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Ding WY, Li YH, Lian H, Ai XY, Zhao YL, Yang YB, Han Q, Liu X, Chen XY, He Z. Sub-Minimum Inhibitory Concentrations of Rhubarb Water Extracts Inhibit Streptococcus suis Biofilm Formation. Front Pharmacol 2017; 8:425. [PMID: 28736523 PMCID: PMC5500959 DOI: 10.3389/fphar.2017.00425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 06/14/2017] [Indexed: 12/28/2022] Open
Abstract
Streptococcus suis is one of the most important swine pathogens, which can cause persistent infection by forming biofilms. In this study, sub-minimum inhibitory concentration (sub-MIC) of rhubarb water extracts were found to inhibit biofilm formation. Two-component signal transduction systems (TCSs), transcriptional regulators, and DNA binding proteins were compared under two conditions: (1) cells treated with sub-MIC rhubarb water extracts and (2) untreated cells. Using an isobaric tags for relative and absolute quantitation (iTRAQ) strategy, we found that TCSs constituent proteins of histidine kinase and response regulator were significantly down-regulated. This down-regulation can affect the transfer of information during biofilm formation. The transcriptional regulators and DNA binding proteins that can interact with TCSs and interrupt gene transcription were also significantly altered. For these reasons, the levels of protein expressions varied in different parts of the treated vs. untreated cells. In summary, rhubarb water extracts might serve as potential inhibitor for the control of S. suis biofilm formation. The change in TCSs, transcriptional regulators, and DNA binding proteins may be important factors in S. suis biofilm inhibition.
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Affiliation(s)
- Wen-Ya Ding
- Department of Pharmacy, Shenyang Pharmaceutical UniversityShenyang, China.,Department of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yan-Hua Li
- Department of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - He Lian
- Department of Pharmacy, Shenyang Pharmaceutical UniversityShenyang, China
| | - Xiao-Yu Ai
- School of Pharmacy, Nankai UniversityTianjin, China
| | - Yu-Lin Zhao
- Department of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yan-Bei Yang
- Department of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Qiang Han
- Department of Pharmacy, Shenyang Pharmaceutical UniversityShenyang, China.,Department of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Xin Liu
- Department of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Xue-Ying Chen
- Department of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Zhonggui He
- Department of Pharmacy, Shenyang Pharmaceutical UniversityShenyang, China
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2
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Jensen IS, Inui K, Drakulic S, Jayaprakash S, Sander B, Golas MM. Expression of Flp Protein in a Baculovirus/Insect Cell System for Biotechnological Applications. Protein J 2017; 36:332-342. [PMID: 28660316 DOI: 10.1007/s10930-017-9724-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The Saccharomyces cerevisiae Flp protein is a site-specific recombinase that recognizes and binds to the Flp recognition target (FRT) site, a specific sequence comprised of at least two inverted repeats separated by a spacer. Binding of four monomers of Flp is required to mediate recombination between two FRT sites. Because of its site-specific cleavage characteristics, Flp has been established as a genome engineering tool. Amongst others, Flp is used to direct insertion of genes of interest into eukaryotic cells based on single and double FRT sites. A Flp-encoding plasmid is thereby typically cotransfected with an FRT-harboring donor plasmid. Moreover, Flp can be used to excise DNA sequences that are flanked by FRT sites. Therefore, the aim of this study was to determine whether Flp protein and its step-arrest mutant, FlpH305L, recombinantly expressed in insect cells, can be used for biotechnological applications. Using a baculovirus system, the proteins were expressed as C-terminally 3 × FLAG-tagged proteins and were purified by anti-FLAG affinity selection. As demonstrated by electrophoretic mobility shift assays (EMSAs), purified Flp and FlpH305L bind to FRT-containing DNA. Furthermore, using a cell assay, purified Flp was shown to be active in recombination and to mediate efficient insertion of a donor plasmid into the genome of target cells. Thus, these proteins can be used for applications such as DNA-binding assays, in vitro recombination, or genome engineering.
