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S41467-017-00439-1.Pdf ARTICLE DOI: 10.1038/s41467-017-00439-1 OPEN Biosynthesis of the nosiheptide indole side ring centers on a cryptic carrier protein NosJ Wei Ding1,2,3,4, Wenjuan Ji2, Yujie Wu2,3, Runze Wu2, Wan-Qiu Liu2, Tianlu Mo2, Junfeng Zhao2, Xiaoyan Ma2,3, Wei Zhang4, Ping Xu5, Zixin Deng6, Boping Tang1,YiYu6 & Qi Zhang 2 Nosiheptide is a prototypal thiopeptide antibiotic, containing an indole side ring in addition to its thiopeptide-characteristic macrocylic scaffold. This indole ring is derived from 3-methyl-2- indolic acid (MIA), a product of the radical S-adenosylmethionine enzyme NosL, but how MIA is incorporated into nosiheptide biosynthesis remains to be investigated. Here we report functional dissection of a series of enzymes involved in nosiheptide biosynthesis. We show NosI activates MIA and transfers it to the phosphopantetheinyl arm of a carrier protein NosJ. NosN then acts on the NosJ-bound MIA and installs a methyl group on the indole C4, and the resulting dimethylindolyl moiety is released from NosJ by a hydrolase-like enzyme NosK. Surface plasmon resonance analysis show that the molecular complex of NosJ with NosN is much more stable than those with other enzymes, revealing an elegant biosynthetic strategy in which the reaction flux is controlled by protein–protein interactions with different binding affinities. 1 Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bioagriculture, Yancheng Teachers University, Yancheng 224002, China. 2 Department of Chemistry, Fudan University, Shanghai 200433, China. 3 Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China. 4 Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou 730000, China. 5 State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China. 6 Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China. Correspondence and requests for materials should be addressed to B.T. (email: [email protected])orto Y.Y. (email: [email protected]) or to Q.Z. (email: [email protected]) NATURE COMMUNICATIONS | 8: 437 | DOI: 10.1038/s41467-017-00439-1 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-00439-1 ibosomally synthesized and posttranslationally modified MIA moiety and this methylation reaction involves a key peptides (RiPPs) are a major class of natural products, as methylene radical derived from 5′-methylthioadenosine, a SAM R 32, 33 revealed by the genome-sequencing programs of the past cleavage product . The nosN-knockout mutant of S. actuosus decade1, 2. These compounds are found in all three domains of produced a nosiheptide analogue (2), which contains an indolyl- life, possessing vast structural diversity ranging from relatively S-cysteine moiety, whereas the side ring is not formed14, 32. simple and linear structures as exemplified by linaridins3, 4 to This result suggests that the thioester bond formation with the highly modified and complex macrocyclic scaffolds. Among Cys8 thiol likely precedes the ester bond formation with the the most extensively modified RiPPs are thiopeptides, a class of Glu6 γ-carboxylate. Notably, lactocillin, a thiopeptide produced sulfur-rich, polyazole-containing macrocyclic peptides featuring a by a vaginal isolate Lactobacillus gasseri JV-V03, contains a dif- central six-membered nitrogen-containing heterocycle5. Similar ferent indolyl-S-cysteine moiety and does not have a side ring to all RiPPs, thiopeptides are produced from a ribosomally syn- system34, demonstrating the diverse biosynthetic chemistry in thesized precursor peptide, involving actions of highly divergent thiopeptide maturation. In this study, we report investigation of biosynthetic enzymes that are organized in a well-orchestrated nosiheptide biosynthesis by a series of genetic and biochemical – process6 12. The complex nature of thiopeptide biosynthesis is analysis. This investigation revealed the functions and substrate further demonstrated by the fact that some thiopeptides, such as specificities of four enzymes (NosI, NosJ, NosN and NosK) that nocathiacin and nosiheptide, contain additional macrocycle rings are involved in the construction of the nosiheptide indole side that are not derived from the ribosomally synthesized precursor ring, showing a well-organized biosynthetic process that centers – peptides13 16. on a previously unknown carrier protein NosJ. Nosiheptide (1) is a prototypic thiopeptide antibiotic produced by Streptomyces actuosus17, which is classified as an e-series thiopeptide, because it contains a hydroxypyridine moiety5. This Results compound blocks bacterial protein translation by targeting the NosI is an adenylating enzyme