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Batista BB, de Lima VM, Picinato BA, Koide T, da Silva Neto JF. A quorum-sensing regulatory cascade for siderophore-mediated iron homeostasis in Chromobacterium violaceum. mSystems 2024; 9:e0139723. [PMID: 38501880 PMCID: PMC11019928 DOI: 10.1128/msystems.01397-23] [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] [Received: 01/02/2024] [Accepted: 02/24/2024] [Indexed: 03/20/2024] Open
Abstract
Iron is a transition metal used as a cofactor in many biochemical reactions. In bacteria, iron homeostasis involves Fur-mediated de-repression of iron uptake systems, such as the iron-chelating compounds siderophores. In this work, we identified and characterized novel regulatory systems that control siderophores in the environmental opportunistic pathogen Chromobacterium violaceum. Screening of a 10,000-transposon mutant library for siderophore halos identified seven possible regulatory systems involved in siderophore-mediated iron homeostasis in C. violaceum. Further characterization revealed a regulatory cascade that controls siderophores involving the transcription factor VitR acting upstream of the quorum-sensing (QS) system CviIR. Mutation of the regulator VitR led to an increase in siderophore halos, and a decrease in biofilm, violacein, and protease production. We determined that these effects occurred due to VitR-dependent de-repression of vioS. Increased VioS leads to direct inhibition of the CviR regulator by protein-protein interaction. Indeed, insertion mutations in cviR and null mutations of cviI and cviR led to an increase of siderophore halos. RNA-seq of the cviI and cviR mutants revealed that CviR regulates CviI-dependent and CviI-independent regulons. Classical QS-dependent processes (violacein, proteases, and antibiotics) were activated at high cell density by both CviI and CviR. However, genes related to iron homeostasis and many other processes were regulated by CviR but not CviI, suggesting that CviR acts without its canonical CviI autoinducer. Our data revealed a complex regulatory cascade involving QS that controls siderophore-mediated iron homeostasis in C. violaceum.IMPORTANCEThe iron-chelating compounds siderophores play a major role in bacterial iron acquisition. Here, we employed a genetic screen to identify novel siderophore regulatory systems in Chromobacterium violaceum, an opportunistic human pathogen. Many mutants with increased siderophore halos had transposon insertions in genes encoding transcription factors, including a novel regulator called VitR, and CviR, the regulator of the quorum-sensing (QS) system CviIR. We found that VitR is upstream in the pathway and acts as a dedicated repressor of vioS, which encodes a direct CviR-inhibitory protein. Indeed, all QS-related phenotypes of a vitR mutant were rescued in a vitRvioS mutant. At high cell density, CviIR activated classical QS-dependent processes (violacein, proteases, and antibiotics production). However, genes related to iron homeostasis and type-III and type-VI secretion systems were regulated by CviR in a CviI- or cell density-independent manner. Our data unveil a complex regulatory cascade integrating QS and siderophores in C. violaceum.
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Affiliation(s)
- Bianca B. Batista
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Vinicius M. de Lima
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Beatriz A. Picinato
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tie Koide
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - José F. da Silva Neto
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Sudhakaran G, Kesavan D, Selvam M, Arasu A, Guru A, Arockiaraj J. Gonorrhea caused due to antimicrobial-resistant bacteria Neisseria gonorrhoeae treated using probiotic peptide. In Silico Pharmacol 2024; 12:17. [PMID: 38525049 PMCID: PMC10957827 DOI: 10.1007/s40203-023-00185-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 03/26/2024] Open
Abstract
Neisseria gonorrhea is a sexually transmitted disease from gonorrhea that lacks treatment; despite the urgency, the absence of adequate drugs, lack of human correlates of protection, and inadequate animal models of infection have delayed progress toward the prevention of gonococcal infection. Lactobacillus crispatus is a lactic acid bacterium typically found in the human vaginal microbiota. Peptides from L. crispatus have shown a potential therapeutic option for targetting N. gonorrhea. Bioinformatics analysis is important for speeding up drug target acquisition, screening refinement, and evaluating adverse effects and drug resistance prediction. Therefore, this study identified an antimicrobial peptide from the bacteriocin immunity protein (BIP) of L. crispatus using the bioinformatics tool and Collection of Antimicrobial Peptide (CAMPR3). Based on the AMP score and highest ADMET properties, the peptide SM20 was chosen for docking analysis. SM20 was docked against multiple proteins from the genome of the AMR bacterium N. gonorrhea using an online tool; protein-peptide interactions were established and visualized using the PyMol visualizing tool. Molecular docking was carried out using the CABSdock tool, and multiple conformations were obtained against the membrane proteins of N. gonorrhoea. The peptide SM20 exhibited higher docking scores and ADMET properties. Therefore, SM20 could be further encapsulated with cellulose; it can be applied topically to the genital tract to target N. gonorrhea infection. The controlled release of the antimicrobial peptide from the gel can provide sustained delivery of the treatment, increasing its efficacy and reducing the risk of resistance development.
