Identification and characterization of andalusicin: N-terminally dimethylated class III lantibiotic from Bacillus thuringiensis sv. andalousiensis Anastasiia Grigoreva, Julia Andreeva, Dmitry Bikmetov, Anastasiia Rusanova, Marina Serebryakova, Andrea Hernandez Garcia, Darya Slonova, Satish Nair, Guy Lippens, Konstantin Severinov, et al. To cite this version: Anastasiia Grigoreva, Julia Andreeva, Dmitry Bikmetov, Anastasiia Rusanova, Marina Serebryakova, et al.. Identification and characterization of andalusicin: N-terminally dimethylated class III lantibiotic from Bacillus thuringiensis sv. andalousiensis. iScience, Elsevier, 2021, 24 (5), 10.1016/j.isci.2021.102480. hal-03270626 HAL Id: hal-03270626 https://hal.inrae.fr/hal-03270626 Submitted on 25 Jun 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License iScience ll OPEN ACCESS Article Identification and characterization of andalusicin: N-terminally dimethylated class III lantibiotic from Bacillus thuringiensis sv. andalousiensis Anastasiia Grigoreva, Julia Andreeva, Dmitry Bikmetov,...,Guy Lippens, Konstantin Severinov, Svetlana Dubiley [email protected] (K.S.) [email protected] (S.D.) Highlights Type III lanthipeptide andalusicin A inhibits the growth of Gram-positive bacteria Andalusicin A has an unusual pastor’s crook structure Genes encoding methyltransferases are frequently found in andalusicin-like BGCs N-terminal methylation is necessary for andalusicin A biological activity Grigoreva et al., iScience 24, 102480 May 21, 2021 ª 2021 The Author(s). https://doi.org/10.1016/ j.isci.2021.102480 iScience ll OPEN ACCESS Article Identification and characterization of andalusicin: N-terminally dimethylated class III lantibiotic from Bacillus thuringiensis sv. andalousiensis Anastasiia Grigoreva,1,2 Julia Andreeva,1,2 Dmitry Bikmetov,3,4 Anastasiia Rusanova,2 Marina Serebryakova,2,5 Andrea Hernandez Garcia,6 Darya Slonova,1 Satish K. Nair,6 Guy Lippens,7 Konstantin Severinov,1,3,4,8,9,* and Svetlana Dubiley1,2,* SUMMARY Lanthipeptides, ribosomally synthesized and post-translationally modified pep- tides (RiPPs), can be divided into five classes based on their structures and biosyn- thetic pathways. Class I and II lanthipeptides have been well characterized, whereas less is known about members of the other three classes. Here, we describe a new family of class III lanthipeptides from Firmicutes. Members of the family are distinguished by the presence of a single carboxy-terminal labionin. We identified and characterized andalusicin, a representative of this family. Anda- lusicin bears two methyl groups at the a-amino terminus, a post-translational 1Center of Life Sciences, modification that has not previously been identified in class III lanthipeptides. Skolkovo Institute of Science and Technology, 121205 Mature andalusicin A shows bioactivity against various Gram-positive bacteria, Moscow, Russia an activity that is highly dependent on the a-N dimethylation. 2Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, INTRODUCTION Russia Lanthipeptides represent the largest known family of ribosomally synthesized and post-translationally 3Center for Precision modified peptides (RiPPs). They are synthesized as linear precursor peptides by the ribosome and then un- Genome Editing and Genetic Technologies for dergo post-translational modifications (PTMs) (Arnison et al., 2013; Montalba´ n-Lo´ pez et al., 2021). The Biomedicine, Institute of PTMs are localized in the core part of the precursor peptide, whereas the leader sequence recruits the Gene Biology, Russian modification enzymes. After the modifications are installed, the leader is cleaved off during (or sometimes Academy of Sciences, Moscow 119334, Russia after) export from the producing cell (Oman and van der Donk, 2010). Genes required for biosynthesis of 4Institute of Molecular bacterial RiPPs usually form compact biosynthetic gene clusters (BGCs). Lanthipeptide BGCs contain Genetics, Russian Academy gene(s) encoding the precursor peptide(s) and enzymes required for post-translational introduction of of Sciences, Moscow 123182, Russia the family-defining lanthionine cross-link in the precursor (Figure 1). In addition, some lanthipeptide 5 BGCs contain accessory genes coding for export pumps and/or self-immunity mechanisms (Stein et al., A.N. Belozersky Institute of Physico-Chemical Biology, 2003), leader peptidases (Lagedroste et al., 2017), and various tailoring enzymes responsible