Synthetic Biology Journal ›› 2023, Vol. 4 ›› Issue (4): 629-650.DOI: 10.12211/2096-8280.2022-073
• Invited Review • Previous Articles Next Articles
Fanzhong ZHANG1,2, Changjun XIANG1,2,3, Lihan ZHANG1,2
Received:
2022-12-08
Revised:
2023-02-21
Online:
2023-09-14
Published:
2023-08-31
Contact:
Lihan ZHANG
张凡忠1,2, 相长君1,2,3, 张骊駻1,2
通讯作者:
张骊駻
作者简介:
基金资助:
CLC Number:
Fanzhong ZHANG, Changjun XIANG, Lihan ZHANG. Advances and applications of evolutionary analysis and big-data guided bioinformatics in natural product research[J]. Synthetic Biology Journal, 2023, 4(4): 629-650.
张凡忠, 相长君, 张骊駻. 进化与大数据导向生物信息学在天然产物研究中的发展及应用[J]. 合成生物学, 2023, 4(4): 629-650.
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URL: https://synbioj.cip.com.cn/EN/10.12211/2096-8280.2022-073
Fig. 5 The structure of polyketides molecules 1 to 10 obtained by phylogeny-guided genome miningCompounds 1 to 5 were aromatic polyketides discovered by genome mining of type Ⅱ PKS. Compounds 6 to 9 were discovered by genome mining of trans-AT PKS. Compound 10 was discovered by genome mining of fungal type Ⅰ PKS. Compounds 11 were enediynes
Fig. 9 The structure of peptide molecules 12~17 obtained by phylogeny-guided genome mining(Compounds 12 was calcium-dependent antibiotic discovered by genome mining of A domain; compounds 13~16 belonged to glycopeptide family of antibiotics discovered by genome mining of C domain;compound 17 was lipopeptide antibiotic discovered by NRPS prediction)
1 | CHEVRETTE M G, GAVRILIDOU A, MANTRI S, et al. The confluence of big data and evolutionary genome mining for the discovery of natural products[J]. Natural Product Reports, 2021, 38(11): 2024-2040. |
2 | CHEVRETTE M G, GUTIÉRREZ-GARCÍA K, SELEM-MOJICA N, et al. Evolutionary dynamics of natural product biosynthesis in bacteria[J]. Natural Product Reports, 2020, 37(4): 566-599. |
3 | JENSEN P R. Natural products and the gene cluster revolution[J]. Trends in Microbiology, 2016, 24(12): 968-977. |
4 | GAVRIILIDOU A, KAUTSAR S A, ZABURANNYI N, et al. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes[J]. Nature Microbiology, 2022, 7(5): 726-735. |
5 | CHEN S C, ZHANG C, ZHANG L H. Investigation of the molecular landscape of bacterial aromatic polyketides by global analysis of typeⅡpolyketide synthases[J]. Angewandte Chemie International Edtion, 2022, 61(24): e202202286. |
6 | ADAMEK M, ALANJARY M, ZIEMERT N. Applied evolution: phylogeny-based approaches in natural products research[J]. Natural Product Reports, 2019, 36(9): 1295-1312. |
7 | PANDE S, KOST C. Bacterial unculturability and the formation of intercellular metabolic networks[J]. Trends in Microbiology, 2017, 25(5): 349-361. |
8 | ZIEMERT N, ALANJARY M, WEBER T. The evolution of genome mining in microbes - a review[J]. Natural Product Reports, 2016, 33(8): 988-1005. |
9 | WALKER J M. Engineering natural products biosynthesis[M]. New York: Humana Imprint, 2022. |
10 | 杨谦, 程伯涛, 汤志军, 等. 基因组挖掘在天然产物发现中的应用和前景[J]. 合成生物学, 2021, 2(5): 697-715. |
YANG Q, CHENG B T, TANG Z J, et al. Applications and prospects of genome mining in the discovery of natural products[J]. Synthetic Biology Journal, 2021, 2(5): 697-715. | |
11 | ZERIKLY M, CHALLIS G L. Strategies for the discovery of new natural products by genome mining[J]. ChemBioChem, 2009, 10(4): 625-633. |
12 | SCHERLACH K, HERTWECK C. Mining and unearthing hidden biosynthetic potential[J]. Nature Communications, 2021, 12(1): 3864. |
13 | BAUMAN K D, BUTLER K S, MOORE B S, et al. Genome mining methods to discover bioactive natural products [J]. Natural Product Reports, 2021, 38(11): 2100-2129. |
14 | CRUZ-MORALES P, KOPP J F, MARTÍNEZ-GUERRERO C, et al. Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model Streptomycetes [J]. Genome Biology and Evolution, 2016, 8(6): 1906-1916. |