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Affiliation(s)
- Ida S Jensen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Ken Inui
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Srdja Drakulic
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Sakthidasan Jayaprakash
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Bjoern Sander
- Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Monika M Golas
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark.
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3
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Characterization of the ATP-Dependent Lon-Like Protease in Methanobrevibacter smithii. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:5759765. [PMID: 27239160 PMCID: PMC4864567 DOI: 10.1155/2016/5759765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/22/2016] [Accepted: 03/28/2016] [Indexed: 11/17/2022]
Abstract
The Lon protease is highly evolutionarily conserved. However, little is known about Lon in the context of gut microbial communities. A gene encoding a Lon-like protease (Lon-like-Ms) was identified and characterized from Methanobrevibacter smithii, the predominant archaeon in the human gut ecosystem. Phylogenetic and sequence analyses showed that Lon-like-Ms and its homologs are newly identified members of the Lon family. A recombinant form of the enzyme was purified by affinity chromatography, and its catalytic properties were examined. Recombinant Lon-like-Ms exhibited ATPase activity and cleavage activity toward fluorogenic peptides and casein. The peptidase activity of Lon-like-Ms relied strictly on Mg(2+) (or other divalent cations) and ATP. These results highlight a new type of Lon-like protease that differs from its bacterial counterpart.
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4
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Abstract
Tyrosine site-specific recombinases (YRs) are widely distributed among prokaryotes and their viruses, and were thought to be confined to the budding yeast lineage among eukaryotes. However, YR-harboring retrotransposons (the DIRS and PAT families) and DNA transposons (Cryptons) have been identified in a variety of eukaryotes. The YRs utilize a common chemical mechanism, analogous to that of type IB topoisomerases, to bring about a plethora of genetic rearrangements with important physiological consequences in their respective biological contexts. A subset of the tyrosine recombinases has provided model systems for analyzing the chemical mechanisms and conformational features of the recombination reaction using chemical, biochemical, topological, structural, and single molecule-biophysical approaches. YRs with simple reaction requirements have been utilized to bring about programmed DNA rearrangements for addressing fundamental questions in developmental biology. They have also been employed to trace the topological features of DNA within high-order DNA interactions established by protein machines. The directed evolution of altered specificity YRs, combined with their spatially and temporally regulated expression, heralds their emergence as vital tools in genome engineering projects with wide-ranging biotechnological and medical applications.
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5
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Abstract
Covalently closed hairpin ends, also known as hairpin telomeres, provide an unusual solution to the end replication problem. The hairpin telomeres are generated from replication intermediates by a process known as telomere resolution. This is a DNA breakage and reunion reaction promoted by hairpin telomere resolvases (also referred to as protelomerases) found in a limited number of phage and bacteria. The reaction promoted by these enzymes is a chemically isoenergetic two-step transesterification without a requirement for divalent metal ions or high-energy cofactors and uses an active site and mechanism similar to that for type IB topoisomerases and tyrosine recombinases. The small number of unrelated telomere resolvases characterized to date all contain a central, catalytic core domain with the active site, but in addition carry variable C- and N-terminal domains with different functions. Similarities and differences in the structure and function of the telomere resolvases are discussed. Of particular interest are the properties of the Borrelia telomere resolvases, which have been studied most extensively at the biochemical level and appear to play a role in shaping the unusual segmented genomes in these organisms and, perhaps, to play a role in recombinational events.