for MIA activation. The nosi- 50S ribosomal subunit18 and thereby exhibits highly potent heptide gene cluster encodes a putative acyl-CoA ligase NosI activity against various contemporary pathogens19. In addition (Fig. 1a), which is a possible candidate for MIA activation. to the ribosomally derived macrocyclic ring, nosiheptide also However, as proposed previously, it could also be possible that possesses a precursor peptide-independent side ring system that NosI activates the γ-carboxylate of Glu6 and forms the intra- mainly consists of an indolyl moiety. This indolyl moiety is molecular ester linkage (Fig. 1b)14. Because the nosN-knockout produced by a radical S-adenosylmethionine (SAM) enzyme mutant strain produces 2, a nosiheptide analogue whose side ring NosL, which converts L-Trp to 3-methyl-2-indolic acid (MIA, 3) is not formed (Fig. 1b), we reasoned that if NosI activates the via an unusual carbon chain rearrangement. NosL exhibits an Glu6 γ-carboxylate, a similar side ring-open analogue could be astonishing substrate and catalytic promiscuity, and its catalytic produced by the nosI-knockout mutant strain. To test this – mechanism has been investigated in detail20 30. It has been hypothesis, we knocked out nosI from S. actuosus by targeted in- shown that the indole side ring is installed before the formation of frame deletion of the 600-bp internal fragment. High-resolution the thiopeptide-characteristic macrocyclic scaffold31, but how (HR)-liquid chromatography (LC)-mass spectrometry (MS) MIA is processed and incorporated into nosiheptide biosynthesis analysis showed that nosiheptide production was completely remains unknown. abolished in the mutant (Fig. 2a, trace ii). However, no signal We recently showed that the radical SAM methyltransferase corresponding to a nosiheptide analog could be found. Instead, NosN is responsible for attaching a methyl group on the C4 of we observed a compound with a retention time much earlier than a A B C D E F G H I J K L M N O P Tailoring Thiopeptide framework Indolyl side ring Precursor peptide Regulation b HO HO NH2 H H N COOH N NH NH N S N S O O S S OH N L-Trp O N H O N O O NH NH O O Glu6 N S Glu6 N S NosL N N N N N SAM N HO S N S. actuosus S. actuosus S N H S H S Cys8 O wild type ΔnosN mutant COOH O OO Cys8 S OH NH S NH NosN Nosl N O O Nosl NosK H O N H N O NosK ? HN O H 2 N ? MIA, 3 H Nosiheptide, 1 2 COOH Fig. 1 Biosynthesis of nosiheptide by S. actuosus. a Organization of the nosiheptide biosynthetic gene cluster. Genes involved in the biosynthesis of the indolyl side ring (nosI, nosJ, nosK, nosL and nosN) are shown in red. b Nosiheptide contains an indolyl side ring that is not derived from the precursor peptide NosM. The NosL-derived indolic acid moiety (highlighted in blue) is a major component of the side ring, and the carbon atom introduced by the radical SAM methyltransferase NosN is highlighted with a red triangle. The nosN-knockout mutant of S. actuosus does not produce nosiheptide but an off-pathway product 2 2 NATURE COMMUNICATIONS | 8: 437 | DOI: 10.1038/s41467-017-00439-1 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-00439-1 ARTICLE a b a 9+ 11+ Nosiheptide, 1 MIA-Pan, 5 [M + 9H] NosJ SH, 7 [M + 11H] [M + 10H]10+ 8+ cal. 1020.51 [M + 8H] obs. 1020.48 iv 11+ iv [M + 11H] MIA, 3 iii iii MIA-AMP, 4 ii ii 800 850 900 950 1000 1050 1020.5 1021.0 1021.5 m/z m/z i i 12 14 16 18 20 22 4 6 8 b Time (min) Time (min) * Fig. 2 NosI is an adenylating enzyme for MIA activation. a HPLC traces 1 of the culture extracts from (i) S. actuosus wild-type strain, (ii) the 2 nosI-knockout mutant and (iv) the nosI-knockout mutant containing a 3 nosI-expressing plasmid; MIA synthetic standard (iii) was also analyzed to 4 confirm the production of MIA by the nosI-knockout mutant. b LC-MS 5 analysis of NosI in vitro activity, showing the extracted ion chromatograms + = (EICs) of [M+H] 505.1 (corresponding to MIA-AMP, 4) for (i) control c reaction with the supernatant of boiled NosI, (ii) NosI reaction with MIA 9+ 10+ 11+ + = [M + 9H] [M + 10H] NosJ S–MIA, 8 [M + 11H] and ATP; and the EICs of [M+H] 436.2 (corresponding to the MIA-Pan, 8+ [M + 8H] [M + 11H]11+ cal. 1034.78 5) for (iii) control reaction with the supernatant of boiled NosI and (iv) NosI obs. 1034.75 reaction with MIA, ATP, and pantetheine that of nosiheptide and a protonated molecular ion at m/z = 176.0708 (1.7 p.p.m. error for a calculated molecule for- 800 850 900 950 1000 1050 1035.5 mula of C10H10NO2) (Fig. 2a, trace ii). This compound was 1035.0 further validated to be MIA by coelution with the synthetic m/z m/z standard (Fig.
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