Abstract
Objectives
To characterize a pyrazinamidase from non-pathogen Pseudonocardia carboxydivorans.
Results
A pyrazinamidase gene pncA encoding a 23-kDa protein PncA-Pse from P. carboxydivorans was over-expressed in Escherichia coli and characterized. This PncA-Pse can convert both pyrazinamide and nicotinamide efficiently with the optimal pH and temperature of pH 8.5 and 45 °C, respectively. Although ferrous iron and manganese were detected in PncA-Pse, the enzymatic activity is not affected by EDTA with the final concentration of 10 mM. Moreover, the enzymatic activity was not significantly affected with the addition of several metal ions, respectively. Based on the structure modeling, the 61st histidine which is associated with the metal binding, was mutated into alanine to get mutant H61A. No activity, iron and manganese were detected for H61A, which implies that PncA-Pse is a metal enzyme with resistance of the metal ion chelator EDTA, which is different from the previous reports.
Conclusion
This is the first characterized pyrazinamidase from the genus Pseudonocardia, a non-pathogen.
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References
Bagshawe KD (2006) Antibody-directed enzyme prodrug therapy (ADEPT) for cancer. Expert Rev Anticancer Ther 6:1421–1431. https://doi.org/10.1586/14737140.6.10.1421
Butterfield CN et al (2016) Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 4:e2687. https://doi.org/10.7717/peerj.2687
Chen WT, Yao ZL (2011) Synthesis and characterization of a dysprosium complex with strong photoluminescence. J Coord Chem 64:996–1005. https://doi.org/10.1080/00958972.2011.560937
Cheng SJ, Thibert L, Sanchez T, Heifets L, Zhang Y (2000) pncA mutations as a major mechanism of pyrazinamide resistance in Mycobacterium tuberculosis: Spread of a monoresistant strain in Quebec, Canada. Antimicrob Agents Ch 44:528–532. https://doi.org/10.1128/Aac.44.3.528-532.2000
Chi WJ, Doong SL, Lin-Shiau SY, Boone CW, Kelloff GJ, Lin JK (1998) Oltipraz, a novel inhibitor of hepatitis B virus transcription through elevation of p53 protein. Carcinogenesis 19:2133–2138. https://doi.org/10.1093/carcin/19.12.2133
Chiu YC, Huang SF, Yu KW, Lee YC, Feng JY, Su WJ (2011) Characteristics of pncA mutations in multidrug-resistant tuberculosis in Taiwan. BMC Infect Dis 11:240. https://doi.org/10.1186/1471-2334-11-240
Doustdar F, Khosravi AD, Farnia P (2009) Mycobacterium tuberculosis genotypic diversity in pyrazinamide-resistant isolates of Iran. Microb Drug Resist 15:251–256. https://doi.org/10.1089/mdr.2009.0066
French JB, Cen Y, Sauve AA, Ealick SE (2010a) High-resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into the catalytic mechanism and inhibition by aldehydes. Biochemistry 49:8803–8812. https://doi.org/10.1021/bi1012436
French JB, Cen Y, Vrablik TL, Xu P, Allen E, Hanna-Rose W, Sauve AA (2010b) Characterization of nicotinamidases: steady state kinetic parameters, classwide inhibition by nicotinaldehydes, and catalytic mechanism. Biochemistry 49:10421–10439. https://doi.org/10.1021/bi1012518
Gagneux S et al (2006) Variable host–pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci 103:2869–2873
Ghislain M, Talla E, Francois JM (2002) Identification and functional analysis of the Saccharomyces cerevisiae nicotinamidase gene. PNCI Yeast 19:215–224. https://doi.org/10.1002/yea.810
Guo M, Sun Z, Zhang Y (2000) Mycobacterium smegmatis has two pyrazinamidase enzymes, PncA and pzaA. J Bacteriol 182:3881–3884
