Applied Microbiology and Biotechnology

, Volume 103, Issue 6, pp 2649–2664 | Cite as

Discovery and characterization of a novel C-terminal peptide carboxyl methyltransferase in a lassomycin-like lasso peptide biosynthetic pathway

  • Yu Su
  • Meng Han
  • Xianbin Meng
  • Yue Feng
  • Shizhong Luo
  • Changyuan Yu
  • Guojun ZhengEmail author
  • Shaozhou ZhuEmail author
Biotechnologically relevant enzymes and proteins


Lasso peptides belong to a peculiar family of ribosomally synthesized and post-translationally modified peptides (RiPPs)—natural products with an unusual isopeptide-bonded slipknot structure. Except for assembling of this unusual lasso fold, several further post-translational modifications of lasso peptides, including C-terminal methylation, phosphorylation/poly-phosphorylation, citrullination, and acetylation, have been reported recently. However, most of their biosynthetic logic have not been elucidated except the phosphorylated paeninodin lasso peptide. Herein, we identified two novel lassomycin-like lasso peptide biosynthetic pathways and, for the first time, characterized a novel C-terminal peptide carboxyl methyltransferase involved in these pathways. Our investigations revealed that this new family of methyltransferase could specifically methylate the C terminus of precursor peptide substrates, eventually leading to lassomycin-like C-terminal methylated lasso peptides. Our studies offer another rare insight into the extraordinary strategies of chemical diversification adopted by lasso peptide biosynthetic machinery and predicated two valuable sources for methylated lasso peptide discovery.


Lasso peptide Lassomycin Methyltransferase Ribosomally synthesized and post-translationally modified peptides 


Funding information

This work was supported by the Fundamental Research Funds for the Central Universities (No. XK1802-8 and XK1803-06), National Natural Science Foundation of China (NSFC, Grant No. 21706005), and National Great Science and Technology Projects (2018ZX09721001).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical statement

This article does not contain any studies with human participants or animals performed by any of the authors

Supplementary material

253_2019_9645_MOESM1_ESM.pdf (2.5 mb)
ESM 1 (PDF 2547 kb)