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The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells. Microbiol Spectr 2016; 2. [PMID: 25541598 DOI: 10.1128/microbiolspec.plas-0003-2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The multi-copy 2 micron plasmid of Saccharomyces cerevisiae, a resident of the nucleus, is remarkable for its high chromosome-like stability. The plasmid does not appear to contribute to the fitness of the host, nor does it impose a significant metabolic burden on the host at its steady state copy number. The plasmid may be viewed as a highly optimized selfish DNA element whose genome design is devoted entirely towards efficient replication, equal segregation and copy number maintenance. A partitioning system comprised of two plasmid coded proteins, Rep1 and Rep2, and a partitioning locus STB is responsible for equal or nearly equal segregation of plasmid molecules to mother and daughter cells. Current evidence supports a model in which the Rep-STB system promotes the physical association of the plasmid with chromosomes and thus plasmid segregation by a hitchhiking mechanism. The Flp site-specific recombination system housed by the plasmid plays a critical role in maintaining steady state plasmid copy number. A decrease in plasmid population due to rare missegregation events is rectified by plasmid amplification via a recombination induced rolling circle replication mechanism. Appropriate plasmid amplification, without runaway increase in copy number, is ensured by positive and negative regulation of FLP gene expression by plasmid coded proteins and by the control of Flp level/activity through host mediated post-translational modification(s) of Flp. The Flp system has been successfully utilized to understand mechanisms of site-specific recombination, to bring about directed genetic alterations for addressing fundamental problems in biology, and as a tool in biotechnological applications.
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7
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Rowley PA, Kachroo AH, Ma CH, Maciaszek AD, Guga P, Jayaram M. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination. Nucleic Acids Res 2015; 43:6023-37. [PMID: 25999343 PMCID: PMC4499138 DOI: 10.1093/nar/gkv513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/21/2015] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Abstract
Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.
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Affiliation(s)
- Paul A Rowley
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Aashiq H Kachroo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Anna D Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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8
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Fan HF, Cheng YS, Ma CH, Jayaram M. Single molecule TPM analysis of the catalytic pentad mutants of Cre and Flp site-specific recombinases: contributions of the pentad residues to the pre-chemical steps of recombination. Nucleic Acids Res 2015; 43:3237-55. [PMID: 25765648 PMCID: PMC4381057 DOI: 10.1093/nar/gkv114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/03/2015] [Indexed: 12/18/2022] Open
Abstract
Cre and Flp site-specific recombinase variants harboring point mutations at their conserved catalytic pentad positions were characterized using single molecule tethered particle motion (TPM) analysis. The findings reveal contributions of these amino acids to the pre-chemical steps of recombination. They suggest functional differences between positionally conserved residues in how they influence recombinase-target site association and formation of ‘non-productive’, ‘pre-synaptic’ and ‘synaptic’ complexes. The most striking difference between the two systems is noted for the single conserved lysine. The pentad residues in Cre enhance commitment to recombination by kinetically favoring the formation of pre-synaptic complexes. These residues in Flp serve a similar function by promoting Flp binding to target sites, reducing non-productive binding and/or enhancing the rate of assembly of synaptic complexes. Kinetic comparisons between Cre and Flp, and between their derivatives lacking the tyrosine nucleophile, are consistent with a stronger commitment to recombination in the Flp system. The effect of target site orientation (head-to-head or head-to-tail) on the TPM behavior of synapsed DNA molecules supports the selection of anti-parallel target site alignment prior to the chemical steps. The integrity of the synapse, whose establishment/stability is fostered by strand cleavage in the case of Flp but not Cre, appears to be compromised by the pentad mutations.
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Affiliation(s)
- Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei 112, Taiwan
| | - Yong-Song Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei 112, Taiwan
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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9
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Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. J Biol Chem 2013; 288:29206-14. [PMID: 23970547 DOI: 10.1074/jbc.m113.508028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the serine family of site-specific DNA recombinases use an unusual constellation of amino acids to catalyze the formation and resolution of a covalent protein-DNA intermediate. A recent high resolution structure of the catalytic domain of Sin, a particularly well characterized family member, provided a detailed view of the catalytic site. To determine how the enzyme might protonate and stabilize the 3'O leaving group in the strand cleavage reaction, we examined how replacing this oxygen with a sulfur affected the cleavage rate by WT and mutant enzymes. To facilitate direct comparison of the cleavage rates, key experiments used suicide substrates that prevented religation after cleavage. The catalytic defect associated with mutation of one of six highly conserved arginine residues, Arg-69 in Sin, was partially rescued by a 3' phosphorothiolate substrate. We conclude that Arg-69 has an important role in stabilizing the 3'O leaving group and is the prime candidate for the general acid that protonates the 3'O, in good agreement with the position it occupies in the high resolution structure of the active site of Sin.
