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Wang Z, Wang H, Mulvenna N, Sanz-Hernandez M, Zhang P, Li Y, Ma J, Wang Y, Matthews S, Wigneshweraraj S, Liu B. A Bacteriophage DNA Mimic Protein Employs a Non-specific Strategy to Inhibit the Bacterial RNA Polymerase. Front Microbiol 2021; 12:692512. [PMID: 34149677 PMCID: PMC8208478 DOI: 10.3389/fmicb.2021.692512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 01/24/2023] Open
Abstract
DNA mimicry by proteins is a strategy that employed by some proteins to occupy the binding sites of the DNA-binding proteins and deny further access to these sites by DNA. Such proteins have been found in bacteriophage, eukaryotic virus, prokaryotic, and eukaryotic cells to imitate non-coding functions of DNA. Here, we report another phage protein Gp44 from bacteriophage SPO1 of Bacillus subtilis, employing mimicry as part of unusual strategy to inhibit host RNA polymerase. Consisting of three simple domains, Gp44 contains a DNA binding motif, a flexible DNA mimic domain and a random-coiled domain. Gp44 is able to anchor to host genome and interact bacterial RNA polymerase via the β and β' subunit, resulting in bacterial growth inhibition. Our findings represent a non-specific strategy that SPO1 phage uses to target different bacterial transcription machinery regardless of the structural variations of RNA polymerases. This feature may have potential applications like generation of genetic engineered phages with Gp44 gene incorporated used in phage therapy to target a range of bacterial hosts.
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Affiliation(s)
- Zhihao Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Hongliang Wang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, China
| | - Nancy Mulvenna
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Maximo Sanz-Hernandez
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Peipei Zhang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yanqing Li
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jia Ma
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Steve Matthews
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Sivaramesh Wigneshweraraj
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Instrument Analysis Centre of Xi’an Jiaotong University, Xi’an, China
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2
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Abstract
Bacteria and archaea use CRISPR-Cas adaptive immune systems to defend themselves from infection by bacteriophages (phages). These RNA-guided nucleases are powerful weapons in the fight against foreign DNA, such as phages and plasmids, as well as a revolutionary gene editing tool. Phages are not passive bystanders in their interactions with CRISPR-Cas systems, however; recent discoveries have described phage genes that inhibit CRISPR-Cas function. More than 20 protein families, previously of unknown function, have been ascribed anti-CRISPR function. Here, we discuss how these CRISPR-Cas inhibitors were discovered and their modes of action were elucidated. We also consider the potential impact of anti-CRISPRs on bacterial and phage evolution. Finally, we speculate about the future of this field.
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Affiliation(s)
- Adair L Borges
- Department of Microbiology and Immunology, University of California, San Francisco, California 94158;
| | - Alan R Davidson
- Department of Molecular Genetics and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, California 94158;
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3
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Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. J Bacteriol 2017; 199:JB.00245-17. [PMID: 28559295 PMCID: PMC5512222 DOI: 10.1128/jb.00245-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022] Open
Abstract
Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems.
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Yüksel D, Bianco PR, Kumar K. De novo design of protein mimics of B-DNA. MOLECULAR BIOSYSTEMS 2016; 12:169-77. [PMID: 26568416 PMCID: PMC4699573 DOI: 10.1039/c5mb00524h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural mimicry of DNA is utilized in nature as a strategy to evade molecular defences mounted by host organisms. One such example is the protein Ocr - the first translation product to be expressed as the bacteriophage T7 infects E. coli. The structure of Ocr reveals an intricate and deliberate arrangement of negative charges that endows it with the ability to mimic ∼24 base pair stretches of B-DNA. This uncanny resemblance to DNA enables Ocr to compete in binding the type I restriction modification (R/M) system, and neutralizes the threat of hydrolytic cleavage of viral genomic material. Here, we report the de novo design and biophysical characterization of DNA mimicking peptides, and describe the inhibitory action of the designed helical bundles on a type I R/M enzyme, EcoR124I. This work validates the use of charge patterning as a design principle for creation of protein mimics of DNA, and serves as a starting point for development of therapeutic peptide inhibitors against human pathogens that employ molecular camouflage as part of their invasion stratagem.
