Abstract
Lantibiotic nukacin ISK-1 is produced by Staphylococcus warneri ISK-1. The dual functional transporter NukT, an ABC transporter maturation and secretion protein, contributes to cleavage of the leader peptide from the prepeptide (modified NukA) and the final transport of nukacin ISK-1. NukT consists of an N-terminal peptidase domain (PEP), a C-terminal nucleotide-binding domain (NBD), and a transmembrane domain (TMD). In this study, NukT and its peptidase-inactive mutant were expressed, purified, and reconstituted into liposomes for analysis of their peptidase and ATPase activities. The ATPase activity of the NBD region was shown to be required for the peptidase activity of the PEP region. Furthermore, we demonstrated for the first time that leader peptide cleavage by the PEP region significantly enhanced the ATPase activity of the NBD region. Taken together, the presented results offer new insights into the processing mechanism of lantibiotic transporters and the necessity of interdomain cooperation.
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References
Al-Shawi MK, Polar MK, Omote H, Figler RA (2003) Transition state analysis of the coupling of drug transport to ATP hydrolysis by P-glycoprotein. J Biol Chem 278(52):52629–52640. https://doi.org/10.1074/jbc.M308175200
Aso Y, Nagao J, Koga H, Okuda K, Kanemasa Y, Sashihara T, Nakayama J, Sonomoto K (2004) Heterologous expression and functional analysis of the gene cluster for the biosynthesis of and immunity to the lantibiotic, nukacin ISK-1. J Biosci Bioeng 98(6):429–436. https://doi.org/10.1016/S1389-1723(05)00308-7
Augustin J, Götz F (1990) Transformation of Staphylococcus epidermidis and other staphylococcal species with plasmid DNA by electroporation. FEMS Microbiol Lett 54(1–3):203–207
Bringel F, Hubert JC (1990) Optimized transformation by electroporation of Lactobacillus plantarum strains with plasmid vectors. Appl Microbiol Biotechnol 33(6):664–670. https://doi.org/10.1007/BF00604934
Choudhury HG, Tong Z, Mathavan I, Li Y, Iwata S, Zirah S, Rebuffat S, van Veen HW, Beis K (2014) Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state. Proc Natl Acad Sci U S A 111(25):9145–9150. https://doi.org/10.1073/pnas.1320506111
Davidson AL, Shuman HA, Nikaido H (1992) Mechanism of maltose transport in Escherichia coli: transmembrane signaling by periplasmic binding proteins. Proc Natl Acad Sci U S A 89(6):2360–2364. https://doi.org/10.1073/pnas.89.6.2360
Franke CM, Tiemersma J, Venema G, Kok J (1999) Membrane topology of the lactococcal bacteriocin ATP-binding cassette transporter protein LcnC. Involvement of LcnC in lactococcin a maturation. J Biol Chem 274(13):8484–8490. https://doi.org/10.1074/jbc.274.13.8484
Furgerson Ihnken LA, Chatterjee C, van der Donk WA (2008) In vitro reconstitution and substrate specificity of a lantibiotic protease. Biochemistry 47(28):7352–7363. https://doi.org/10.1021/bi800278n
Gebhard S (2012) ABC transporters of antimicrobial peptides in Firmicutes bacteria—phylogeny, function and regulation. Mol Microbiol 86(6):1295–1317. https://doi.org/10.1111/mmi.12078
Geertsma ER, Nik Mahmood NA, Schuurman-Wolters GK, Poolman B (2008) Membrane reconstitution of ABC transporters and assays of translocator function. Nat Protoc 3(2):256–266. https://doi.org/10.1038/nprot.2007.519
Ghobrial O, Derendorf H, Hillman JD (2010) Pharmacokinetic and pharmacodynamic evaluation of the lantibiotic MU1140. J Pharm Sci 99(5):2521–2528. https://doi.org/10.1002/jps.22015
Havarstein LS, Diep DB, Nes IF (1995) A family of bacteriocin ABC transporters carry out proteolytic processing of their substrates concomitant with export. Mol Microbiol 16(2):229–240. https://doi.org/10.1111/j.1365-2958.1995.tb02295.x
