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Bell RT, Sahakyan H, Makarova KS, Wolf YI, Koonin EV. CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA. eLife 2024; 13:RP94800. [PMID: 38739430 PMCID: PMC11090510 DOI: 10.7554/elife.94800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with three distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.
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Affiliation(s)
- Ryan T Bell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Harutyun Sahakyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
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2
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Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins. Proc Natl Acad Sci U S A 2022; 119:2116278119. [PMID: 35193978 PMCID: PMC8892312 DOI: 10.1073/pnas.2116278119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
Abstract
Histone-like protein from Escherichia coli strain U93 (HU) protein is the most abundant nucleoid-associated protein in bacteria, which plays a fundamental role in chromosomal compaction and organization. It is essential for most bacteria as well as Apicomplexans, thus an important target for the development of antimicrobial and antimalaria drugs. We report Gp46 as a phage protein HU inhibitor. It inhibits HU of Bacillus subtilis by occupying its DNA binding site, thus preventing chromosome segregation during cell division. As key residues for the interaction are highly conserved, Gp46 interacts with HUs of a broad range of pathogens, including many pathogenic bacteria and Apicomplexan parasites like Plasmodium falciparum. Thus, this cross-species property could benefit antibiotic and antimalaria drug development that targets HU. The architectural protein histone-like protein from Escherichia coli strain U93 (HU) is the most abundant bacterial DNA binding protein and highly conserved among bacteria and Apicomplexan parasites. It not only binds to double-stranded DNA (dsDNA) to maintain DNA stability but also, interacts with RNAs to regulate transcription and translation. Importantly, HU is essential to cell viability for many bacteria; hence, it is an important antibiotic target. Here, we report that Gp46 from bacteriophage SPO1 of Bacillus subtilis is an HU inhibitor whose expression prevents nucleoid segregation and causes filamentous morphology and growth defects in bacteria. We determined the solution structure of Gp46 and revealed a striking negatively charged surface. An NMR-derived structural model for the Gp46–HU complex shows that Gp46 occupies the DNA binding motif of the HU and therefore, occludes DNA binding, revealing a distinct strategy for HU inhibition. We identified the key residues responsible for the interaction that are conserved among HUs of bacteria and Apicomplexans, including clinically significant Mycobacterium tuberculosis, Acinetobacter baumannii, and Plasmodium falciparum, and confirm that Gp46 can also interact with these HUs. Our findings provide detailed insight into a mode of HU inhibition that provides a useful foundation for the development of antibacteria and antimalaria drugs.
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3
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Dennehy R, Duggan N, Dignam S, McCormack S, Dillon E, Molony J, Romano M, Hou Y, Ardill L, Whelan MVX, Drulis‐Kawa Z, Ó'Cróinín T, Valvano MA, Berisio R, McClean S. Protein with negative surface charge distribution, Bnr1, shows characteristics of a DNA-mimic protein and may be involved in the adaptation of Burkholderia cenocepacia. Microbiologyopen 2022; 11:e1264. [PMID: 35212475 PMCID: PMC9060813 DOI: 10.1002/mbo3.1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/14/2022] [Indexed: 11/11/2022] Open
Abstract
Adaptation of opportunistic pathogens to their host environment requires reprogramming of a vast array of genes to facilitate survival in the host. Burkholderia cenocepacia, a Gram-negative bacterium with a large genome of ∼8 Mb that colonizes environmental niches, is exquisitely adaptable to the hypoxic environment of the cystic fibrosis lung and survives in macrophages. We previously identified an immunoreactive acidic protein encoded on replicon 3, BCAS0292. Deletion of the BCAS0292 gene significantly altered the abundance of 979 proteins by 1.5-fold or more; 19 proteins became undetectable while 545 proteins showed ≥1.5-fold reduced abundance, suggesting the BCAS0292 protein is a global regulator. Moreover, the ∆BCAS0292 mutant showed a range of pleiotropic effects: virulence and host-cell attachment were reduced, antibiotic susceptibility was altered, and biofilm formation enhanced. Its growth and survival were impaired in 6% oxygen. In silico prediction of its three-dimensional structure revealed BCAS0292 presents a dimeric β-structure with a negative surface charge. The ΔBCAS0292 mutant displayed altered DNA supercoiling, implicated in global regulation of gene expression. Three proteins were identified in pull-downs with FLAG-tagged BCAS0292, including the Histone H1-like protein, HctB, which is recognized as a global transcriptional regulator. We propose that BCAS0292 protein, which we have named Burkholderia negatively surface-charged regulatory protein 1 (Bnr1), acts as a DNA-mimic and binds to DNA-binding proteins, altering DNA topology and regulating the expression of multiple genes, thereby enabling the adaptation of B. cenocepacia to highly diverse environments.
