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Wang Y, Wang S, Nie X, Yang K, Xu P, Wang X, Liu M, Yang Y, Chen Z, Wang S. Molecular and structural basis of nucleoside diphosphate kinase-mediated regulation of spore and sclerotia development in the fungus Aspergillus flavus. J Biol Chem 2019; 294:12415-12431. [PMID: 31243100 DOI: 10.1074/jbc.ra119.007505] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
The fundamental biological function of nucleoside diphosphate kinase (NDK) is to catalyze the reversible exchange of the γ-phosphate between nucleoside triphosphate (NTP) and nucleoside diphosphate (NDP). This kinase also has functions that extend beyond its canonically defined enzymatic role as a phosphotransferase. However, the role of NDK in filamentous fungi, especially in Aspergillus flavus (A. flavus), is not yet known. Here we report that A. flavus has two NDK-encoding gene copies as assessed by qPCR. Using gene-knockout and complementation experiments, we found that AfNDK regulates spore and sclerotia development and is involved in plant virulence as assessed in corn and peanut seed-based assays. An antifungal test with the inhibitor azidothymidine suppressed AfNDK activity in vitro and prevented spore production and sclerotia formation in A. flavus, confirming AfNDK's regulatory functions. Crystallographic analysis of AfNDK, coupled with site-directed mutagenesis experiments, revealed three residues (Arg-104, His-117, and Asp-120) as key sites that contribute to spore and sclerotia development. These results not only enrich our knowledge of the regulatory role of this important protein in A. flavus, but also provide insights into the prevention of A. flavus infection in plants and seeds, as well as into the structural features relevant for future antifungal drug development.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sen Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyi Nie
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kunlong Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Xu
- State Key Laboratory of Structural Chemistry and CAS Key Laboratory, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Xiuna Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengxin Liu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongshuai Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; State Key Laboratory of Structural Chemistry and CAS Key Laboratory, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zhuo Chen
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; State Key Laboratory of Structural Chemistry and CAS Key Laboratory, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Yu H, Rao X, Zhang K. Nucleoside diphosphate kinase (Ndk): A pleiotropic effector manipulating bacterial virulence and adaptive responses. Microbiol Res 2017; 205:125-134. [PMID: 28942838 DOI: 10.1016/j.micres.2017.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/23/2017] [Accepted: 09/02/2017] [Indexed: 12/11/2022]
Abstract
Nucleoside diphosphate kinase (Ndk) is a housekeeping enzyme that balances cellular nucleoside triphosphate (NTP) pools by catalyzing the reversible transfer of γ-phosphate from NTPs to nucleoside diphosphates (NDPs). In addition to its fundamental role in nucleotide metabolism, Ndk has roles in protein histidine phosphorylation, DNA cleavage/repair, and gene regulation. Recent studies have also revealed that Ndk secreted from bacteria is important in modulating virulence-associated phenotypes including quorum sensing regulation, type III secretion system activation, and virulence factor production. Moreover, after infection, Ndks released from bacteria are involved in regulating host defense activities, such as cell apoptosis, phagocytosis, and inflammatory responses. Given that Ndk exerts a pleiotropic effect on bacterial virulence and bacteria-host interactions, the biological significance of the bacterial Ndks during infection is intriguing. This review will provide a synopsis of the current knowledge regarding the biological properties and roles of Ndks in regulating bacterial virulence and adaptation and will discuss in depth the biological significance of Ndk during bacteria-host interactions.
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Affiliation(s)
- Hua Yu
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China; Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China.
| | - Kebin Zhang
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China.