Ishii S, Yano T, Ebihara A, Okamoto A, Manzoku M, Hayashi H (2010) Crystal structure of the peptidase domain of Streptococcus ComA, a bifunctional ATP-binding cassette transporter involved in the quorum-sensing pathway. J Biol Chem 285(14):10777–10785. https://doi.org/10.1074/jbc.M109.093781
Ishii S, Yano T, Hayashi H (2006) Expression and characterization of the peptidase domain of Streptococcus pneumoniae ComA, a bifunctional ATP-binding cassette transporter involved in quorum sensing pathway. J Biol Chem 281(8):4726–4731. https://doi.org/10.1074/jbc.M512516200
Ishii S, Yano T, Okamoto A, Murakawa T, Hayashi H (2013) Boundary of the nucleotide-binding domain of Streptococcus ComA based on functional and structural analysis. Biochemistry 52(15):2545–2555. https://doi.org/10.1021/bi3017069
Islam MR, Nagao J, Zendo T, Sonomoto K (2012) Antimicrobial mechanism of lantibiotics. Biochem Soc Trans 40(6):1528–1533. https://doi.org/10.1042/BST20120190
Jabes D, Brunati C, Candiani G, Riva S, Romano G, Donadio S (2011) Efficacy of the new lantibiotic NAI-107 in experimental infections induced by multidrug-resistant Gram-positive pathogens. Antimicrob Agents Chemother 55(4):1671–1676. https://doi.org/10.1128/AAC.01288-10
Jin MS, Oldham ML, Zhang Q, Chen J (2012) Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans. Nature 490(7421):566–569. https://doi.org/10.1038/nature11448
Kimura H, Nagano R, Matsusaki H, Sonomoto K, Ishizaki A (1997) A bacteriocin of strain Pediococcus sp. ISK-1 isolated from Nukadoko, bed of fermented rice bran. Biosci Biotechnol Biochem 61(6):1049–1051. https://doi.org/10.1271/bbb.61.1049
Lecher J, Schwarz CK, Stoldt M, Smits SH, Willbold D, Schmitt L (2012) An RTX transporter tethers its unfolded substrate during secretion via a unique N-terminal domain. Structure 20(10):1778–1787. https://doi.org/10.1016/j.str.2012.08.005
Letzel AC, Pidot SJ, Hertweck C (2014) Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics 15(1):983. https://doi.org/10.1186/1471-2164-15-983
Lin DY, Huang S, Chen J (2015) Crystal structures of a polypeptide processing and secretion transporter. Nature 523(7561):425–430. https://doi.org/10.1038/nature14623
Locher KP (2016) Mechanistic diversity in ATP-binding cassette (ABC) transporters. Nat Struct Mol Biol 23(6):487–493. https://doi.org/10.1038/nsmb.3216
Nagao J, Asaduzzaman SM, Aso Y, Okuda K, Nakayama J, Sonomoto K (2006) Lantibiotics: insight and foresight for new paradigm. J Biosci Bioeng 102(3):139–149. https://doi.org/10.1263/jbb.102.139
Nagao J, Aso Y, Sashihara T, Shioya K, Adachi A, Nakayama J, Sonomoto K (2005a) Localization and interaction of the biosynthetic proteins for the lantibiotic, Nukacin ISK-1. Biosci Biotechnol Biochem 69(7):1341–1347. https://doi.org/10.1271/bbb.69.1341
Nagao J, Harada Y, Shioya K, Aso Y, Zendo T, Nakayama J, Sonomoto K (2005b) Lanthionine introduction into nukacin ISK-1 prepeptide by co-expression with modification enzyme NukM in Escherichia coli. Biochem Biophys Res Commun 336(2):507–513. https://doi.org/10.1016/j.bbrc.2005.08.125
Nishie M, Sasaki M, Nagao J, Zendo T, Nakayama J, Sonomoto K (2011) Lantibiotic transporter requires cooperative functioning of the peptidase domain and the ATP binding domain. J Biol Chem 286(13):11163–11169. https://doi.org/10.1074/jbc.M110.212704
Nishie M, Shioya K, Nagao J, Jikuya H, Sonomoto K (2009) ATP-dependent leader peptide cleavage by NukT, a bifunctional ABC transporter, during lantibiotic biosynthesis. J Biosci Bioeng 108(6):460–464. https://doi.org/10.1016/j.jbiosc.2009.06.002