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Affiliation(s)
- Ruth Dennehy
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Niamh Duggan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Simon Dignam
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Sarah McCormack
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Eugene Dillon
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Jessica Molony
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Maria Romano
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Yueran Hou
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Laura Ardill
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Matthew V. X. Whelan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and MicrobiologyUniversity of WroclawWroclawPoland
| | - Tadhg Ó'Cróinín
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Miguel A. Valvano
- School of Medicine, Dentistry and Biomedical Sciences, Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
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4
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Liao YT, Lin SS, Lin SJ, Sun WT, Shen BN, Cheng HP, Lin CP, Ko TP, Chen YF, Wang HC. Structural insights into the interaction between phytoplasmal effector causing phyllody 1 and MADS transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:706-719. [PMID: 31323156 DOI: 10.1111/tpj.14463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/24/2019] [Accepted: 07/02/2019] [Indexed: 05/21/2023]
Abstract
Phytoplasmas are bacterial plant pathogens which can induce severe symptoms including dwarfism, phyllody and virescence in an infected plant. Because phytoplasmas infect many important crops such as peanut and papaya they have caused serious agricultural losses. The phytoplasmal effector causing phyllody 1 (PHYL1) is an important phytoplasmal pathogenic factor which affects the biological function of MADS transcription factors by interacting with their K (keratin-like) domain, thus resulting in abnormal plant developments such as phyllody. Until now, lack of information on the structure of PHYL1 has prevented a detailed understanding of the binding mechanism between PHYL1 and the MADS transcription factors. Here, we present the crystal structure of PHYL1 from peanut witches'-broom phytoplasma (PHYL1PnWB ). This protein was found to fold into a unique α-helical hairpin with exposed hydrophobic residues on its surface that may play an important role in its biological function. Using proteomics approaches, we propose a binding mode of PHYL1PnWB with the K domain of the MADS transcription factor SEPALLATA3 (SEP3_K) and identify the residues of PHYL1PnWB that are important for this interaction. Furthermore, using surface plasmon resonance we measure the binding strength of PHYL1PnWB proteins to SEP3_K. Lastly, based on confocal images, we found that α-helix 2 of PHYL1PnWB plays an important role in PHYL1-mediated degradation of SEP3. Taken together, these results provide a structural understanding of the specific binding mechanism between PHYL1PnWB and SEP3_K.