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Zhu X, Poghosyan E, Gopal R, Liu Y, Ciruelas KS, Maizy Y, Diener DR, King SM, Ishikawa T, Yang P. General and specific promotion of flagellar assembly by a flagellar nucleoside diphosphate kinase. Mol Biol Cell 2017; 28:3029-3042. [PMID: 28877983 PMCID: PMC5662260 DOI: 10.1091/mbc.e17-03-0156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
NDK5 promotes assembly of motile cilia and flagella with its structure and protein phosphorylation–related reactions instead of the canonical NDK activity. The novel mechanisms and dominant-negative effect of mutated functional NDK5 reveal the remarkable versatility of a molecular platform that is used in diverse cellular processes. Nucleoside diphosphate kinases (NDKs) play a central role in diverse cellular processes using the canonical NDK activity or alternative mechanisms that remain poorly defined. Our study of dimeric NDK5 in a flagellar motility control complex, the radial spoke (RS), has revealed new modalities. The flagella in Chlamydomonas ndk5 mutant were paralyzed, albeit only deficient in three RS subunits. RS morphology appeared severely changed in averaged cryo-electron tomograms, suggesting that NDK5 is crucial for the intact spokehead formation as well as RS structural stability. Intriguingly, ndk5’s flagella were also short, resembling those of an allelic spoke-less mutant. All ndk5’s phenotypes were rescued by expressions of NDK5 or a mutated NDK5 lacking the canonical kinase activity. Importantly, the mutated NDK5 that appeared fully functional in ndk5 cells elicited a dominant-negative effect in wild-type cells, causing paralyzed short flagella with hypophosphorylated, less abundant, but intact RSs, and accumulated hypophosphorylated NDK5 in the cell body. We propose that NDK5 dimer is an RS structural subunit with an additional mechanism that uses cross-talk between the two NDK monomers to accelerate phosphorylation-related assembly of RSs and entire flagella.
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Affiliation(s)
- Xiaoyan Zhu
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Emiliya Poghosyan
- Biomolecular Research Laboratory, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Radhika Gopal
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Yi Liu
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Kristine S Ciruelas
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Yousif Maizy
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Dennis R Diener
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
| | - Takashi Ishikawa
- Biomolecular Research Laboratory, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
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Mishra S, Jakkala K, Srinivasan R, Arumugam M, Ranjeri R, Gupta P, Rajeswari H, Ajitkumar P. NDK Interacts with FtsZ and Converts GDP to GTP to Trigger FtsZ Polymerisation--A Novel Role for NDK. PLoS One 2015; 10:e0143677. [PMID: 26630542 PMCID: PMC4668074 DOI: 10.1371/journal.pone.0143677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 11/09/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction Nucleoside diphosphate kinase (NDK), conserved across bacteria to humans, synthesises NTP from NDP and ATP. The eukaryotic homologue, the NDPK, uses ATP to phosphorylate the tubulin-bound GDP to GTP for tubulin polymerisation. The bacterial cytokinetic protein FtsZ, which is the tubulin homologue, also uses GTP for polymerisation. Therefore, we examined whether NDK can interact with FtsZ to convert FtsZ-bound GDP and/or free GDP to GTP to trigger FtsZ polymerisation. Methods Recombinant and native NDK and FtsZ proteins of Mycobacterium smegmatis and Mycobacterium tuberculosis were used as the experimental samples. FtsZ polymersation was monitored using 90° light scattering and FtsZ polymer pelleting assays. The γ32P-GTP synthesised by NDK from GDP and γ32P-ATP was detected using thin layer chromatography and quantitated using phosphorimager. The FtsZ bound 32P-GTP was quantitated using phosphorimager, after UV-crosslinking, followed by SDS-PAGE. The NDK-FtsZ interaction was determined using Ni2+-NTA-pulldown assay and co-immunoprecipitation of the recombinant and native proteins in vitro and ex vivo, respectively. Results NDK triggered instantaneous polymerisation of GDP-precharged recombinant FtsZ in the presence of ATP, similar to the polymerisation of recombinant FtsZ (not GDP-precharged) upon the direct addition of GTP. Similarly, NDK triggered polymerisation of recombinant FtsZ (not GDP-precharged) in the presence of free GDP and ATP as well. Mutant NDK, partially deficient in GTP synthesis from ATP and GDP, triggered low level of polymerisation of MsFtsZ, but not of MtFtsZ. As characteristic of NDK’s NTP substrate non-specificity, it used CTP, TTP, and UTP also to convert GDP to GTP, to trigger FtsZ polymerisation. The NDK of one mycobacterial species could trigger the polymerisation of the FtsZ of another mycobacterial species. Both the recombinant and the native NDK and FtsZ showed interaction with each other in vitro and ex vivo, alluding to the possibility of direct phosphorylation of FtsZ-bound GDP by NDK. Conclusion Irrespective of the bacterial species, NDK interacts with FtsZ in vitro and ex vivo and, through the synthesis of GTP from FtsZ-bound GDP and/or free GDP, and ATP (CTP/TTP/UTP), triggers FtsZ polymerisation. The possible biological context of this novel activity of NDK is presented.
