环番合成酶PacB催化Xye类核糖体肽翻译后修饰研究

韩沅均; 莫天录; 邓子新; 张琪; 丁伟

doi:10.12211/2096-8280.2021-080

您当前的位置：

首页 >

文章列表页 >

环番合成酶PacB催化Xye类核糖体肽翻译后修饰研究

研究论文 | 更新时间：2026-03-18

- 环番合成酶PacB催化Xye类核糖体肽翻译后修饰研究
- Study on the post-translational modification of RiPPs Xye catalyzed by CyFE PacB
- 合成生物学 2021年2卷第5期页码：826-836
- 作者机构：
  
  1.上海交通大学生命科学技术学院，微生物代谢国家重点实验室，上海 200240
  2.复旦大学化学系，上海 200243
- 作者简介：
  
  韩沅均（1998—），博士研究生。研究方向为化学生物学。
  丁伟（1981—），男，博士生导师，副教授。研究方向为微生物代谢及合成生物学。
- 基金信息：
  
  科技部重点研发计划(2018YFA0900402)
- DOI：10.12211/2096-8280.2021-080
  中图分类号： Q936
- 收稿：2021-08-01，
  
  修回：2021-08-12，
  
  纸质出版：2021-10-31
- 稿件说明：
移动端阅览
韩沅均，莫天录，邓子新，张琪，丁伟. 环番合成酶PacB催化Xye类核糖体肽翻译后修饰研究［J］. 合成生物学， 2021， 2（5）： 826-836

HAN Yuanjun， MO Tianlu， DENG Zixin， ZHANG Qi， DING Wei. Study on the post-translational modification of RiPPs Xye catalyzed by CyFE PacB［J］. Synthetic Biology Journal， 2021， 2（5）： 826-836
韩沅均，莫天录，邓子新，张琪，丁伟. 环番合成酶PacB催化Xye类核糖体肽翻译后修饰研究［J］. 合成生物学， 2021， 2（5）： 826-836 DOI： 10.12211/2096-8280.2021-080.

HAN Yuanjun， MO Tianlu， DENG Zixin， ZHANG Qi， DING Wei. Study on the post-translational modification of RiPPs Xye catalyzed by CyFE PacB［J］. Synthetic Biology Journal， 2021， 2（5）： 826-836 DOI： 10.12211/2096-8280.2021-080.

摘要

近年来，一类含有分子内三残基环番结构的新型核糖体肽引起了广泛关注。这类化合物通常由一类

-腺苷甲硫氨酸自由基酶催化核心肽中芳香氨基酸的sp

碳和相邻第三位氨基酸残基侧链的sp

碳之间形成C—C或C—O键，这类酶被称为三残基环番合成酶（3-CyFEs）。目前发现Xye类核糖体肽天然产物生物合成基因簇中普遍含有此类三残基环番合成酶。本文报道从

Photorhabdus australis

DSM 17609中发现一个新的Xye类核糖体肽生物合成基因簇

pac

。异源表达和体外活性重建表明其生物合成基因簇编码的三残基环番合成酶PacB负责pacpeptide核心肽内的三个分子内环的生成。体内和体外实验结果初步表明PacB具有较高的底物容忍性，三个环番结构相互独立形成，但形成效率存在明显的差异，从而初步揭示了三个环番的形成顺序。本研究拓展了对Xye类核糖体肽化合物家族翻译后修饰以及三

残基环番合成酶催化功能的了解。

Abstract

Cyclic ribosomally synthesized and post-translationally modified peptides (RiPPs) with macrocycles derived from three amino acid residues have attracted intense interest in recent years. Biosynthesis of these peptides usually involves a radical (

)-adenosylmethionine (rSAM) enzyme that catalyzes the formation of a C—C or C—O bond between an aromatic carbon and a side chain carbon of another residue. Such enzymes are named three-residue cyclophane forming enzymes (3-CyFEs). The rSAM enzyme family is known as one of the largest enzyme super families

which consists of more than 22000 members. rSAM enzymes are widely found in all three life domains as one of the earliest biocatalysts on earth. A large amount of microbial genomic information shows that many RiPPs biosynthesis gene clusters contain rSAM enzymes. Recently

several 3-CyFEs from Xye gene clusters

which form three cyclizations on the precursor peptides

were reported. In this paper

we report a new Xye RiPP pacpeptide and its key biosynthetic enzyme PacB from

Photorhabdus australis

DSM 17609. We coexpressed the

pacA

and

pacB

Escherichia coli

and reconstituted the activity of heterologously expressed protein to investigate the bioactivity of 3-CyFEs PacB. The high-resolution mass spectrometry assay indicates that PacB indeed led to forming all three cyclophanes of pacpeptide. Additionally

the mutation of Asn/Argto Gly on the precursor peptide resulted in only two cyclophane was found

which demonstrated that three cyclization reactions were generated independently with different efficiency. PacB also catalyzed all three cyclophanes formation on the precursor peptide with Asn/Arg mutated to Ala. These results expand our understanding of 3-CyFEs chemistry in natural product biosynthesis and provide insights into the post-modification of cyclic RiPPs with three-residue cyclophanes.

关键词

Keywords

references

ARNISON P G , BIBB M J , BIERBAUM G , et al . Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature [J ] . Natural Product Reports , 2013 , 30 ( 1 ): 108 - 160 .

MONTALBÁN-LÓPEZ M , SCOTT T A , RAMESH S , et al . New developments in RiPP discovery, enzymology and engineering [J ] . Natural Product Reports , 2021 , 38 ( 1 ): 130 - 239 .