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Affiliation(s)
- Yi-Ting Liao
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
- Center of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
| | - Shin-Jen Lin
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wan-Ting Sun
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Bing-Nan Shen
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Han-Pin Cheng
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Chan-Pin Lin
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Fan Chen
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Hao-Ching Wang
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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5
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Wang H, Chou C, Hsu K, Lee C, Wang AH. New paradigm of functional regulation by DNA mimic proteins: Recent updates. IUBMB Life 2018; 71:539-548. [DOI: 10.1002/iub.1992] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Hao‐Ching Wang
- Graduate Institute of Translational MedicineCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
| | - Chia‐Cheng Chou
- National Center for High‐performance ComputingNational Applied Research Laboratories Hsinchu 300 Taiwan
| | - Kai‐Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
| | - Chi‐Hua Lee
- Institute of Biological Chemistry, Academia Sinica Taipei 115 Taiwan
| | - Andrew H.‐J. Wang
- Graduate Institute of Translational MedicineCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
- Institute of Biological Chemistry, Academia Sinica Taipei 115 Taiwan
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6
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Huang MF, Lin SJ, Ko TP, Liao YT, Hsu KC, Wang HC. The monomeric form of Neisseria DNA mimic protein DMP19 prevents DNA from binding to the histone-like HU protein. PLoS One 2017; 12:e0189461. [PMID: 29220372 PMCID: PMC5722371 DOI: 10.1371/journal.pone.0189461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/28/2017] [Indexed: 12/12/2022] Open
Abstract
DNA mimicry is a direct and effective strategy by which the mimic competes with DNA for the DNA binding sites on other proteins. Until now, only about a dozen proteins have been shown to function via this strategy, including the DNA mimic protein DMP19 from Neisseria meningitides. We have shown previously that DMP19 dimer prevents the operator DNA from binding to the transcription factor NHTF. Here, we provide new evidence that DMP19 monomer can also interact with the Neisseria nucleoid-associated protein HU. Using BS3 crosslinking, gel filtration and isothermal titration calorimetry assays, we found that DMP19 uses its monomeric form to interact with the Neisseria HU dimer. Crosslinking conjugated mass spectrometry was used to investigate the binding mode of DMP19 monomer and HU dimer. Finally, an electrophoretic mobility shift assay (EMSA) confirmed that the DNA binding affinity of HU is affected by DMP19. These results showed that DMP19 is bifunctional in the gene regulation of Neisseria through its variable oligomeric forms.
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Affiliation(s)
- Ming-Fen Huang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Shin-Jen Lin
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Ting Liao
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Hao-Ching Wang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- * E-mail:
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7
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Chou CC, Wang AHJ. Structural D/E-rich repeats play multiple roles especially in gene regulation through DNA/RNA mimicry. MOLECULAR BIOSYSTEMS 2016; 11:2144-51. [PMID: 26088262 DOI: 10.1039/c5mb00206k] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aspartic acid and glutamic acid repeats in proteins exhibit strong negative charge distribution and they may play special biological roles. From 39,684 unique structural data in the RCSB Protein Data Bank (PDB), 173 structures were found to contain ordered D/E-rich repeat structures, and 57 of them were related to DNA/RNA functions. The frequency of occurrence of glutamic acid (36.90%) was higher than that of aspartic acid (27.02%). Glycine (2.38%), alanine (2.68%), valine (3.54%), leucine (5.57%), and isoleucine (3.34%), but not methionine (0.91%), were the most abundant hydrophobic residues. The available complex structures suggested that D/E-rich proteins might be involved in DNA mimicry, mRNA processing and regulation of the transcription complex. The region surrounding the D/E-rich repeat sequences plays important roles in the binding specificity toward the target proteins. The numbers and composition of aspartic acid and glutamic acid might also affect binding properties. Aspartic acid and glutamic acid are disorder-promoting residues in the intrinsically disorder proteins. Our findings suggest that the D/E-rich repeats are unique components of intrinsically disordered proteins, which are involved in the gene regulation and could serve as potential druggable fragments or drug targets.
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Affiliation(s)
- Chia-Cheng Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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8
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Wang HC, Ho CH, Chou CC, Ko TP, Huang MF, Hsu KC, Wang AHJ. Using structural-based protein engineering to modulate the differential inhibition effects of SAUGI on human and HSV uracil DNA glycosylase. Nucleic Acids Res 2016; 44:4440-9. [PMID: 26980279 PMCID: PMC4872100 DOI: 10.1093/nar/gkw185] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/09/2016] [Indexed: 02/06/2023] Open
Abstract
Uracil-DNA glycosylases (UDGs) are highly conserved proteins that can be found in a wide range of organisms, and are involved in the DNA repair and host defense systems. UDG activity is controlled by various cellular factors, including the uracil-DNA glycosylase inhibitors, which are DNA mimic proteins that prevent the DNA binding sites of UDGs from interacting with their DNA substrate. To date, only three uracil-DNA glycosylase inhibitors, phage UGI, p56, and Staphylococcus aureus SAUGI, have been determined. We show here that SAUGI has differential inhibitory effects on UDGs from human, bacteria, Herpes simplex virus (HSV; human herpesvirus 1) and Epstein-Barr virus (EBV; human herpesvirus 4). Newly determined crystal structures of SAUGI/human UDG and a SAUGI/HSVUDG complex were used to explain the differential binding activities of SAUGI on these two UDGs. Structural-based protein engineering was further used to modulate the inhibitory ability of SAUGI on human UDG and HSVUDG. The results of this work extend our understanding of DNA mimics as well as potentially opening the way for novel therapeutic applications for this kind of protein.