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Affiliation(s)
- Saurabh Mishra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Ramanujam Srinivasan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Muthu Arumugam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Raghavendra Ranjeri
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Prabuddha Gupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Haryadi Rajeswari
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- * E-mail:
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Neeld D, Jin Y, Bichsel C, Jia J, Guo J, Bai F, Wu W, Ha UH, Terada N, Jin S. Pseudomonas aeruginosa injects NDK into host cells through a type III secretion system. MICROBIOLOGY-SGM 2014; 160:1417-1426. [PMID: 24699069 DOI: 10.1099/mic.0.078139-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen possessing a type III secretion system (T3SS) which injects toxic effector proteins into mammalian host cells. In previous studies, P. aeruginosa strains lacking all of the known type III effectors were shown to cause cytotoxicity upon prolonged infection time. In this study, we report the identification of a new cytotoxin, nucleoside diphosphate kinase (NDK), which is injected into eukaryotic cells in a T3SS-dependent manner. Injection of NDK is inhibited by the presence of previously known effectors of the T3SS, with an effectorless strain injecting the highest amount, suggesting active competition with the known T3SS effectors. NDK is shown to cause a cytotoxic response when expressed in eukaryotic cells, and P. aeruginosa strains harbouring NDK also show a greater toxicity than strains lacking it. Interestingly, the cytotoxic effect of intracellular NDK is independent of its kinase activity. In previous studies, NDK was shown to be secreted into culture supernatants via a type I secretion system and cause cytotoxicity in a kinase-dependent manner. Therefore, the current study highlights an alternative route of NDK secretion as well as two different cytotoxic mechanisms of NDK, depending on the extra- or intra-cellular location of the protein.
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Affiliation(s)
- Dennis Neeld
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Yongxin Jin
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Candace Bichsel
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Jinghua Jia
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Jianhui Guo
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Fang Bai
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Weihui Wu
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Un-Hwan Ha
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Naohiro Terada
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Shouguang Jin
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
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Georgescauld F, Moynié L, Habersetzer J, Cervoni L, Mocan I, Borza T, Harris P, Dautant A, Lascu I. Intersubunit ionic interactions stabilize the nucleoside diphosphate kinase of Mycobacterium tuberculosis. PLoS One 2013; 8:e57867. [PMID: 23526954 PMCID: PMC3589492 DOI: 10.1371/journal.pone.0057867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/27/2013] [Indexed: 01/10/2023] Open
Abstract
Most nucleoside diphosphate kinases (NDPKs) are hexamers. The C-terminal tail interacting with the neighboring subunits is crucial for hexamer stability. In the NDPK from Mycobacterium tuberculosis (Mt) this tail is missing. The quaternary structure of Mt-NDPK is essential for full enzymatic activity and for protein stability to thermal and chemical denaturation. We identified the intersubunit salt bridge Arg80-Asp93 as essential for hexamer stability, compensating for the decreased intersubunit contact area. Breaking the salt bridge by the mutation D93N dramatically decreased protein thermal stability. The mutation also decreased stability to denaturation by urea and guanidinium. The D93N mutant was still hexameric and retained full activity. When exposed to low concentrations of urea it dissociated into folded monomers followed by unfolding while dissociation and unfolding of the wild type simultaneously occur at higher urea concentrations. The dissociation step was not observed in guanidine hydrochloride, suggesting that low concentration of salt may stabilize the hexamer. Indeed, guanidinium and many other salts stabilized the hexamer with a half maximum effect of about 0.1 M, increasing protein thermostability. The crystal structure of the D93N mutant has been solved.