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Affiliation(s)
- Deniz Yüksel
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA.
| | - Piero R Bianco
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA.
| | - Krishna Kumar
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA. and Cancer Center, Tufts Medical Center, Boston, MA 02111, USA
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5
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Ruer S, Pinotsis N, Steadman D, Waksman G, Remaut H. Virulence-targeted Antibacterials: Concept, Promise, and Susceptibility to Resistance Mechanisms. Chem Biol Drug Des 2015; 86:379-99. [DOI: 10.1111/cbdd.12517] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/23/2014] [Accepted: 01/06/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Ségolène Ruer
- Structural and Molecular Microbiology; Structural Biology Research Center; VIB; Pleinlaan 2 Brussels 1050 Belgium
- Structural Biology Brussels; Vrije Universiteit Brussel; Pleinlaan 2 Brussels 1050 Belgium
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology (ISMB); UCL and Birkbeck College; London WC1E 7HX UK
| | - David Steadman
- Wolfson Institute for Biomedical Research (WIBR); UCL; London WC1E 6BT UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology (ISMB); UCL and Birkbeck College; London WC1E 7HX UK
| | - Han Remaut
- Structural and Molecular Microbiology; Structural Biology Research Center; VIB; Pleinlaan 2 Brussels 1050 Belgium
- Structural Biology Brussels; Vrije Universiteit Brussel; Pleinlaan 2 Brussels 1050 Belgium
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6
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Sugitani N, Chazin WJ. Characteristics and concepts of dynamic hub proteins in DNA processing machinery from studies of RPA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 117:206-211. [PMID: 25542993 DOI: 10.1016/j.pbiomolbio.2014.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
DNA replication, damage response and repair require the coordinated action of multi-domain proteins operating within dynamic multi-protein machines that act upon the DNA substrate. These modular proteins contain flexible linkers of various lengths, which enable changes in the spatial distribution of the globular domains (architecture) that harbor their essential biochemical functions. This mobile architecture is uniquely suited to follow the evolving substrate landscape present over the course of the specific process performed by the multi-protein machinery. A fundamental advance in understanding of protein machinery is the realization of the pervasive role of dynamics. Not only is the machine undergoing dynamic transformations, but the proteins themselves are flexible and constantly adapting to the progression through the steps of the overall process. Within this dynamic context the activity of the constituent proteins must be coordinated, a role typically played by hub proteins. A number of important characteristics of modular proteins and concepts about the operation of dynamic machinery have been discerned. These provide the underlying basis for the action of the machinery that reads DNA, and responds to and repairs DNA damage. Here, we introduce a number of key characteristics and concepts, including the modularity of the proteins, linkage of weak binding sites, direct competition between sites, and allostery, using the well recognized hub protein replication protein A (RPA).
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Affiliation(s)
- Norie Sugitani
- Center for Structural Biology and Departments of Biochemistry and Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Walter J Chazin
- Center for Structural Biology and Departments of Biochemistry and Chemistry, Vanderbilt University, Nashville, TN, USA.
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7
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Ho CH, Wang HC, Ko TP, Chang YC, Wang AHJ. The T4 phage DNA mimic protein Arn inhibits the DNA binding activity of the bacterial histone-like protein H-NS. J Biol Chem 2014; 289:27046-27054. [PMID: 25118281 DOI: 10.1074/jbc.m114.590851] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The T4 phage protein Arn (Anti restriction nuclease) was identified as an inhibitor of the restriction enzyme McrBC. However, until now its molecular mechanism remained unclear. In the present study we used structural approaches to investigate biological properties of Arn. A structural analysis of Arn revealed that its shape and negative charge distribution are similar to dsDNA, suggesting that this protein could act as a DNA mimic. In a subsequent proteomic analysis, we found that the bacterial histone-like protein H-NS interacts with Arn, implying a new function. An electrophoretic mobility shift assay showed that Arn prevents H-NS from binding to the Escherichia coli hns and T4 p8.1 promoters. In vitro gene expression and electron microscopy analyses also indicated that Arn counteracts the gene-silencing effect of H-NS on a reporter gene. Because McrBC and H-NS both participate in the host defense system, our findings suggest that T4 Arn might knock down these mechanisms using its DNA mimicking properties.
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Affiliation(s)
- Chun-Han Ho
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan,; Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Hao-Ching Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Core Facilities for Protein Structural Analysis, and Academia Sinica, Taipei 115, Taiwan
| | - Yuan-Chih Chang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan, and
| | - Andrew H-J Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan,; Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; Core Facilities for Protein Structural Analysis, and Academia Sinica, Taipei 115, Taiwan.
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8
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Mruk I, Kobayashi I. To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res 2013; 42:70-86. [PMID: 23945938 PMCID: PMC3874152 DOI: 10.1093/nar/gkt711] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
One of the simplest classes of genes involved in programmed death is that containing the toxin–antitoxin (TA) systems of prokaryotes. These systems are composed of an intracellular toxin and an antitoxin that neutralizes its effect. These systems, now classified into five types, were initially discovered because some of them allow the stable maintenance of mobile genetic elements in a microbial population through postsegregational killing or the death of cells that have lost these systems. Here, we demonstrate parallels between some TA systems and restriction–modification systems (RM systems). RM systems are composed of a restriction enzyme (toxin) and a modification enzyme (antitoxin) and limit the genetic flux between lineages with different epigenetic identities, as defined by sequence-specific DNA methylation. The similarities between these systems include their postsegregational killing and their effects on global gene expression. Both require the finely regulated expression of a toxin and antitoxin. The antitoxin (modification enzyme) or linked protein may act as a transcriptional regulator. A regulatory antisense RNA recently identified in an RM system can be compared with those RNAs in TA systems. This review is intended to generalize the concept of TA systems in studies of stress responses, programmed death, genetic conflict and epigenetics.