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Affiliation(s)
- Hao-Ching Wang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Chun-Han Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Cheng Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Ming-Fen Huang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Andrew H-J Wang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan
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9
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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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10
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Shah S, Heddle JG. Squaring up to DNA: pentapeptide repeat proteins and DNA mimicry. Appl Microbiol Biotechnol 2014; 98:9545-60. [PMID: 25343976 DOI: 10.1007/s00253-014-6151-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 02/01/2023]
Abstract
Pentapeptide repeats are a class of proteins characterized by the presence of multiple repeating sequences five amino acids in length. The sequences fold into a right-handed β-helix with a roughly square-shaped cross section. Pentapeptide repeat proteins include a number of examples which are thought to function as structural mimics of DNA and act to competitively bind to the type II topoisomerase DNA gyrase, an important antibacterial target. DNA gyrase-targeting pentapeptide repeat proteins can both inhibit DNA gyrase-a potentially useful therapeutic property-and contribute to resistance to quinolone antibacterials (by acting to prevent them forming a lethal complex with the DNA and enzyme). Pentapeptide repeat proteins are therefore of wide interest not only because of their unusual structure, function, and potential as an antibacterial target, but also because knowledge of their mechanism of action may lead to both a greater understanding of the details of DNA gyrase function as well as being a useful template for the design of new DNA gyrase inhibitors. However, many puzzling aspects as to how these DNA mimics function and indeed even their ability to act as DNA mimics itself remains open to question. This review summarizes the current state of knowledge regarding pentapeptide repeat proteins, focusing on those that are thought to mimic DNA, and speculates on potential structure-function relationships which may account for their differing specificities.
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Affiliation(s)
- Shama Shah
- Heddle Initiative Research Unit, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
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11
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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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12
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Tucker AT, Bobay BG, Banse AV, Olson AL, Soderblom EJ, Moseley MA, Thompson RJ, Varney KM, Losick R, Cavanagh J. A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA. J Mol Biol 2014; 426:1911-24. [PMID: 24534728 PMCID: PMC4017629 DOI: 10.1016/j.jmb.2014.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/07/2014] [Accepted: 02/07/2014] [Indexed: 12/25/2022]
Abstract
Bacteria respond to adverse environmental conditions by switching on the expression of large numbers of genes that enable them to adapt to unfavorable circumstances. In Bacillus subtilis, many adaptive genes are under the negative control of the global transition state regulator, the repressor protein AbrB. Stressful conditions lead to the de-repression of genes under AbrB control. Contributing to this de-repression is AbbA, an anti-repressor that binds to and blocks AbrB from binding to DNA. Here, we have determined the NMR structure of the functional AbbA dimer, confirmed that it binds to the N-terminal DNA-binding domain of AbrB, and have provided an initial description for the interaction using computational docking procedures. Interestingly, we show that AbbA has structural and surface characteristics that closely mimic the DNA phosphate backbone, enabling it to readily carry out its physiological function.