  1. Aldemir H, Gulder TAM (2017) Expanding the structural space of ribosomal peptides: autocatalytic N-methylation in Omphalotin biosynthesis. Angew Chem Int Edit 56(44):13570–13572. CrossRefGoogle Scholar
  2. Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian K-D, Fischbach MA, Garavelli JS, Goransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Muller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl H-G, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Sussmuth RD, Tagg JR, Tang G-L, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA (2013) Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 30(1):108–160. CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bayro MJ, Mukhopadhyay J, Swapna GVT, Huang JY, Ma L-C, Sineva E, Dawson PE, Montelione GT, Ebright RH (2003) Structure of antibacterial peptide Microcin J25: a 21-residue lariat Protoknot. J Am Chem Soc 125(41):12382–12383. CrossRefPubMedGoogle Scholar
  4. Burkhart BJ, Hudson GA, Dunbar KL, Mitchell DA (2015) A prevalent peptide-binding domain guides ribosomal natural product biosynthesis. Nat Chem Biol 11(8):564–570. CrossRefPubMedPubMedCentralGoogle Scholar
  5. Cano-Muniz S, Anthony R, Niemann S, Alffenaar JC (2018) New approaches and therapeutic options for Mycobacterium tuberculosis in a dormant state. Clin Microbiol Rev 31(1).
  6. Challis GL (2008) Genome Mining for Novel Natural Product Discovery. J Med Chem 51(9):2618–2628. CrossRefPubMedGoogle Scholar
  7. Corre C, Challis GL (2009) New natural product biosynthetic chemistry discovered by genome mining. Nat Prod Rep 26(8):977–986. CrossRefPubMedGoogle Scholar
  8. Demain LA (1999) Pharmaceutically active secondary metabolites of microorganisms. Appl Microbiol Biotechnol 52(4):455–463. CrossRefPubMedGoogle Scholar
  9. Duquesne S, Destoumieux-Garzón D, Zirah S, Goulard C, Peduzzi J, Rebuffat S (2007) Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli. Chem Biol 14(7):793–803. CrossRefPubMedGoogle Scholar
  10. Elsayed SS, Trusch F, Deng H, Raab A, Prokes I, Busarakam K, Asenjo JA, Andrews BA, van West P, Bull AT, Goodfellow M, Yi Y, Ebel R, Jaspars M, Rateb ME (2015) Chaxapeptin, a lasso peptide from Extremotolerant Streptomyces leeuwenhoekii strain C58 from the Hyperarid Atacama Desert. J Org Chem 80(20):10252–10260. CrossRefPubMedGoogle Scholar
  11. Feng Z, Ogasawara Y, Nomura S, Dairi T (2018) Biosynthetic gene cluster of a d-tryptophan-containing lasso peptide, MS-271. Chembiochem : a European journal of chemical biology 19(19):2045–2048. CrossRefPubMedGoogle Scholar
  12. Gavrish E, Sit Clarissa S, Cao S, Kandror O, Spoering A, Peoples A, Ling L, Fetterman A, Hughes D, Bissell A, Torrey H, Akopian T, Mueller A, Epstein S, Goldberg A, Clardy J, Lewis K (2014) Lassomycin, a Ribosomally synthesized cyclic peptide, kills Mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. Chem Biol 21(4):509–518. CrossRefPubMedPubMedCentralGoogle Scholar
  13. Harvey AL, Edrada-Ebel R, Quinn RJ (2015) The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 14(2):111–129. CrossRefPubMedGoogle Scholar
  14. Hegemann JD, Zimmermann M, Xie X, Marahiel MA (2013a) Caulosegnins I–III: a highly diverse Group of Lasso Peptides Derived from a single biosynthetic gene cluster. J Am Chem Soc 135(1):210–222. CrossRefPubMedGoogle Scholar
  15. Hegemann JD, Zimmermann M, Zhu S, Klug D, Marahiel MA (2013b) Lasso peptides from proteobacteria: genome mining employing heterologous expression and mass spectrometry. J Pept Sci 100(5):527–542. CrossRefGoogle Scholar
  16. Hegemann JD, Zimmermann M, Zhu S, Steuber H, Harms K, Xie X, Marahiel MA (2014) Xanthomonins I-III: a new class of lasso peptides with a seven-residue macrolactam ring. Angew Chem Int Ed 53(8):2230–2234. CrossRefGoogle Scholar
  17. Hegemann JD, Zimmermann M, Xie X, Marahiel MA (2015) Lasso peptides: an intriguing class of bacterial natural products. Acc Chem Res 48(7):1909–1919. CrossRefPubMedGoogle Scholar
  18. Inokoshi J, Matsuhama M, Miyake M, Ikeda H, Tomoda H (2012) Molecular cloning of the gene cluster for lariatin biosynthesis of Rhodococcus jostii K01-B0171. Appl Microbiol Biotechnol 95(2):451–460. CrossRefPubMedGoogle Scholar
  19. Inokoshi J, Koyama N, Miyake M, Shimizu Y, Tomoda H (2016) Structure-activity analysis of gram-positive bacterium-producing lasso peptides with anti-mycobacterial activity. Sci Rep 6:30375. CrossRefPubMedPubMedCentralGoogle Scholar