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Affiliation(s)
- Iwona Mruk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, Gdansk, 80-308, Poland, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
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9
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Bapteste E, Dupré J. Towards a processual microbial ontology. BIOLOGY & PHILOSOPHY 2013; 28:379-404. [PMID: 23487350 PMCID: PMC3591535 DOI: 10.1007/s10539-012-9350-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 10/17/2012] [Indexed: 05/26/2023]
Abstract
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely "processually equivalent" entities, "processually versatile" entities, and "stabilized" entities.
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Affiliation(s)
- Eric Bapteste
- />UMR CNRS 7138, Université Pierre et Marie Curie, 75005 Paris, France
| | - John Dupré
- />ESRC Centre for Genomics in Society (Egenis), University of Exeter, Exeter, UK
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10
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Abstract
Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. Here, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.
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Affiliation(s)
- Adi Stern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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11
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Merkel L, Hoesl MG, Albrecht M, Schmidt A, Budisa N. Blue Fluorescent Amino Acids as In Vivo Building Blocks for Proteins. Chembiochem 2010; 11:305-14. [DOI: 10.1002/cbic.200900651] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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Rajagopalan S, Andreeva A, Teufel DP, Freund SM, Fersht AR. Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics. J Biol Chem 2009; 284:21728-37. [PMID: 19525231 PMCID: PMC2755895 DOI: 10.1074/jbc.m109.006429] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/11/2009] [Indexed: 12/03/2022] Open
Abstract
The tumor suppressor p53 regulates cell cycle arrest and apoptosis by transactivating several genes that are critical for these processes. The transcriptional activity of p53 is often regulated by post-translational modifications and its interactions with various transcriptional coactivators. Here we report a physical interaction between the N-terminal transactivation domain (TAD) of p53 and the C-terminal DNA-binding domain of positive cofactor 4 (PC4(CTD)). Using NMR spectroscopy, we showed that residues 35-57 (TAD2) interact with PC4. (15)N,(1)H HSQC and fluorescence competition experiments indicated that TAD binds to the DNA-binding site of PC4. Hepta-phosphorylation of the TAD peptide increased its binding affinity. Computer modeling of the p53N-PC4 complex revealed several important interactions that are reminiscent of those in the single-stranded DNA-PC4 complex. The ubiquitous nature of the acidic transactivation domain of p53 in mediating interactions with several transcription cofactors is also manifested as a DNA mimetic.
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Affiliation(s)
| | - Antonina Andreeva
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
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13
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McMahon SA, Roberts GA, Johnson KA, Cooper LP, Liu H, White JH, Carter LG, Sanghvi B, Oke M, Walkinshaw MD, Blakely GW, Naismith JH, Dryden DTF. Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. Nucleic Acids Res 2009; 37:4887-97. [PMID: 19506028 PMCID: PMC2731889 DOI: 10.1093/nar/gkp478] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The ardA gene, found in many prokaryotes including important pathogenic species, allows associated mobile genetic elements to evade the ubiquitous Type I DNA restriction systems and thereby assist the spread of resistance genes in bacterial populations. As such, ardA contributes to a major healthcare problem. We have solved the structure of the ArdA protein from the conjugative transposon Tn916 and find that it has a novel extremely elongated curved cylindrical structure with defined helical grooves. The high density of aspartate and glutamate residues on the surface follow a helical pattern and the whole protein mimics a 42-base pair stretch of B-form DNA making ArdA by far the largest DNA mimic known. Each monomer of this dimeric structure comprises three alpha–beta domains, each with a different fold. These domains have the same fold as previously determined proteins possessing entirely different functions. This DNA mimicry explains how ArdA can bind and inhibit the Type I restriction enzymes and we demonstrate that 6 different ardA from pathogenic bacteria can function in Escherichia coli hosting a range of different Type I restriction systems.