Han L et al (2011) Synthesis, structure and thermal behavior of a new coordination polymer based on mixed pyrazine-2-carboxylate and oxalate ligands. J Chem Crystallogr 41:596–600. https://doi.org/10.1007/s10870-011-0002-1
Henssen A (1957) Morphology and system of thermophilic actinomycetes. Archiv fur Mikrobiologie 26:373–414
Hou L, Osei-Hyiaman D, Zhang Z, Wang B, Yang A, Kano K (2000) Molecular characterization of pncA gene mutations in Mycobacterium tuberculosis clinical isolates from China. Epidemiol Infect 124:227–232
Jewett MW, Jain S, Linowski AK, Sarkar A, Rosa PA (2011) Molecular characterization of the Borrelia burgdorferi in vivo-essential protein PncA. Microbiology 157:2831–2840. https://doi.org/10.1099/mic.0.051706-0
Joshi JG, Handler P (1962) Purification and properties of nicotinamidase from Torula cremoris. J Biol Chem 237:929–935
Khan MT et al (2018) Pyrazinamide-resistant mycobacterium tuberculosis isolates from Khyber Pakhtunkhwa and rpsA mutations. J Biol Regul Homeost Agents 32:705–709
Konno K, Feldmann FM, McDermott W (1967) Pyrazinamide susceptibility and amidase activity of tubercle bacilli. Am Rev Respir Dis 95:461–469. https://doi.org/10.1164/arrd.1967.95.3.461
Lee KW, Lee JM, Jung KS (2001) Characterization of pncA mutations of pyrazinamide-resistant Mycobacterium tuberculosis in Korea. J Korean Med Sci 16:537–543. https://doi.org/10.3346/jkms.2001.16.5.537
Malik SI, Ali S, Masood N, Nadeem T, Khan AS, Afzal MT (2019) Pyrazinamide resistance and mutations in pncA among isolates of Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan. BMC Infect Dis 19:116. https://doi.org/10.1186/s12879-019-3764-2
Moolten FL (1986) Tumor chemosensitivity conferred by inserted herpes thymidine kinase genes—paradigm for a prospective cancer control strategy. Cancer Res 46:5276–5281
Mukhopadhyay S, Chandalia SB (1999) Kinetics of the highly selective liquid-phase oxidation of side chain alkyl groups in 2-methylpyrazine and picolines by selenium dioxide. Org Process Res Dev 3:455–459. https://doi.org/10.1021/Op990042b
Mullen CA, Kilstrup M, Blaese RM (1992) Transfer of the bacterial gene for cytosine deaminase to mammalian-cells confers lethal sensitivity to 5-fluorocytosine—a negative selection system. P Natl Acad Sci USA 89:33–37. https://doi.org/10.1073/Pnas.89.1.33
Pardee AB, Benz EJ Jr, St Peter DA, Krieger JN, Meuth M, Trieshmann HW Jr (1971) Hyperproduction and purification of nicotinamide deamidase, a microconstitutive enzyme of Escherichia coli. J Biol Chem 246:6792–6796
Park SK et al (2001) pncA mutations in clinical Mycobacterium tuberculosis isolates from Korea. BMC Infect Dis 1:4
Petrella S, Gelus-Ziental N, Maudry A, Laurans C, Boudjelloul R, Sougakoff W (2011) Crystal structure of the pyrazinamidase of Mycobacterium tuberculosis: insights into natural and acquired resistance to pyrazinamide. PLoS ONE 6:e15785. https://doi.org/10.1371/journal.pone.0015785
Ping X, Li W, Xu L, Jiang C (2003) A microwave-based method for genomic DNA extraction from actinomycetes. Microbiology 30:82–84
Portugal I, Barreiro L, Moniz-Pereira J, Brum L (2004) pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis isolates in Portugal. Antimicrob Agents Chemother 48:2736–2738. https://doi.org/10.1128/aac.48.7.2736-2738.2004
Prochaska HJ, Chavan SJ, Baron P, Polsky B (1995) Oltipraz, a novel inhibitor of human immunodeficiency virus type 1 (HIV-1) replication. J Cell Biochem Suppl 22:117–125