  20. Knappe TA, Linne U, Zirah S, Rebuffat S, Xie X, Marahiel MA (2008) Isolation and structural characterization of capistruin, a lasso peptide predicted from the genome sequence of Burkholderia thailandensis E264. J Am Chem Soc 130(34):11446–11454. CrossRefPubMedGoogle Scholar
  21. Koehn FE, Carter GT (2005) The evolving role of natural products in drug discovery. Nat Rev Drug Discov 4(3):206–220. CrossRefPubMedGoogle Scholar
  22. Lear S, Munshi T, Hudson AS, Hatton C, Clardy J, Mosely JA, Bull TJ, Sit CS, Cobb SL (2016) Total chemical synthesis of lassomycin and lassomycin-amide. Org Biomol Chem 14(19):4534–4541. CrossRefPubMedGoogle Scholar
  23. Lee H, Suh JW (2016) Anti-tuberculosis lead molecules from natural products targeting Mycobacterium tuberculosis ClpC1. J Ind Microbiol Biotechnol 43(2–3):205–212. CrossRefPubMedGoogle Scholar
  24. Letzel A-C, Pidot SJ, Hertweck C (2014) Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics 15(1):983. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Li Y, Ducasse R, Zirah S, Blond A, Goulard C, Lescop E, Giraud C, Hartke A, Guittet E, Pernodet J-L, Rebuffat S (2015) Characterization of Sviceucin from Streptomyces provides insight into enzyme exchangeability and disulfide bond formation in lasso peptides. ACS Chem Biol 10(11):2641–2649. CrossRefPubMedGoogle Scholar
  26. Mahanta N, Zhang Z, Hudson GA, van der Donk WA, Mitchell DA (2017) Reconstitution and substrate specificity of the radical S-Adenosyl-methionine Thiazole C-methyltransferase in Thiomuracin biosynthesis. J Am Chem Soc 139(12):4310–4313. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Maksimov MO, Link AJ (2014) Prospecting genomes for lasso peptides. J Ind Microbiol Biotechnol 41(2):333–344. CrossRefPubMedGoogle Scholar
  28. Maksimov MO, Pan SJ, James Link A (2012a) Lasso peptides: structure, function, biosynthesis, and engineering. Nat Prod Rep 29(9):996–1006. CrossRefPubMedGoogle Scholar
  29. Maksimov MO, Pelczer I, Link AJ (2012b) Precursor-centric genome-mining approach for lasso peptide discovery. Proc Natl Acad Sci USA 109(38):15223–15228. CrossRefPubMedGoogle Scholar
  30. Metelev M, Tietz Jonathan I, Melby Joel O, Blair Patricia M, Zhu L, Livnat I, Severinov K, Mitchell Douglas A (2015) Structure, bioactivity, and resistance mechanism of Streptomonomicin, an unusual lasso peptide from an understudied halophilic Actinomycete. Chem Biol 22(2):241–250. CrossRefPubMedPubMedCentralGoogle Scholar
  31. Metelev M, Arseniev A, Bushin LB, Kuznedelov K, Artamonova TO, Kondratenko R, Khodorkovskii M, Seyedsayamdost MR, Severinov K (2017) Acinetodin and Klebsidin, RNA polymerase targeting lasso peptides produced by human isolates of Acinetobacter gyllenbergii and Klebsiella pneumoniae. ACS Chem Biol 12(3):814–824. CrossRefPubMedGoogle Scholar
  32. Mevaere J, Goulard C, Schneider O, Sekurova ON, Ma H, Zirah S, Afonso C, Rebuffat S, Zotchev SB, Li Y (2018) An orthogonal system for heterologous expression of actinobacterial lasso peptides in Streptomyces hosts. Sci Rep 8(1):8232. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Newman DJ, Cragg GM (2016) Natural products as sources of new drugs from 1981 to 2014. J Nat Prod 79(3):629–661. CrossRefPubMedGoogle Scholar
  34. Ogawa T, Ochiai K, Tanaka T, Tsukuda E, Chiba S, Yano K, Yamasaki M, Yoshida M, Matsuda Y (1995) RES-701-2, −3 and −4, novel and selective endothelin type B receptor antagonists produced by Streptomyces sp. I. Taxonomy of producing strains, fermentation, isolation, and biochemical properties. J Antibiot 48(11):1213–1220CrossRefGoogle Scholar
  35. Oman TJ, van der Donk WA (2010) Follow the leader: the use of leader peptides to guide natural product biosynthesis. Nat Chem Biol 6(1):9–18CrossRefGoogle Scholar
  36. Ongpipattanakul C, Nair SK (2018) Molecular basis for autocatalytic backbone N-methylation in RiPP natural product biosynthesis. ACS Chem Biol 13(10):2989–2999. CrossRefPubMedPubMedCentralGoogle Scholar
  37. Parent A, Guillot A, Benjdia A, Chartier G, Leprince J, Berteau O (2016) The B12-radical SAM enzyme PoyC catalyzes valine Cbeta-methylation during Polytheonamide biosynthesis. J Am Chem Soc 138(48):15515–15518. CrossRefPubMedPubMedCentralGoogle Scholar
  38. Parish T (2014) Targeting mycobacterial proteolytic complexes with natural products. Chem Biol 21(4):437–438. CrossRefPubMedGoogle Scholar
  39. Piscotta FJ, Tharp JM, Liu WR, Link AJ (2015) Expanding the chemical diversity of lasso peptide MccJ25 with genetically encoded noncanonical amino acids. Chem Commun 51(2):409–412. CrossRefGoogle Scholar