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Affiliation(s)
- Florian Georgescauld
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Lucile Moynié
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Johann Habersetzer
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Laura Cervoni
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi “La Sapienza”, Roma, Italy
| | - Iulia Mocan
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Tudor Borza
- Laboratoire de Chimie Structurale des Macromolécules, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Pernile Harris
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alain Dautant
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
- * E-mail: (AD); (IL)
| | - Ioan Lascu
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
- * E-mail: (AD); (IL)
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Arumugam M, Ajitkumar P. Histidine 117 in the His-Gly-Ser-Asp motif is Required for the Biochemical Activities of Nucleoside Diphosphate Kinase of Mycobacterium smegmatis. Open Biochem J 2012; 6:71-7. [PMID: 22888372 PMCID: PMC3414718 DOI: 10.2174/1874091x01206010071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 04/16/2012] [Accepted: 04/19/2012] [Indexed: 11/28/2022] Open
Abstract
Nucleoside diphosphate kinase (NDK), which is widely conserved in both prokaryotes and eukaryotes, maintains a balanced pool of nucleotide triphosphates and their deoxy derivatives. NDKs from bacterial and other systems contain the conserved HGSD motif, where the His residue is required for the biochemical activities, namely the NTPase (AT-Pase and GTPase), NTP synthesising, and autophosphorylation activities of the enzyme. Amino acid sequence homology comparison of the NDK of Mycobacterium smegmatis (MsmNDK) with the NDKs of other bacterial genera showed the presence of H117GSD motif. While the recombinant wild type MsmNDK showed the NTPase, NTP synthesising, and autophosphorylation activities, the H117Q mutation abolished the biochemical activities of the recombinant MsmNDK-H117Q mutant protein in vitro. These observations demonstrate that the H117 residue in the HGSD motif is required for the biochemical activities of MsmNDK.
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Affiliation(s)
- Muthu Arumugam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
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Mittal P, Karthikeyan S, Chakraborti PK. Amino acids involved in polyphosphate synthesis and its mobilization are distinct in polyphosphate kinase-1 from Mycobacterium tuberculosis. PLoS One 2011; 6:e27398. [PMID: 22110640 PMCID: PMC3215733 DOI: 10.1371/journal.pone.0027398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/16/2011] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In bacteria polyphosphates (poly-P) are involved in cellular metabolism and development especially during stress. The enzyme, principally involved in polyphosphate biosynthesis and its mobilization leading to generation of NTPs, is known as polyphosphate kinase (PPK). PRINCIPAL FINDINGS Among two genes of polyphosphate kinases present in Mycobacterium tuberculosis, we cloned and expressed PPK1 in Escherichia coli as histidine-tagged protein. This ∼86 kDa protein is capable of autophosphorylation and synthesis of poly-P as well as NTP. Among 22 conserved histidine residues, we found only His-491 is autophosphorylated and crucial for any enzymatic activity. Substitution of His-510 caused mPPK1 protein deficient but not defective in autophosphorylation, thereby contrary to earlier reports negating any role of this residue in the process. However, mutation of His-510 with either Ala or Gln affected ATP or poly-P synthesis depending on the substitution; while such effects were severe with H510A but mild with H510Q. Furthermore, mPPK1 also renders auxiliary nucleotide diphosphate kinase function by synthesizing virtually all NTPs/dNTPs from their cognate NDPs/dNDPs by utilizing poly-P as the phosphate donor albeit with varied efficiency. To assess the influence of other catalytic domain residues of mPPK1 towards its functionality, we designed mutations based on E. coli PPK1 crystal structure since it owes 68% amino acid sequence similarity with mPPK1. Interestingly, our results revealed that mutations in mPPK1 affecting poly-P synthesis always affected its ATP synthesizing ability; however, the reverse may not be true. CONCLUSIONS/SIGNIFICANCE We conclude that amino acid residues involved in poly-P and ATP synthesizing activities of mPPK1 are distinct. Considering conserved nature of PPK1, it seems our observations have broader implications and not solely restricted to M. tuberculosis only.