Rehman AU, Khan MT, Liu H, Wadood A, Malik SI, Chen H-F (2019) Exploring the pyrazinamide drug resistance mechanism of clinical mutants T370P and W403G in ribosomal protein S1 of Mycobacterium tuberculosis. J Chem Inf Model 59:1584–1597. https://doi.org/10.1021/acs.jcim.8b00956
Rodrigues Vde F, Telles MA, Ribeiro MO, Cafrune PI, Rossetti ML, Zaha A (2005) Characterization of pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis in Brazil. Antimicrob Agents Chemother 49:444–446. https://doi.org/10.1128/aac.49.1.444-446.2005
Scorpio A, Zhang Y (1996) Mutations in pncA, a gene encoding pyrazinamidase/nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in tubercle bacillus. Nat Med 2:662–667
Shi W et al (2011) Pyrazinamide inhibits trans-translation in Mycobacterium tuberculosis. Science 333:1630–1632. https://doi.org/10.1126/science.1208813
Stekhanova TN, Bezsudnova EY, Mardanov AV, Osipov EM, Ravin NV, Skryabin KG, Popov VO (2014) Nicotinamidase from the thermophilic archaeon Acidilobus saccharovorans: structural and functional characteristics. Biochem Biokhimiia 79:54–61. https://doi.org/10.1134/S0006297914010088
Sun ZZY (1999) Reduced pyrazinamidase activity and the natural resistance of Mycobacterium kansasii to the antituberculosis drug pyrazinamide. Antimicrob Agents Chemother 43(3):537–542
Sun Z, Scorpio A, Zhang Y (1997) The pncA gene from naturally pyrazinamide-resistant Mycobacterium avium encodes pyrazinamidase and confers pyrazinamide susceptibility to resistant M. tuberculosis complex organisms. Microbiology 143(10):3367–3373. https://doi.org/10.1099/00221287-143-10-3367
Tanigawa Y, Shimoyama M, Dohi K, Ueda I (1972) Purification and properties of nicotinamide deamidase from Flavobacterium peregrinum. J Biol Chem 247:8036–8042
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. https://doi.org/10.1093/nar/25.24.4876
Williams EM et al (2015) Nitroreductase gene-directed enzyme prodrug therapy: insights and advances toward clinical utility. Biochem J 471:131–153. https://doi.org/10.1042/BJ20150650
Xu J et al (2014) Functional and structural studies of pullulanase from Anoxybacillus sp. LM18-11. Proteins 82:1685–1693. https://doi.org/10.1002/prot.24498
Zhang H, Bi L, Li C, Sun Z, Deng J, Zhang X (2009) Mutations found in the pncA gene of Mycobacterium tuberculosis in clinical pyrazinamide-resistant isolates from a local region of China. J Int Med Res 37:1430–1435
Zhang H et al (2008) Characterization of Mycobacterium tuberculosis nicotinamidase/pyrazinamidase. FEBS J 275:753–762. https://doi.org/10.1111/j.1742-4658.2007.06241.x
Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinform 9:40. https://doi.org/10.1186/1471-2105-9-40
Zhang Y, Shi W, Zhang W, Mitchison D (2014) Mechanisms of pyrazinamide action and resistance. Microbiol Spec. https://doi.org/10.1128/microbiolspec.MGM2-0023-2013
Acknowledgements
This study was supported by National Key R&D Program of China (Grant No. 2018YFA090091-02) and 2016 Wuhan Yellow Crane Talents (Science) Program.
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Yan, C., Zhang, J., Wu, P. et al. An EDTA-resistant pyrazinamidase from non-pathogen Pseudonocardia carboxydivorans. Biotechnol Lett 42, 1707–1718 (2020). https://doi.org/10.1007/s10529-020-02890-5
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DOI: https://doi.org/10.1007/s10529-020-02890-5