for secondary Lomonosov Moscow State PTMs (Acedo et al., 2019; Iorio et al., 2014; Wiebach et al., 2018). University, Moscow 119991, Russia b 6Department of The lanthionine (a -thioether linkage) is installed in two steps, which are catalyzed by a multifunctional lan- Biochemistry, University of thionine synthetase (in class IIÀIV lanthipeptides), the sequential action of dehydratase and cyclase (in class Illinois at I lanthipeptides) (Repka et al., 2017), or putative lyase, kinase, and cyclase (in class V) (Xu et al., 2020). Select Urbana-Champaign, Champaign, IL 61801 USA Ser or Thr residues of the precursor are dehydrated to dehydroalanine (Dha)/dehydrobutyrine (Dhb). Next, 7Toulouse Biotechnology a thiol group of a Cys is added to the double bond in a 1,4 conjugate addition reaction to form either a Institute (TBI), Universite´ de lanthionine (Lan) or a methyl-lanthionine (MeLan), respectively (Knerr and van der Donk, 2012). C-terminal Toulouse, CNRS, INRA, INSA, lanthionine and MeLan can undergo decarboxylation resulting in (2-aminovynyl)-cysteine (AviCys) and 2- Toulouse 31077, France aminovinyl-3-methyl-cysteine (AviMeCys), respectively (Ortega et al., 2017; Schneider et al., 2000). In 8Waksman Institute for Microbiology, Piscataway, NJ some cases lanthipeptides contain more complex labionin (Lab)/methyllabionin (MeLab) structures, which 08854-8020, USA form upon the dehydration and macrocyclization of three residues, Ser/Ser/Cys or Ser/Thr/Cys, respec- 9Lead contact tively (Figure 1)(Meindl et al., 2010). *Correspondence: [email protected]. Class IIIÀV lanthipeptides are the least studied, and only a handful of representatives of either of these clas- edu (K.S.), À [email protected] sesareknown.ClassIII IV lanthipeptides are synthetized by a multifunctional lanthionine synthetase (S.D.) composed of three domains (Figure 1): the central kinase domain that activates Ser and Thr residues https://doi.org/10.1016/j.isci. through phosphorylation; the N-terminal lyase domain, responsible for phosphate elimination; and the 2021.102480 iScience 24, 102480, May 21, 2021 ª 2021 The Author(s). 1 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). ll iScience OPEN ACCESS Article Figure 1. Five classes of lanthipeptides Schematic domain organizations of lanthionine synthetases from different classes are depicted above representative lanthipeptides from each class. Conserved zinc-binding residues in the cyclase domains are marked by vertical lines. Post- translational modifications common for Ser, Thr, and Cys residues of lanthipeptides are shown in magenta, blue, and green colors, respectively. C-terminal cyclization domain (LanC) that catalyzes the conjugate addition (Hegemann et al., 2019). The latter domain discriminates class III (LanKC) and IV (LanL) enzymes, as LanKC C-terminal domains do not contain the characteristic zinc-binding residues conserved in other cyclases (Wang and van der Donk, 2012). The unique feature of LanKC enzymes is the ability to install labionin/methyllabionin structures; how- ever, the exact mechanism of this process remains unknown (Hegemann and Su¨ ssmuth, 2020). Here, we report the identification and functional characterization of a novel lanthipeptide biosynthetic gene cluster from Bacillus thuringiensis sv. andalousiensis NRRL B23139 and structural characterization 2 iScience 24, 102480, May 21, 2021 iScience ll Article OPEN ACCESS Figure 2. B. thuringiensis sv. andalousiensis NRRL B23139 produces lanthipeptides (A) Antimicrobial activity assay of B. thuringiensis sv. andalousiensis NRRL B23139 against B. cereus ATCC 4342. A small clear halo around a patch of B. thuringiensis NRRL B23139 cells indicates the production of a secreted antimicrobial compound active against B. cereus ATCC 4342 cells forming the surrounding lawn. A patch of B. cereus ATCC 4342 cells was used as a negative control (no production of inhibitory compounds expected). (B) MALDI-TOF-MS analysis of a B. thuringiensis cellular extract. (C) MALDI-TOF-MS/MS spectrum of andalusicin A. Only b-ions are labeled for clarity. Amino acids are marked according to standard classification; Dhb stands for dehydrobutyrine. A difference in 683 Da between the precursor ion and the first b-ion matches the mass of the C-terminal STISNCC fragment of AncA1/A2 peptides assuming that all Ser and Thr residues are dehydrated. (D) A scheme of B. thuringiensis sv. andalousiensis NRRL B23139 lanthipeptide biosynthesis