possibly suggests that the MutS clamps are trapped in the closed DNA heteroduplex. These studies, therefore, serve as the basis for a detailed investigation of the structure-function relationship among the protein partners of the mismatch repair pathway of H. influenzae.
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Affiliation(s)
- Nimesh Joseph
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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17
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Giron-Monzon L, Manelyte L, Ahrends R, Kirsch D, Spengler B, Friedhoff P. Mapping protein-protein interactions between MutL and MutH by cross-linking. J Biol Chem 2004; 279:49338-45. [PMID: 15371440 DOI: 10.1074/jbc.m409307200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Strand discrimination in Escherichia coli DNA mismatch repair requires the activation of the endonuclease MutH by MutL. There is evidence that MutH binds to the N-terminal domain of MutL in an ATP-dependent manner; however, the interaction sites and the molecular mechanism of MutH activation have not yet been determined. We used a combination of site-directed mutagenesis and site-specific cross-linking to identify protein interaction sites between the proteins MutH and MutL. Unique cysteine residues were introduced in cysteine-free variants of MutH and MutL. The introduced cysteines were modified with the cross-linking reagent 4-maleimidobenzophenone. Photoactivation resulted in cross-links verified by mass spectrometry of some of the single cysteine variants to their respective Cys-free partner proteins. Moreover, we mapped the site of interaction by cross-linking different combinations of single cysteine MutH and MutL variants with thiol-specific homobifunctional cross-linkers of varying length. These results were used to model the MutH.MutL complex and to explain the ATP dependence of this interaction.
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Affiliation(s)
- Luis Giron-Monzon
- Institut für Biochemie (FB 08), Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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