LU J X , LI Y Q , BAI Z B , et al . Enzymatic macrocyclization of ribosomally synthesized and posttranslational modified peptides via C-S and C-C bond formation [J ] . Natural Product Reports , 2021 , 38 ( 5 ): 981 - 992 .

VAN DER DONK W A , NAIR S K . Structure and mechanism of lanthipeptide biosynthetic enzymes [J ] . Current Opinion in Structural Biology , 2014 , 29 : 58 - 66 .

ZHANG Q , YU Y , VÉLASQUEZ J E , et al . Evolution of lanthipeptide synthetases [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2012 , 109 ( 45 ): 18361 - 18366 .

VAN KRAAIJ C , DE VOS W M , SIEZEN R J , et al . Lantibiotics: biosynthesis, mode of action and applications [J ] . Natural Product Reports , 1999 , 16 ( 5 ): 575 - 587 .

FLUHE L , MARAHIEL M A . Radical S -adenosylmethionine enzyme catalyzed thioether bond formation in sactipeptide biosynthesis [J ] . Current Opinion in Structural Biology , 2013 , 17 ( 4 ): 605 - 612 .

CHEN Y L , WANG J X , LI G Q , et al . Current advancements in sactipeptide natural products [J ] . Frontiers in Chemistry , 2021 , 9 : 595991 .

MO T L , JI X J , YUAN W , et al . Thuricin Z: A narrow-spectrum sactibiotic that targets the cell membrane [J ] . Angewandte Chemie International Edition , 2019 , 58 ( 52 ): 18793 - 18797 .

DALY N L , CRAIK D J . Bioactive cystine knot proteins [J ] . Current Opinion in Structural Biology , 2011 , 15 : 362 - 368 .

CHEKAN J R , ESTRADA P , COVELLO P S , et al . Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2017 , 114 ( 25 ): 6551 - 6556 .

BURNETT P G , JADHAV P D , OKINYO-OWITI D P , et al . Glycine-containing flaxseed orbitides [J ] . Journal of Natural Products , 2015 , 78 : 681 - 688 .

SHIM Y Y , YOUNG L W , ARNISON P G , et al . Proposed systematic nomenclature for orbitides [J ] . Journal of Natural Products , 2015 , 78 ( 4 ): 645 - 652 .

DE VEER S J , KAN M W , CRAIK D J . Cyclotides: from structure to function [J ] . Chemical Reviews , 2019 , 119 ( 24 ): 12375 - 12421 .

BURMAN R , GUNASEKERA S , STRÖMSTEDT A A , et al . Chemistry and biology of cyclotides: circular plant peptides outside the box [J ] . Journal of Natural Products , 2014 , 77 ( 3 ): 724 - 736 .

CRAIK D J , CEMAZAR M , DALY N L . The chemistry and biology of cyclotides [J ] . Current Opinion in Drug Discovery & Development , 2007 , 10 ( 2 ): 176 - 184 .

MARTINS J , VASCONCELOS V . Cyanobactins from cyanobacteria: current genetic and chemical state of knowledge [J ] . Marine Drugs , 2015 , 13 ( 11 ): 6910 - 6946 .

HUDSON G A , MITCHELL D A . RiPP antibiotics: biosynthesis and engineering potential [J ] . Current Opinion in Microbiology , 2018 , 45 : 61 - 69 .[PubMed ]

DONIA M S , RAVEL J , SCHMIDT E W . A global assembly line for cyanobactins [J ] . Nature Chemical Biology , 2008 , 4 ( 6 ): 341 - 343 .

VINOGRADOV A A , SUGA H . Introduction to thiopeptides: biological activity, biosynthesis, and strategies for functional reprogramming [J ] . Cell Chemical Biology , 2020 , 27 ( 8 ): 1032 - 1051 .

MA S , CHEN H , LI H , et al . Post-translational formation of aminomalonate by a promiscuous peptide-modifying radical SAM enzyme [J ] . Angewandte Chemie International Edition , 2021 , 60 ( 36 ): 19957 - 19964 .

NGUYEN T Q N , TOOH Y W , SUGIYAMA R , et al . Post-translational formation of strained cyclophanes in bacteria [J ] . Nature Chemistry , 2020 , 12 : 1042 - 1053 .

SCHRAMMA K R , BUSHIN L B , SEYEDSAYAMDOST M R . Structure and biosynthesis of a macrocyclic peptide containing an unprecedented lysine-to-tryptophan crosslink [J ] . Nature Chemistry , 2015 , 7 ( 5 ): 431 - 437 .

KAUR H , JAKOB R P , MARZINEK J K , et al . The antibiotic darobactin mimics a beta-strand to inhibit outer membrane insertase [J ] . Nature , 2021 , 593 : 125 - 129 .

BUSHIN L B , SEYEDSAYAMDOST M R . Guidelines for determining the structures of radical SAM enzyme catalyzed modifications in the biosynthesis of RiPP natural products [J ] . Methods in Enzymology , 2018 , 606 : 439 - 460 .

BENJDIA A , BALTY C , BERTEAU O . Radical SAM enzymes in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs) [J ] . Frontiers in Chemistry , 2017 , 5 : 87 .

ZHANG Q , ORTEGA M , SHI Y X , et al . Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2014 , 111 ( 33 ): 12031 - 12036 .

STROHALM M , HASSMAN M , KOSATA B , et al . mMass data miner: an open source alternative for mass spectrometric data analysis [J ] . Rapid Communications in Mass Spectrometry , 2008 , 22 ( 6 ): 905 - 908 .

浏览量

下载量

CSCD

文章被引用时，请邮件提醒。

提交

工具集

关联资源

含氨基乙烯半胱氨酸核糖体肽的生物合成与化学合成