  40. Ramm S, Krawczyk B, Muhlenweg A, Poch A, Mosker E, Sussmuth RD (2017) A self-sacrificing N-methyltransferase is the precursor of the fungal natural product Omphalotin. Angew Chem Int Ed 56(33):9994–9997. CrossRefGoogle Scholar
  41. Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5(4):725–738. CrossRefPubMedPubMedCentralGoogle Scholar
  42. Schon T, Miotto P, Koser CU, Viveiros M, Bottger E, Cambau E (2017) Mycobacterium tuberculosis drug-resistance testing: challenges, recent developments and perspectives. Clin Microbiol Infect 23(3):154–160. CrossRefPubMedGoogle Scholar
  43. Selvaraj A, Chen H-T, Ya-Ting Huang A, Kao C-L (2018) Expedient on-resin modification of a peptide C-terminus through a benzotriazole linker. Chem Sci 9(2):345–349. CrossRefPubMedGoogle Scholar
  44. Shen B (2015) A new Golden age of natural products drug discovery. Cell 163(6):1297–1300. CrossRefPubMedPubMedCentralGoogle Scholar
  45. Singh S, Chang A, Goff RD, Bingman CA, Gruschow S, Sherman DH, Phillips GN Jr, Thorson JS (2011) Structural characterization of the mitomycin 7-O-methyltransferase. Proteins 79(7):2181–2188. CrossRefPubMedPubMedCentralGoogle Scholar
  46. Tietz JI, Schwalen CJ, Patel PS, Maxson T, Blair PM, Tai HC, Zakai UI, Mitchell DA (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat Chem Biol 13(5):470–478. CrossRefPubMedPubMedCentralGoogle Scholar
  47. van der Velden NS, Kalin N, Helf MJ, Piel J, Freeman MF, Kunzler M (2017) Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products. Nat Chem Biol 13(8):833–835. CrossRefPubMedGoogle Scholar
  48. Velásquez JE, van der Donk WA (2011) Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol 15(1):11–21. CrossRefPubMedGoogle Scholar
  49. Wilson K-A, Kalkum M, Ottesen J, Yuzenkova J, Chait BT, Landick R, Muir T, Severinov K, Darst SA (2003) Structure of Microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail. J Am Chem Soc 125(41):12475–12483. CrossRefPubMedGoogle Scholar
  50. Wu B, Wijma HJ, Song L, Rozeboom HJ, Poloni C, Tian Y, Arif MI, Nuijens T, Quaedflieg PJLM, Szymanski W, Feringa BL, Janssen DB (2016) Versatile peptide C-terminal functionalization via a computationally engineered peptide amidase. ACS Catal 6(8):5405–5414. CrossRefGoogle Scholar
  51. Zerikly M, Challis GL (2009) Strategies for the discovery of new natural products by genome mining. ChemBioChem 10(4):625–633. CrossRefPubMedGoogle Scholar
  52. Zhang Q, van der Donk WA (2012) Catalytic promiscuity of a bacterial alpha-N-methyltransferase. FEBS Lett 586(19):3391–3397. CrossRefPubMedPubMedCentralGoogle Scholar
  53. Zhang Z, Mahanta N, Hudson GA, Mitchell DA, van der Donk WA (2017) Mechanism of a class C radical S-Adenosyl-l-methionine Thiazole methyl transferase. J Am Chem Soc 139(51):18623–18631. CrossRefPubMedPubMedCentralGoogle Scholar
  54. Zheng Q, Fang H, Liu W (2017) Post-translational modifications involved in the biosynthesis of thiopeptide antibiotics. Org Biomol Chem 15(16):3376–3390. CrossRefPubMedGoogle Scholar
  55. Zhou S, Alkhalaf LM, de Los Santos EL, Challis GL (2016) Mechanistic insights into class B radical-S-adenosylmethionine methylases: ubiquitous tailoring enzymes in natural product biosynthesis. Curr Opin Chem Biol 35:73–79. CrossRefPubMedGoogle Scholar
  56. Zhu S, Fage CD, Hegemann JD, Mielcarek A, Yan D, Linne U, Marahiel MA (2016a) The B1 protein guides the biosynthesis of a lasso peptide. Sci Rep 6:35604. CrossRefPubMedPubMedCentralGoogle Scholar
  57. Zhu S, Fage CD, Hegemann JD, Yan D, Marahiel MA (2016b) Dual substrate-controlled kinase activity leads to polyphosphorylated lasso peptides. FEBS Lett 590(19):3323–3334. CrossRefPubMedGoogle Scholar
  58. Zhu S, Hegemann JD, Fage CD, Zimmermann M, Xie X, Linne U, Marahiel MA (2016c) Insights into the unique phosphorylation of the lasso peptide Paeninodin. J Biol Chem 291(26):13662–13678. CrossRefPubMedPubMedCentralGoogle Scholar
  59. Zimmermann M, Hegemann Julian D, Xie X, Marahiel Mohamed A (2013) The Astexin-1 lasso peptides: biosynthesis, stability, and structural studies. Chem Biol 20(4):558–569. CrossRefPubMedGoogle Scholar
  60. Zong C, Cheung-Lee WL, Elashal HE, Raj M, Link AJ (2018) Albusnodin: an acetylated lasso peptide from Streptomyces albus. Chem Commun 54(11):1339–1342. CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Chemical Resources EngineeringBeijing University of Chemical TechnologyBeijingPeople’s Republic of China
  2. 2.College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingPeople’s Republic of China
  3. 3.MOE Key Laboratory of Bioinformatics, School of Life SciencesTsinghua UniversityBeijingPeople’s Republic of China

Personalised recommendations