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10
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Abstract
The processes of DNA topoisomerization and site-specific recombination are fundamentally similar: DNA cleavage by forming a phospho-protein covalent linkage, DNA topological rearrangement, and DNA ligation coupled with protein regeneration. Type IB DNA topoisomerases are structurally and mechanistically homologous to tyrosine recombinases. Both enzymes nick DNA double helices independent of metal ions, form 3'-phosphotyrosine intermediates, and rearrange the free 5' ends relative to the uncut strands by swiveling. In contrast, serine recombinases generate 5'-phospho-serine intermediates. A 180° relative rotation of the two halves of a 100 kDa terameric serine recombinase and DNA complex has been proposed as the mechanism of strand exchange. Here I propose an alternative mechanism. Interestingly, the catalytic domain of serine recombinases has structural similarity to the TOPRIM domain, conserved among all Type IA and Type II topoisomerases and responsible for metal binding and DNA cleavage. TOPRIM topoisomerases also cleave DNA to generate 5'-phosphate and 3'-OH groups. Based on the existing biochemical data and crystal structures of topoisomerase II and serine recombinases bound to pre- and post-cleavage DNA, I suggest a strand passage mechanism for DNA recombination by serine recombinases. This mechanism is reminiscent of DNA topoisomerization and does not require subunit rotation.
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Affiliation(s)
- Wei Yang
- 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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11
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Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C. Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J Biol Chem 2010; 285:35675-84. [PMID: 20826810 PMCID: PMC2975192 DOI: 10.1074/jbc.m110.131037] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 09/03/2010] [Indexed: 11/06/2022] Open
Abstract
Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-Å resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-β-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and β-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within β-N-acetylglucosaminidases but otherwise absent in β-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 β-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of β-lactamase.
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Affiliation(s)
| | - Stefanie Fischer
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Patrick Polzer
- the Max-Planck-Institute of Quantum Optics, 85748 Garching, Germany
| | - Kay Diederichs
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Wolfram Welte
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
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12
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Mouw KW, Steiner AM, Ghirlando R, Li NS, Rowland SJ, Boocock MR, Stark WM, Piccirilli JA, Rice PA. Sin resolvase catalytic activity and oligomerization state are tightly coupled. J Mol Biol 2010; 404:16-33. [PMID: 20868695 DOI: 10.1016/j.jmb.2010.08.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 08/18/2010] [Accepted: 08/30/2010] [Indexed: 11/18/2022]
Abstract
Serine recombinases promote specific DNA rearrangements by a cut-and-paste mechanism that involves cleavage of all four DNA strands at two sites recognized by the enzyme. Dissecting the order and timing of these cleavage events and the steps leading up to them is difficult because the cleavage reaction is readily reversible. Here, we describe assays using activated Sin mutants and a DNA substrate with a 3'-bridging phosphorothiolate modification that renders Sin-mediated DNA cleavage irreversible. We find that activating Sin mutations promote DNA cleavage rather than simply stabilize the cleavage product. Cleavage events at the scissile phosphates on complementary strands of the duplex are tightly coupled, and the overall DNA cleavage rate is strongly dependent on Sin concentration. When combined with analytical ultracentrifugation data, these results suggest that Sin catalytic activity and oligomerization state are tightly linked, and that activating mutations promote formation of a cleavage-competent oligomeric state that is normally formed only transiently within the full synaptic complex.