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Affiliation(s)
- Gokul Sudhakaran
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600077 Tamil Nadu India
| | - D. Kesavan
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, 603203 Tamil Nadu India
| | - Madesh Selvam
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, 603203 Tamil Nadu India
| | - Abirami Arasu
- Department of Microbiology, SRM Arts and Science College, Kattankulathur, Chennai, 603203 Tamil Nadu India
| | - Ajay Guru
- Department of Cariology, Saveetha Dental College and Hospitals, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600077 Tamil Nadu India
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, 603203 Tamil Nadu India
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Holley CL, Dhulipala V, Maurakis SA, Greenawalt AN, Read TD, Cornelissen CN, Shafer WM. Transcriptional activation of ompA in Neisseria gonorrhoeae mediated by the XRE family member protein NceR. mBio 2023; 14:e0124423. [PMID: 37387605 PMCID: PMC10470515 DOI: 10.1128/mbio.01244-23] [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] [Received: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 07/01/2023] Open
Abstract
Increasing antibiotic resistance of Neisseria gonorrhoeae, the causative agent of gonorrhea, is a growing global concern that has renewed vaccine development efforts. The gonococcal OmpA protein was previously identified as a vaccine candidate due to its surface exposure, conservation, stable expression, and involvement in host-cell interactions. We previously demonstrated that the transcription of ompA can be activated by the MisR/MisS two-component system. Interestingly, earlier work suggested that the availability of free iron also influences ompA expression, which we confirmed in this study. In the present study, we found that iron regulation of ompA was independent of MisR and searched for additional regulators. A DNA pull-down assay with the ompA promoter from gonococcal lysates obtained from bacteria grown in the presence or absence of iron identified an XRE (Xenobiotic Response Element) family member protein encoded by NGO1982. We found that an NGO1982 null mutant of N. gonorrhoeae strain FA19 displayed a reduced level of ompA expression compared to the wild-type (WT) parent strain. Given this regulation, and the capacity of this XRE-like protein to regulate a gene involved in peptidoglycan biosynthesis (ltgA), along with its presence in other Neisseria sp., we termed the NGO1982-encoded protein as NceR (Neisseria cell envelope regulator). Critically, results from DNA-binding studies indicated that NceR regulates ompA through a direct mechanism. Thus, ompA expression is subject to both iron-dependent (NceR) and -independent (MisR/MisS) pathways. Hence, levels of the vaccine antigen candidate OmpA in circulating gonococcal strains could be influenced by transcriptional regulatory systems and the availability of iron. IMPORTANCE Herein, we report that the gene encoding a conserved gonococcal surface-exposed vaccine candidate (OmpA) is activated by a heretofore undescribed XRE family transcription factor, which we term NceR. We report that NceR regulation of ompA expression in N. gonorrhoeae is mediated by an iron-dependent mechanism, while the previously described MisR regulatory system is iron-independent. Our study highlights the importance of defining the complexity of coordinated genetic and physiologic systems that regulate genes encoding vaccine candidates to better understand their availability during infection.