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Affiliation(s)
- Payal Mittal
- Council of Scientific and Industrial Research—Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Subramanian Karthikeyan
- Council of Scientific and Industrial Research—Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Pradip K. Chakraborti
- Council of Scientific and Industrial Research—Institute of Microbial Technology, Sector 39A, Chandigarh, India
- * E-mail:
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9
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Dar HH, Prasad D, Varshney GC, Chakraborti PK. Secretory nucleoside diphosphate kinases from both intra- and extracellular pathogenic bacteria are functionally indistinguishable. MICROBIOLOGY-SGM 2011; 157:3024-3035. [PMID: 21816881 DOI: 10.1099/mic.0.049221-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nucleoside diphosphate kinase (NDK), responsible for the maintenance of NTP pools, is an ATP-utilizing enzyme secreted by different pathogens. We found that NDK from Salmonella enterica serovar Typhimurium (S. Typhimurium) is also secretory in nature. Secretory NDK is known to play a crucial role in the survival of pathogenic microbes within host cells through their interaction with extracellular ATP. To elucidate this aspect, we assessed the contribution of secretory products containing NDK from intracellular (Mycobacterium tuberculosis and S. Typhimurium) and extracellular (Vibrio cholerae) pathogens to the process of ATP-induced J774 mouse macrophage cell lysis by monitoring lactate dehydrogenase (LDH) release in the culture medium. Compared with an untreated control, our results demonstrate that S. Typhimurium secretory products caused a greater than twofold decrease in LDH release from J774 macrophage cells treated with ATP. Furthermore, the secretory products from an ndk-deleted strain of S. Typhimurium did not display such behaviour. Contrary to this observation, the secretory products containing NDK of V. cholerae were found to be cytotoxic to J774 cells. At the amino acid level, the sequences of both the NDKs (S. Typhimurium and V. cholerae) exhibited 65 % identity, and their biochemical characteristics (autophosphorylation and phosphotransfer activities) were indistinguishable. However, to our surprise, the secretory product of an ndk-deleted strain of S. Typhimurium, when complemented with V. cholerae ndk, was able to prevent ATP-induced cytolysis. Taken together, our results unambiguously imply that the intrinsic properties of secretory NDKs are identical in intra- and extracellular pathogens, irrespective of their mode of manifestation.
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Affiliation(s)
- Haider Hussain Dar
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160 036, India
| | - Deepshikha Prasad
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160 036, India
| | - Grish C Varshney
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160 036, India
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10
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Intermolecular phosphotransfer is crucial for efficient catalytic activity of nucleoside diphosphate kinase. Biochem J 2010; 430:539-49. [PMID: 20575762 DOI: 10.1042/bj20100026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
NDK (nucleoside diphosphate kinase) is primarily involved in maintaining cellular nucleotide pools in both prokaryotes and eukaryotes. We cloned ndk from Salmonella typhimurium and expressed it in Escherichia coli as a histidine-tagged protein. The Ni-NTA (Ni(2+)-nitrilotriacetate)-purified protein (sNDK) was found to be tetrameric with a monomeric unit molecular mass of approximately 18 kDa. The sNDK exhibited bivalent-cation-dependent autophosphorylation at a wide range of pH values and the phosphorylation withstands acid or alkali treatment. Surprisingly, nucleoside diphosphates did not behave as 'true inhibitors' of autophosphorylation activity. The sNDK displayed phosphotransfer activity from nucleoside triphosphates to nucleoside diphosphates; however, it was Mg(2+)/Mn(2+)-dependent. Mutational analysis established His(117) as the predominantly phosphorylating residue in sNDK. Although it is a histidine kinase, we found that substitution of Ser(119) with alanine/glutamate significantly affected the autophosphorylation, as well as the NTP-synthesizing ability of sNDK. Interestingly, the mixture of inactive (H117A) and partially active (S119A) proteins was found to be catalytically more efficient than the presence of corresponding amounts of active population, advocating transfer of phosphate from phospho-His(117) to Ser(119). Consistent with this observation, the Ni-NTA-purified H117A protein, obtained following co-expression of both of the mutant constructs [His-tagged H117A and GST (glutathione transferase)-tagged S119A] in E. coli, exhibited autophosphorylation, thereby alluding to intermolecular phosphotransfer between His(117) and Ser(119). Although this housekeeping enzyme has long been discovered and characterized from different sources, the results of the present study portray how Ser(119) in sNDK is phosphorylated. Furthermore, our findings illustrate for the first time that the intermolecular phosphotransfer is mandatory for the efficient NTP synthesis in any NDK.