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Affiliation(s)
- Ashley T Tucker
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, 128 Polk Hall, Raleigh, NC 27695, USA
| | - Benjamin G Bobay
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, 128 Polk Hall, Raleigh, NC 27695, USA
| | - Allison V Banse
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Andrew L Olson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, 128 Polk Hall, Raleigh, NC 27695, USA
| | - Erik J Soderblom
- Duke Proteomics Core Facility, Institute for Genome Sciences and Policy, Duke University School of Medicine, Duke University, B02 Levine Sciences Research Center, 450 Research Drive, Durham, NC 27708, USA
| | - M Arthur Moseley
- Duke Proteomics Core Facility, Institute for Genome Sciences and Policy, Duke University School of Medicine, Duke University, B02 Levine Sciences Research Center, 450 Research Drive, Durham, NC 27708, USA
| | - Richele J Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, 128 Polk Hall, Raleigh, NC 27695, USA
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - John Cavanagh
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, 128 Polk Hall, Raleigh, NC 27695, USA.
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Wang HC, Ho CH, Hsu KC, Yang JM, Wang AHJ. DNA mimic proteins: functions, structures, and bioinformatic analysis. Biochemistry 2014; 53:2865-74. [PMID: 24766129 DOI: 10.1021/bi5002689] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.
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Affiliation(s)
- Hao-Ching Wang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University , Taipei 110, Taiwan
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Silmon de Monerri NC, Kim K. Pathogens hijack the epigenome: a new twist on host-pathogen interactions. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:897-911. [PMID: 24525150 DOI: 10.1016/j.ajpath.2013.12.022] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 12/01/2013] [Accepted: 12/05/2013] [Indexed: 02/07/2023]
Abstract
Pathogens have evolved strategies to promote their survival by dramatically modifying the transcriptional profile and protein content of the host cells they infect. Modifications of the host transcriptome and proteome are mediated by pathogen-encoded effector molecules that modulate host cells through a variety of different mechanisms. Recent studies highlight the importance of the host chromatin and other epigenetic regulators as targets of pathogens. Host gene regulatory mechanisms may be targeted through cytoplasmic signaling, directly by pathogen effector proteins, and possibly by pathogen RNA. Although many of these changes are short-lived and persist only during the course of infection, several studies indicate that pathogens are able to induce long-term, heritable changes that are essential to pathogenesis of infectious diseases and persistence of pathogens within their hosts. In this review, we discuss how pathogens modulate the epigenome of host cells, a new and flourishing avenue of host-pathogen interaction studies.
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Affiliation(s)
- Natalie C Silmon de Monerri
- Departments of Medicine, Pathology, and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Kami Kim
- Departments of Medicine, Pathology, and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York.
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Wang HC, Hsu KC, Yang JM, Wu ML, Ko TP, Lin SR, Wang AHJ. Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor. Nucleic Acids Res 2013; 42:1354-64. [PMID: 24150946 PMCID: PMC3902945 DOI: 10.1093/nar/gkt964] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA mimic proteins are unique factors that control the DNA binding activity of target proteins by directly occupying their DNA binding sites. The extremely divergent amino acid sequences of the DNA mimics make these proteins hard to predict, and although they are likely to be ubiquitous, to date, only a few have been reported and functionally analyzed. Here we used a bioinformatic approach to look for potential DNA mimic proteins among previously reported protein structures. From ∼14 candidates, we selected the Staphylococcus conserved hypothetical protein SSP0047, and used proteomic and structural approaches to show that it is a novel DNA mimic protein. In Staphylococcus aureus, we found that this protein acts as a uracil-DNA glycosylase inhibitor, and therefore named it S. aureus uracil-DNA glycosylase inhibitor (SAUGI). We also determined and analyzed the complex structure of SAUGI and S. aureus uracil-DNA glycosylase (SAUDG). Subsequent BIAcore studies further showed that SAUGI has a high binding affinity to both S. aureus and human UDG. The two uracil-DNA glycosylase inhibitors (UGI and p56) previously known to science were both found in Bacillus phages, and this is the first report of a bacterial DNA mimic that may regulate SAUDG’s functional roles in DNA repair and host defense.
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Affiliation(s)
- 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, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan, Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30050, Taiwan, Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 30050, Taiwan and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan
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