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Affiliation(s)
- Kent W Mouw
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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13
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Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD. Requirements for catalysis in the Cre recombinase active site. Nucleic Acids Res 2010; 38:5817-32. [PMID: 20462863 PMCID: PMC2943603 DOI: 10.1093/nar/gkq384] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Members of the tyrosine recombinase (YR) family of site-specific recombinases catalyze DNA rearrangements using phosphoryl transfer chemistry that is identical to that used by the type IB topoisomerases (TopIBs). To better understand the requirements for YR catalysis and the relationship between the YRs and the TopIBs, we have analyzed the in vivo and in vitro recombination activities of all substitutions of the seven active site residues in Cre recombinase. We have also determined the structure of a vanadate transition state mimic for the Cre-loxP reaction that facilitates interpretation of mutant activities and allows for a comparison with similar structures from the related topoisomerases. We find that active site residues shared by the TopIBs are most sensitive to substitution. Only two, the tyrosine nucleophile and a conserved lysine residue that activates the 5'-hydroxyl leaving group, are strictly required to achieve >5% of wild-type activity. The two conserved arginine residues each tolerate one substitution that results in modest recombination activity and the remaining three active site positions can be substituted with several alternative amino acids while retaining a significant amount of activity. The results are discussed in the context of YR and TopIB structural models and data from related YR systems.
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Affiliation(s)
- Bryan Gibb
- Department of Biochemistry and Biophysics and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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14
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Vanhooff V, Normand C, Galloy C, Segall AM, Hallet B. Control of directionality in the DNA strand-exchange reaction catalysed by the tyrosine recombinase TnpI. Nucleic Acids Res 2009; 38:2044-56. [PMID: 20044348 PMCID: PMC2847244 DOI: 10.1093/nar/gkp1187] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In DNA site-specific recombination catalysed by tyrosine recombinases, two pairs of DNA strands are sequentially exchanged between separate duplexes and the mechanisms that confer directionality to this theoretically reversible reaction remain unclear. The tyrosine recombinase TnpI acts at the internal resolution site (IRS) of the transposon Tn4430 to resolve intermolecular transposition products. Recombination is catalysed at the IRS core sites (IR1–IR2) and is regulated by adjacent TnpI-binding motifs (DR1 and DR2). These are dispensable accessory sequences that confer resolution selectivity to the reaction by stimulating synapsis between directly repeated IRSs. Here, we show that formation of the DR1–DR2-containing synapse imposes a specific order of activation of the TnpI catalytic subunits in the complex so that the IR1-bound subunits catalyse the first strand exchange and the IR2-bound subunits the second strand exchange. This ordered pathway was demonstrated for a complete recombination reaction using a TnpI catalytic mutant (TnpI-H234L) partially defective in DNA rejoining. The presence of the DR1- and DR2-bound TnpI subunits was also found to stabilize transient recombination intermediates, further displacing the reaction equilibrium towards product formation. Implication of TnpI/IRS accessory elements in the initial architecture of the synapse and subsequent conformational changes taking place during strand exchange is discussed.
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Affiliation(s)
- Virginie Vanhooff
- Unité de Génétique, Institut des Sciences de la Vie, UCLouvain, 5/6 Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
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15
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Chan PHW, Lairson LL, Lee HJ, Wakarchuk WW, Strynadka NCJ, Withers SG, McIntosh LP. NMR Spectroscopic Characterization of the Sialyltransferase CstII from Campylobacter jejuni: Histidine 188 Is the General Base. Biochemistry 2009; 48:11220-30. [DOI: 10.1021/bi901606n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick H. W. Chan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Luke L. Lairson
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1 Canada
| | - Ho Jun Lee
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Warren W. Wakarchuk
- Institute for Biological Sciences, National Research Council Canada, Ottawa, ON, K1A 0R6 Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Stephen G. Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1 Canada
| | - Lawrence P. McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1 Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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16
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Active site electrostatics protect genome integrity by blocking abortive hydrolysis during DNA recombination. EMBO J 2009; 28:1745-56. [PMID: 19440204 DOI: 10.1038/emboj.2009.131] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 04/21/2009] [Indexed: 11/08/2022] Open
Abstract
Water, acting as a rogue nucleophile, can disrupt transesterification steps of important phosphoryl transfer reactions in DNA and RNA. We have unveiled this risk, and identified safeguards instituted against it, during strand cleavage and joining by the tyrosine site-specific recombinase Flp. Strand joining is threatened by a latent Flp endonuclease activity (type I) towards the 3'-phosphotyrosyl intermediate resulting from strand cleavage. This risk is not alleviated by phosphate electrostatics; neutralizing the negative charge on the scissile phosphate through methylphosphonate (MeP) substitution does not stimulate type I endonuclease. Rather, protection derives from the architecture of the recombination synapse and conformational dynamics within it. Strand cleavage is protected against water by active site electrostatics. Replacement of the catalytic Arg-308 of Flp by alanine, along with MeP substitution, elicits a second Flp endonuclease activity (type II) that directly targets the scissile phosphodiester bond in DNA. MeP substitution, combined with appropriate active site mutations, will be useful in revealing anti-hydrolytic mechanisms engendered by systems that mediate DNA relaxation, DNA transposition, site-specific recombination, telomere resolution, RNA splicing and retrohoming of mobile introns.