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Affiliation(s)
- Concerta L. Holley
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Vijaya Dhulipala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stavaros A. Maurakis
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | | | - Timothy D. Read
- Department of Medicine (Division of Infectious Diseases), Emory University School of Medicine, Atlanta, Georgia, USA
- The Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - William M. Shafer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Medicine (Division of Infectious Diseases), Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratories of Bacterial Pathogenesis, Veterans Affairs Medical Center, Decatur, Georgia, USA
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Zhao B, He D, Gao S, Zhang Y, Wang L. Hypothetical protein FoDbp40 influences the growth and virulence of Fusarium oxysporum by regulating the expression of isocitrate lyase. Front Microbiol 2022; 13:1050637. [DOI: 10.3389/fmicb.2022.1050637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022] Open
Abstract
Fungal growth is closely related to virulence. Finding the key genes and pathways that regulate growth can help elucidate the regulatory mechanisms of fungal growth and virulence in efforts to locate new drug targets. Fusarium oxysporum is an important plant pathogen and human opportunistic pathogen that has research value in agricultural and medicinal fields. A mutant of F. oxysporum with reduced growth was obtained by Agrobacterium tumefaciens-mediated transformation, the transferred DNA (T-DNA) interrupted gene in this mutant coded a hypothetical protein that we named FoDbp40. FoDbp40 has an unknown function, but we chose to explore its possible functions as it may play a role in fungal growth regulatory mechanisms. Results showed that F. oxysporum growth and virulence decreased after FoDbp40 deletion. FOXG_05529 (NCBI Gene ID, isocitrate lyase, ICL) was identified as a key gene that involved in the reduced growth of this mutant. Deletion of FoDbp40 results in a decrease of more than 80% in ICL expression and activity, succinate level, and energy level, plus a decrease in phosphorylated mammalian target of rapamycin level and an increase in phosphorylated 5′-adenosine monophosphate activated protein kinase level. In summary, our study found that the FoDbp40 regulates the expression of ICL at a transcriptional level and affects energy levels and downstream related pathways, thereby regulating the growth and virulence of F. oxysporum.
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Li M, Chen Q, Wu C, Li Y, Wang S, Chen X, Qiu B, Li Y, Mao D, Lin H, Yu D, Cao Y, Huang Z, Cui C, Zhong Z. A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571. Genes (Basel) 2022; 13:genes13101895. [PMID: 36292780 PMCID: PMC9601964 DOI: 10.3390/genes13101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/02/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICEAc) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICEAc, but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICEAc and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host’s flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICEAc by 18.5%. We propose the feasibility of constructing a minimal ICEAc element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.
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Affiliation(s)
- Mingxu Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qianqian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanhui Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyang Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Sanle Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuelian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bowen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxin Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongmei Mao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Lin
- Animal, Plant and Food Inspection Center, Nanjing Customs, No. 39, Chuangzhi Road, Nanjing 210019, China
| | - Daogeng Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, Danzhou 571737, China
| | - Yajun Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Chunhong Cui
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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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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Lu H, Wang L, Li S, Pan C, Cheng K, Luo Y, Xu H, Tian B, Zhao Y, Hua Y. Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO. Nucleic Acids Res 2019; 47:9925-9933. [PMID: 31410466 PMCID: PMC6765133 DOI: 10.1093/nar/gkz720] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 12/25/2022] Open
Abstract
DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-terminal domain is stabilized by hydrophobic interactions of leucine/isoleucine-rich helices, which is critical for DdrO dimerization. Our findings suggest that DdrO is a novel XRE family transcriptional regulator that forms a distinctive dimer. The structure also provides insight into the mechanism of DdrO-PprI-mediated DNA damage response in Deinococcus.
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Affiliation(s)
- Huizhi Lu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Shengjie Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Chaoming Pan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Kaiying Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuxia Luo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
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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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Kawalek A, Modrzejewska M, Zieniuk B, Bartosik AA, Jagura-Burdzy G. Interaction of ArmZ with the DNA-binding domain of MexZ induces expression of mexXY multidrug efflux pump genes and antimicrobial resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.01199-19. [PMID: 31527038 PMCID: PMC6879243 DOI: 10.1128/aac.01199-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/13/2019] [Indexed: 12/17/2022] Open
Abstract
Multidrug efflux pumps play an important role in antibiotic resistance in bacteria. In Pseudomonas aeruginosa, MexXY pump provides intrinsic resistance to many antimicrobials, including aminoglycosides. The expression of mexXY operon is negatively regulated by MexZ repressor. The repression is alleviated in response to the antibiotic-induced ribosome stress, which results in increased synthesis of anti-repressor ArmZ, interacting with MexZ. The molecular mechanism of MexZ inactivation by ArmZ is not known. Here, we showed that the N-terminal part of MexZ, encompassing the DNA-binding domain, is required for interaction with ArmZ. Using the bacterial two hybrid system based mutant screening and pull-down analyses we identified substitutions in MexZ that diminished (R3S, K6E, R13H) or completely impaired (K53E) the interaction with ArmZ without blocking MexZ activity as a transcriptional repressor. Introduction of corresponding mexZ missense mutations into P aeruginosa PAO1161 chromosome impaired (mexZ K6E, mexZ R13H) or blocked (mexZ K53E) tetracycline mediated induction of mexY expression. Concomitantly, PAO1161 mexZ K53E strain was more susceptible to aminoglycosides. The identified residues are highly conserved in MexZ-like transcriptional regulators found in bacterial genomes encoding both MexX/MexY/MexZ and ArmZ/PA5470 orthologs, suggesting that a similar mechanism may contribute to induction of efflux mediated resistance in other bacterial species. Overall, our data shed light on the molecular mechanism of ArmZ mediated induction of intrinsic antimicrobial resistance in P. aeruginosa.