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Affiliation(s)
- Stephen A McMahon
- Centre for Biomolecular Science, The University, St Andrews KY16 9ST, UK
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14
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Zavilgelsky GB, Rastorguev SM. Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes. Mol Biol 2009. [DOI: 10.1134/s0026893309020071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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A mutational analysis of DNA mimicry by ocr, the gene 0.3 antirestriction protein of bacteriophage T7. Biochem Biophys Res Commun 2008; 378:129-32. [PMID: 19013430 DOI: 10.1016/j.bbrc.2008.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 11/06/2008] [Indexed: 11/24/2022]
Abstract
The ocr protein of bacteriophage T7 is a structural and electrostatic mimic of approximately 24 base pairs of double-stranded B-form DNA. As such, it inhibits all Type I restriction and modification (R/M) enzymes by blocking their DNA binding grooves and inactivates them. This allows the infection of the bacterial cell by T7 to proceed unhindered by the action of the R/M defence system. We have mutated aspartate and glutamate residues on the surface of ocr to investigate their contribution to the tight binding between the EcoKI Type I R/M enzyme and ocr. Contrary to expectations, all of the single and double site mutations of ocr constructed were active as anti-R/M proteins in vivo and in vitro indicating that the mimicry of DNA by ocr is very resistant to change.
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16
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Zavilgelsky GB, Rastorguev SM. DNA mimicry by proteins as effective mechanism for regulation of activity of DNA-dependent enzymes. BIOCHEMISTRY (MOSCOW) 2007; 72:913-9, 4 p. following 982. [DOI: 10.1134/s0006297907090015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Lepthien S, Wiltschi B, Bolic B, Budisa N. In vivo engineering of proteins with nitrogen-containing tryptophan analogs. Appl Microbiol Biotechnol 2007; 73:740-54. [PMID: 17269153 DOI: 10.1007/s00253-006-0665-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recently, it has become possible to reprogram the protein synthesis machinery such that numerous noncanonical amino acids can be translated into target sequences yielding tailor-made proteins. The canonical amino acid tryptophan (Trp) encoded by a single nucleotide triplet (UGG) is a particularly interesting target for protein engineering and design. Trp-residues can be substituted with a variety of analogs and surrogates generated biosynthetically or by organic chemistry. Among them, nitrogen-containing tryptophan analogs occupy a central position, as they have distinct chemical properties in comparison with aliphatic amines and imines. They resemble purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. These special properties of the analogs can be directly transmitted into related protein structures via in vivo ribosome-mediated translation. Proteins expressed in this way are further endowed with unique properties like new spectral, altered redox and titration features or might serve as useful biomaterials. We present and discuss current works and future developments in protein engineering with nitrogen-containing tryptophan analogs and related compounds as well as their relevance for academic and applicative research.
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Affiliation(s)
- Sandra Lepthien
- Molecular Biotechnology, Max-Planck-Institut für Biochemie, BioFuture Independent Research Group, Am Klopferspitz 18, 82152 Martinsreid, Germany
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18
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Ghosh M, Meiss G, Pingoud A, London RE, Pedersen LC. The nuclease a-inhibitor complex is characterized by a novel metal ion bridge. J Biol Chem 2007; 282:5682-90. [PMID: 17138564 PMCID: PMC2072808 DOI: 10.1074/jbc.m605986200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nonspecific, extracellular nucleases have received enhanced attention recently as a consequence of the critical role that these enzymes can play in infectivity by overcoming the host neutrophil defense system. The activity of the cyanobacterial nuclease NucA, a member of the betabetaalpha Me superfamily, is controlled by the specific nuclease inhibitor, NuiA. Here we report the 2.3-A resolution crystal structure of the NucA-NuiA complex, showing that NucA inhibition by NuiA involves an unusual divalent metal ion bridge that connects the nuclease with its inhibitor. The C-terminal Thr-135(NuiA) hydroxyl oxygen is directly coordinated with the catalytic Mg(2+) of the nuclease active site, and Glu-24(NuiA) also extends into the active site, mimicking the charge of a scissile phosphate. NuiA residues Asp-75 and Trp-76 form a second interaction site, contributing to the strength and specificity of the interaction. The crystallographically defined interface is shown to be consistent with results of studies using site-directed NuiA mutants. This mode of inhibition differs dramatically from the exosite mechanism of inhibition seen with the DNase colicins E7/E9 and from other nuclease-inhibitor complexes that have been studied. The structure of this complex provides valuable insights for the development of inhibitors for related nonspecific nucleases that share the DRGH active site motif such as the Streptococcus pneumoniae nuclease EndA, which mediates infectivity of this pathogen, and mitochondrial EndoG, which is involved in recombination and apoptosis.
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Affiliation(s)
- Mahua Ghosh
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Gregor Meiss
- Institut für Biochemie (FB 08), Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392, Giessen, Germany
| | - Alfred Pingoud
- Institut für Biochemie (FB 08), Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392, Giessen, Germany
| | - Robert E. London
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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