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Sun J, Wang X, Lau A, Liao TYA, Bucci C, Hmama Z. Mycobacterial nucleoside diphosphate kinase blocks phagosome maturation in murine RAW 264.7 macrophages. PLoS One 2010; 5:e8769. [PMID: 20098737 PMCID: PMC2808246 DOI: 10.1371/journal.pone.0008769] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 12/29/2009] [Indexed: 11/30/2022] Open
Abstract
Background Microorganisms capable of surviving within macrophages are rare, but represent very successful pathogens. One of them is Mycobacterium tuberculosis (Mtb) whose resistance to early mechanisms of macrophage killing and failure of its phagosomes to fuse with lysosomes causes tuberculosis (TB) disease in humans. Thus, defining the mechanisms of phagosome maturation arrest and identifying mycobacterial factors responsible for it are key to rational design of novel drugs for the treatment of TB. Previous studies have shown that Mtb and the related vaccine strain, M. bovis bacille Calmette-Guérin (BCG), disrupt the normal function of host Rab5 and Rab7, two small GTPases that are instrumental in the control of phagosome fusion with early endosomes and late endosomes/lysosomes respectively. Methodology/Principal Findings Here we show that recombinant Mtb nucleoside diphosphate kinase (Ndk) exhibits GTPase activating protein (GAP) activity towards Rab5 and Rab7. Then, using a model of latex bead phagosomes, we demonstrated that Ndk inhibits phagosome maturation and fusion with lysosomes in murine RAW 264.7 macrophages. Maturation arrest of phagosomes containing Ndk-beads was associated with the inactivation of both Rab5 and Rab7 as evidenced by the lack of recruitment of their respective effectors EEA1 (early endosome antigen 1) and RILP (Rab7-interacting lysosomal protein). Consistent with these findings, macrophage infection with an Ndk knocked-down BCG strain resulted in increased fusion of its phagosome with lysosomes along with decreased survival of the mutant. Conclusion Our findings provide evidence in support of the hypothesis that mycobacterial Ndk is a putative virulence factor that inhibits phagosome maturation and promotes survival of mycobacteria within the macrophage.
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Affiliation(s)
- Jim Sun
- Division of Infectious Diseases, Department of Medicine, University of British Columbia and Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
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Sureka K, Sanyal S, Basu J, Kundu M. Polyphosphate kinase 2: a modulator of nucleoside diphosphate kinase activity in mycobacteria. Mol Microbiol 2009; 74:1187-97. [PMID: 19843229 DOI: 10.1111/j.1365-2958.2009.06925.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mycobacteria encode putative class II polyphosphate kinases (PPKs). We report that recombinant PPK2 of Mycobacterium tuberculosis catalyses the synthesis of GTP from GDP using polyphosphate rather than ATP as phosphate donor. Unlike that of PPK1, this is the favoured reaction of PPK2. The sites of autophosphorylation, H115 and H247, as well as G74 were critical for GTP-synthesizing activity. Compromised survival of a ppk2 knockout (PPK2-KO) of Mycobacterium smegmatis under heat or acid stress or hypoxia, and the ability of ppk2 of M. tuberculosis to complement this, confirmed that PPK2 plays a role in mycobacterial survival under stress. Intracellular ATP : GTP ratio was higher in PPK2-KO compared with the wild-type M. smegmatis, bringing to light a role of PPK2 in regulating the intracellular nucleotide pool. We present evidence that PPK2 does so by interacting with nucleoside diphosphate kinase (Ndk). Pull-down assays and analysis by surface plasmon resonance demonstrated that the interaction requires G74 of PPK2(MTB) and (109)LET(111) of Ndk(MTB). In summary, we unravel a novel mechanism of regulation of nucleotide pools in mycobacteria. Downregulation of ppk2 impairs survival of M. tuberculosis in macrophages, suggesting that PPK2 plays an important role in the physiology of the bacteria residing within macrophages.