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Affiliation(s)
- Adam Kawalek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Warsaw, Poland
| | - Magdalena Modrzejewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Warsaw, Poland
| | - Bartlomiej Zieniuk
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Aneta Agnieszka Bartosik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Warsaw, Poland
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10
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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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11
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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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12
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Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor. Proc Natl Acad Sci U S A 2016; 113:E2480-8. [PMID: 27099293 DOI: 10.1073/pnas.1602618113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92-198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant.
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13
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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: 43] [Impact Index Per Article: 5.4] [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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14
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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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15
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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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16
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Gasparini R, Panatto D, Bragazzi NL, Lai PL, Bechini A, Levi M, Durando P, Amicizia D. How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines. J Immunol Res 2015; 2015:189153. [PMID: 26351643 PMCID: PMC4553322 DOI: 10.1155/2015/189153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/09/2015] [Indexed: 01/17/2023] Open
Abstract
In the last decades, tremendous advancement in dissecting the mechanisms of pathogenicity of Neisseria meningitidis at a molecular level has been achieved, exploiting converging approaches of different disciplines, ranging from pathology to microbiology, immunology, and omics sciences (such as genomics and proteomics). Here, we review the molecular biology of the infectious agent and, in particular, its interactions with the immune system, focusing on both the innate and the adaptive responses. Meningococci exploit different mechanisms and complex machineries in order to subvert the immune system and to avoid being killed. Capsular polysaccharide and lipooligosaccharide glycan composition, in particular, play a major role in circumventing immune response. The understanding of these mechanisms has opened new horizons in the field of vaccinology. Nowadays different licensed meningococcal vaccines are available and used: conjugate meningococcal C vaccines, tetravalent conjugate vaccines, an affordable conjugate vaccine against the N. menigitidis serogroup A, and universal vaccines based on multiple antigens each one with a different and peculiar function against meningococcal group B strains.
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Affiliation(s)
- R. Gasparini
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Panatto
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - N. L. Bragazzi
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - P. L. Lai
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - A. Bechini
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - M. Levi
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - P. Durando
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Amicizia
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
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17
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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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18
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Lee CC, Maestre-Reyna M, Hsu KC, Wang HC, Liu CI, Jeng WY, Lin LL, Wood R, Chou CC, Yang JM, Wang AHJ. Crowning proteins: modulating the protein surface properties using crown ethers. Angew Chem Int Ed Engl 2014; 53:13054-8. [PMID: 25287606 PMCID: PMC4288931 DOI: 10.1002/anie.201405664] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/16/2014] [Indexed: 11/18/2022]
Abstract
Crown ethers are small, cyclic polyethers that have found wide-spread use in phase-transfer catalysis and, to a certain degree, in protein chemistry. Crown ethers readily bind metallic and organic cations, including positively charged amino acid side chains. We elucidated the crystal structures of several protein-crown ether co-crystals grown in the presence of 18-crown-6. We then employed biophysical methods and molecular dynamics simulations to compare these complexes with the corresponding apoproteins and with similar complexes with ring-shaped low-molecular-weight polyethylene glycols. Our studies show that crown ethers can modify protein surface behavior dramatically by stabilizing either intra- or intermolecular interactions. Consequently, we propose that crown ethers can be used to modulate a wide variety of protein surface behaviors, such as oligomerization, domain–domain interactions, stabilization in organic solvents, and crystallization.
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Affiliation(s)
- Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan); Core Facilities for Protein Structural Analysis, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan)
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19
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Lee CC, Maestre-Reyna M, Hsu KC, Wang HC, Liu CI, Jeng WY, Lin LL, Wood R, Chou CC, Yang JM, Wang AHJ. Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405664] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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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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21
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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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22
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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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23
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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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Wang HC, Wu ML, Ko TP, Wang AHJ. Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein. Nucleic Acids Res 2013; 41:5127-38. [PMID: 23531546 PMCID: PMC3643605 DOI: 10.1093/nar/gkt201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 12/16/2022] Open
Abstract
DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.
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Affiliation(s)
- Hao-Ching Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Mao-Lun Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for 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, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan, and Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
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