Ortega MA, van der Donk WA (2016) New insights into the biosynthetic logic of ribosomally synthesized and post-translationally modified peptide natural products. Cell Chem Biol 23(1):31–44. https://doi.org/10.1016/j.chembiol.2015.11.012
Ortega MA, Velasquez JE, Garg N, Zhang Q, Joyce RE, Nair SK, van der Donk WA (2014) Substrate specificity of the lanthipeptide peptidase ElxP and the oxidoreductase ElxO. ACS Chem Biol 9(8):1718–1725. https://doi.org/10.1021/cb5002526
Pag U, Sahl HG (2002) Multiple activities in lantibiotics—models for the design of novel antibiotics? Curr Pharm Des 8(9):815–833. https://doi.org/10.2174/1381612023395439
Reimann S, Poschmann G, Kanonenberg K, Stuhler K, Smits SH, Schmitt L (2016) Interdomain regulation of the ATPase activity of the ABC transporter haemolysin B from Escherichia coli. Biochem J 473(16):2471–2483. https://doi.org/10.1042/BCJ20160154
Sahl HG, Bierbaum G (1998) Lantibiotics: biosynthesis and biological activities of uniquely modified peptides from gram-positive bacteria. Annu Rev Microbiol 52(1):41–79. https://doi.org/10.1146/annurev.micro.52.1.41
Sambrook J, Russell DW, Sambrook J (2006) The condensed protocols from molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
Shimafuji C, Noguchi M, Nishie M, Nagao J, Shioya K, Zendo T, Nakayama J, Sonomoto K (2015) In vitro catalytic activity of N-terminal and C-terminal domains in NukM, the post-translational modification enzyme of nukacin ISK-1. J Biosci Bioeng 120(6):624–629. https://doi.org/10.1016/j.jbiosc.2015.03.020
Tang WX, Dong SH, Repka LM, He C, Nair SK, van der Donk WA (2015) Applications of the class II lanthipeptide protease LicP for sequence-specific, traceless peptide bond cleavage. Chem Sci 6(11):6270–6279. https://doi.org/10.1039/c5sc02329g
Wang B, Dukarevich M, Sun EI, Yen MR, Saier MH Jr (2009) Membrane porters of ATP-binding cassette transport systems are polyphyletic. J Membr Biol 231(1):1–10. https://doi.org/10.1007/s00232-009-9200-6
Wang H, Fewer DP, Sivonen K (2011) Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria. PLoS One 6(7):e22384. https://doi.org/10.1371/journal.pone.0022384
Willey JM, van der Donk WA (2007) Lantibiotics: peptides of diverse structure and function. Annu Rev Microbiol 61(1):477–501. https://doi.org/10.1146/annurev.micro.61.080706.093501
Wu KH, Tai PC (2004) Cys32 and His105 are the critical residues for the calcium-dependent cysteine proteolytic activity of CvaB, an ATP-binding cassette transporter. J Biol Chem 279(2):901–909. https://doi.org/10.1074/jbc.M308296200
Xie L, van der Donk WA (2004) Post-translational modifications during lantibiotic biosynthesis. Curr Opin Chem Biol 8(5):498–507. https://doi.org/10.1016/j.cbpa.2004.08.005
Zhang Q, Doroghazi JR, Zhao X, Walker MC, van der Donk WA (2015) Expanded natural product diversity revealed by analysis of lanthipeptide-like gene clusters in actinobacteria. Appl Environ Microbiol 81(13):4339–4350. https://doi.org/10.1128/AEM.00635-15
Acknowledgements
Sen Zheng acknowledges the Ajinomoto Scholarship Foundation, Japan, fellowship for the financial aid through the study.
Funding
This work was partially supported by the Grants-in-Aid for Scientific Research (KAKENHI) from the Japan Society for the Promotion of Science (JSPS), grant number JP26292040.
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Zheng, S., Nagao, Ji., Nishie, M. et al. ATPase activity regulation by leader peptide processing of ABC transporter maturation and secretion protein, NukT, for lantibiotic nukacin ISK-1. Appl Microbiol Biotechnol 102, 763–772 (2018). https://doi.org/10.1007/s00253-017-8645-2
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DOI: https://doi.org/10.1007/s00253-017-8645-2