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Aihara H, Huang WM, Ellenberger T. An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres. Mol Cell 2007; 27:901-13. [PMID: 17889664 PMCID: PMC2041798 DOI: 10.1016/j.molcel.2007.07.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 06/11/2007] [Accepted: 07/25/2007] [Indexed: 12/27/2022]
Abstract
The termini of linear chromosomes are protected by specialized DNA structures known as telomeres that also facilitate the complete replication of DNA ends. The simplest type of telomere is a covalently closed DNA hairpin structure found in linear chromosomes of prokaryotes and viruses. Bidirectional replication of a chromosome with hairpin telomeres produces a catenated circular dimer that is subsequently resolved into unit-length chromosomes by a dedicated DNA cleavage-rejoining enzyme known as a hairpin telomere resolvase (protelomerase). Here we report a crystal structure of the protelomerase TelK from Klebsiella oxytoca phage varphiKO2, in complex with the palindromic target DNA. The structure shows the TelK dimer destabilizes base pairing interactions to promote the refolding of cleaved DNA ends into two hairpin ends. We propose that the hairpinning reaction is made effectively irreversible by a unique protein-induced distortion of the DNA substrate that prevents religation of the cleaved DNA substrate.
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Affiliation(s)
- Hideki Aihara
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8231, St. Louis, MO 63110
| | - Wai Mun Huang
- Department of Pathology, EEJ Medical Research Building, Room 5200B 15 N. Medical Dr. East, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8231, St. Louis, MO 63110
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Zalatan JG, Catrina I, Mitchell R, Grzyska PK, O’Brien PJ, Herschlag D, Hengge AC. Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis. J Am Chem Soc 2007; 129:9789-98. [PMID: 17630738 PMCID: PMC3171187 DOI: 10.1021/ja072196+] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested to proceed through transition states that are altered from their solution counterparts, with the alterations presumably arising from interactions with active-site functional groups. In particular, the phosphate monoester hydrolysis reaction catalyzed by Escherichia coli alkaline phosphatase (AP) has been the subject of intensive scrutiny. Recent linear free energy relationship (LFER) studies suggest that AP catalyzes phosphate monoester hydrolysis through a loose transition state, similar to that in solution. To gain further insight into the nature of the transition state and active-site interactions, we have determined kinetic isotope effects (KIEs) for AP-catalyzed hydrolysis reactions with several phosphate monoester substrates. The LFER and KIE data together provide a consistent picture for the nature of the transition state for AP-catalyzed phosphate monoester hydrolysis and support previous models suggesting that the enzymatic transition state is similar to that in solution. Moreover, the KIE data provides unique information regarding specific interactions between the transition state and the active-site Zn2+ ions. These results provide strong support for a model in which electrostatic interactions between the bimetallo Zn2+ site and a nonbridging phosphate ester oxygen atom make a significant contribution to the large rate enhancement observed for AP-catalyzed phosphate monoester hydrolysis.
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