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Affiliation(s)
- Kamakshi Sureka
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
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13
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Coutinho-Silva R, Corrêa G, Sater AA, Ojcius DM. The P2X(7) receptor and intracellular pathogens: a continuing struggle. Purinergic Signal 2009; 5:197-204. [PMID: 19214779 DOI: 10.1007/s11302-009-9130-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 09/16/2008] [Indexed: 02/07/2023] Open
Abstract
The purinergic receptor, P2X(7), has recently emerged as an important component of the innate immune response against microbial infections. Ligation of P2X(7) by ATP can stimulate inflammasome activation and secretion of proinflammatory cytokines, but it can also lead directly to killing of intracellular pathogens in infected macrophages and epithelial cells. Thus, while some intracellular pathogens evade host defense responses by modulating with membrane trafficking or cell signaling in the infected cells, the host cells have also developed mechanisms for inhibiting infection. This review will focus on the effects of P2X(7) on control of infection by intracellular pathogens, microbial virulence factors that interfere with P2X(7) activity, and recent evidence linking polymorphisms in human P2X(7) with susceptibility to infection.
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Affiliation(s)
- Robson Coutinho-Silva
- Immunobiology Program, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, 21941-902, RJ, Brazil,
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Thakur RK, Kumar P, Halder K, Verma A, Kar A, Parent JL, Basundra R, Kumar A, Chowdhury S. Metastases suppressor NM23-H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression. Nucleic Acids Res 2008; 37:172-83. [PMID: 19033359 PMCID: PMC2615625 DOI: 10.1093/nar/gkn919] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulatory influence of the G-quadruplex or G4 motif present within the nuclease hypersensitive element (NHE) in the promoter of c-MYC has been noted. On the other hand, association of NM23-H2 to the NHE leads to c-MYC activation. Therefore, NM23-H2 interaction with the G4 motif within the c-MYC NHE presents an interesting mechanistic possibility. Herein, using luciferase reporter assay and chromatin immunoprecipitation we show NM23-H2 mediated c-MYC activation involves NM23-H2-G4 motif binding within the c-MYC NHE. G4 motif complex formation with recombinant NM23-H2 was independently confirmed using fluorescence energy transfer, which also indicated that the G4 motif was resolved to an unfolded state within the protein-bound complex. Taken together, this supports transcriptional role of NM23-H2 via a G4 motif.
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Affiliation(s)
- Ram Krishna Thakur
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
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Mattoo AR, Saif Zaman M, Dubey GP, Arora A, Narayan A, Jailkhani N, Rathore K, Maiti S, Singh Y. Spo0B of Bacillus anthracis - a protein with pleiotropic functions. FEBS J 2008; 275:739-52. [PMID: 18190531 DOI: 10.1111/j.1742-4658.2007.06240.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spo0B is an important component of the phosphorelay signal transduction pathway, the pathway involved in the initiation of sporulation in Bacillus subtilis. Bioinformatic, phylogenetic and biochemical studies showed that Spo0B of Bacillus anthracis has evolved from citrate/malate kinases. During the course of evolution, Spo0B has retained the characteristic histidine kinase boxes H, N, F, G(1) and G(2), and has acquired nucleotide-binding domains, Walker A and Walker B, of ATPases. Owing to the presence of these domains, autophosphorylation and ATPase activity was observed in Spo0B of B. anthracis. Mutational studies showed that among the six histidine residues, His13 of the H-box is involved in the autophosphorylation activity of Spo0B, whereas Lys33 of the Walker A domain is associated with the ATPase activity of the protein. Thermodynamic and binding studies of the binding of Mg-ATP to Spo0B using isothermal titration calorimetry (ITC) suggested that the binding is driven by favorable entropy changes and that the reaction is exothermic, with an apparent dissociation constant (K(d)) equal to 0.02 mm. The value of the dissociation constant (K(d) = 0.05 mm) determined by the intrinsic fluorescence of trytophan of Spo0B was similar to that obtained by ITC studies. The purified Spo0B of B. anthracis also showed nucleoside diphosphate kinase-like activity of phosphate transfer from nucleoside triphosphate to nucleoside diphosphate. This is the first evidence for Spo0B of B. anthracis as an enzyme with histidine kinase and ATPase activities, which may have important roles to play in sporulation and pathogenesis.
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Affiliation(s)
- Abid R Mattoo
- Allergy and Infectious Diseases, Institute of Genomics and Integrative Biology, Delhi, India
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Kumar P, Verma A, Saini AK, Chopra P, Chakraborti PK, Singh Y, Chowdhury S. Nucleoside diphosphate kinase from Mycobacterium tuberculosis cleaves single strand DNA within the human c-myc promoter in an enzyme-catalyzed reaction. Nucleic Acids Res 2005; 33:2707-14. [PMID: 15888727 PMCID: PMC1097768 DOI: 10.1093/nar/gki568] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The reason for secretion of nucleoside diphosphate kinase (NdK), an enzyme involved in maintaining the cellular pool of nucleoside triphosphates in both prokaryotes and eukaryotes, by Mycobacterium tuberculosis is intriguing. We recently observed that NdK from M.tuberculosis (mNdK) localizes within nuclei of HeLa and COS-1 cells and also nicks chromosomal DNA in situ (A. K. Saini, K. Maithal, P. Chand, S. Chowdhury, R. Vohra, A. Goyal, G. P. Dubey, P. Chopra, R. Chandra, A. K. Tyagi, Y. Singh and V. Tandon (2004) J. Biol. Chem., 279, 50142–50149). In the current study, using a molecular beacon approach, we demonstrate that the mNdK catalyzes the cleavage of single strand DNA. It displays Michaelis–Menten kinetics with a kcat/KM of 9.65 (±0.88) × 106 M−1 s−1. High affinity (Kd ≈ KM of ∼66 nM) and sequence-specific binding to the sense strand of the nuclease hypersensitive region in the c-myc promoter was observed. This is the first study demonstrating that the cleavage reaction is also enzyme-catalyzed in addition to the enzymatic kinase activity of multifunctional NdK. Using our approach, we demonstrate that GDP competitively inhibits the nuclease activity with a KI of ∼1.9 mM. Recent evidence implicates mNdK as a potent virulence factor in tuberculosis owing to its DNase-like activity. In this context, our results demonstrate a molecular mechanism that could be the basis for assessing in situ DNA damage by secretory mNdK.
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Affiliation(s)
| | | | | | | | | | | | - Shantanu Chowdhury
- To whom correspondence should be addressed. Tel: +91 11 2766 6156; Fax: +91 11 2766 7471;
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Saini AK, Maithal K, Chand P, Chowdhury S, Vohra R, Goyal A, Dubey GP, Chopra P, Chandra R, Tyagi AK, Singh Y, Tandon V. Nuclear Localization and in Situ DNA Damage by Mycobacterium tuberculosis Nucleoside-diphosphate Kinase. J Biol Chem 2004; 279:50142-9. [PMID: 15377659 DOI: 10.1074/jbc.m409944200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleoside-diphosphate kinase of Mycobacterium tuberculosis (mNdK) is a secretory protein, but the rationale behind secreting an enzyme involved in the maintenance of cellular pool of nucleoside triphosphates is not clearly understood. To elucidate the biological significance of mNdK secretion, we expressed mNdK fused to green fluorescent protein in HeLa and COS-1 cells. Interestingly, mNdK was detected in the nuclei of HeLa and COS-1 cells. Incubation of mNdK with nuclei isolated from HeLa and COS-1 cells led to in situ damage of chromosomal DNA. Surface plasmon resonance studies demonstrated that mNdK binds supercoiled plasmid DNA lacking apurinic/apyrimidinic sites with a dissociation constant of 30 +/- 3.2 mum. Plasmid cleavage by mNdK was found to be dependent on the specific divalent metal ion and inhibited by a metal ion chelator. Moreover, the metal ion-dependent DNA cleavage by mNdK was mediated by superoxide radicals as detected by electron paramagnetic resonance. The cleavage reaction was inhibited under nitrogen atmosphere confirming the necessity of molecular oxygen for DNA cleavage. In view of the findings that mNdK is secreted by intracellular mycobacteria and damages the nuclear DNA, it can be postulated that mNdK may cause cell death that could help in the dissemination of the pathogen.
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Affiliation(s)
- Adesh Kumar Saini
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
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