15 | KANG H S. Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products[J]. Journal of Industrial Microbiology & Biotechnology, 2017, 44(2): 285-293. |
16 | ALANJARY M, KRONMILLER B, ADAMEK M, et al. The antibiotic resistant target seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery[J]. Nucleic Acids Research, 2017, 45(W1): W42-W48. |
17 | DIRENÇ MUNGAN M, ALANJARY M, BLIN K, et al. ARTS 2.0: feature updates and expansion of the antibiotic resistant target seeker for comparative genome mining[J]. Nucleic Acids Research, 2020, 48(W1): W546-W552. |
18 | ZIEMERT N, PODELL S, PENN K, et al. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity[J]. PLoS One, 2012, 7(3): e34064. |
19 | KLAU L J, PODELL S, CREAMER K E, et al. The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function[J]. Journal of Biological Chemistry, 2022, 298(10): 102480. |
20 | SÉLEM-MOJICA N, AGUILAR C, GUTIÉRREZ-GARCÍA K, et al. EvoMining reveals the origin and fate of natural product biosynthetic enzymes[J]. Microbial Genomics, 2019, 5(12): e000260. |
21 | NAVARRO-MUÑOZ J C, SELEM-MOJICA N, MULLOWNEY M W, et al. A computational framework to explore large-scale biosynthetic diversity[J]. Nature Chemical Biology, 2020, 16(1): 60-68. |
22 | MEDEMA M H, KOTTMANN R, YILMAZ P, et al. Minimum information about a biosynthetic gene cluster[J]. Nature Chemical Biology, 2015, 11(9): 625-631. |
23 | KAUTSAR S A, BLIN K, SHAW S, et al. MIBiG 2.0: a repository for biosynthetic gene clusters of known function[J]. Nucleic Acids Research, 2020, 48(D1): D454-D458. |
24 | BLIN K, SHAW S, KAUTSAR S A, et al. The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes[J]. Nucleic Acids Research, 2021, 49(D1): D639-D643. |
25 | RAWLINGS B J. Type I polyketide biosynthesis in bacteria (part A—erythromycin biosynthesis)[J]. Natural Product Reports, 2001, 18(2): 190-227. |
26 | HERTWECK C, LUZHETSKYY A, REBETS Y, et al. TypeⅡpolyketide synthases: gaining a deeper insight into enzymatic teamwork[J]. Natural Product Reports, 2007, 24(1): 162-190. |
27 | ABE I, MORITA H. Structure and function of the chalcone synthase superfamily of plant typeⅢpolyketide synthases[J]. Natural Product Reports, 2010, 27(6): 809-838. |
28 | YU D Y, XU F C, ZENG J, et al. TypeⅢpolyketide synthases in natural product biosynthesis[J]. IUBMB Life, 2012, 64(4): 285-295. |
29 | NIVINA A, YUET K P, HSU J, et al. Evolution and diversity of assembly-line polyketide synthases[J]. Chemical Reviews, 2019, 119(24): 12524-12547. |
30 | JENKE-KODAMA H, DITTMANN E. Evolution of metabolic diversity: insights from microbial polyketide synthases[J]. Phytochemistry, 2009, 70(15-16): 1858-1866. |
31 | NIVINA A, HERRERA PAREDES S, FRASER H B, et al. GRINS: genetic elements that recode assembly-line polyketide synthases and accelerate their diversification[J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(26): e2100751118. |
32 | JENKE-KODAMA H, SANDMANN A, MÜLLER R, et al. Evolutionary implications of bacterial polyketide synthases[J]. Molecular Biology and Evolution, 2005, 22(10): 2027-2039. |
33 | NGUYEN T, ISHIDA K, JENKE-KODAMA H, et al. Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection[J]. Nature Biotechnology, 2008, 26(2): 225-233. |
34 | LOPEZ J V. Naturally mosaic operons for secondary metabolite biosynthesis: variability and putative horizontal transfer of discrete catalytic domains of the epothilone polyketide synthase locus[J]. Molecular Genetics and Genomics, 2004, 270(5): 420-431. |
35 | ZHANG L H, HASHIMOTO T, QIN B, et al. Characterization of giant modular PKSs provides insight into genetic mechanism for structural diversification of aminopolyol polyketides[J]. Angewandte Chemie International Edtion, 2017, 56(7): 1740-1745. |
36 | KEATINGE-CLAY A T. Polyketide synthase modules redefined[J]. Angewandte Chemie International Edtion, 2017, 56(17): 4658-4660. |
37 | VANDER WOOD D A, KEATINGE-CLAY A T. The modules of trans-acyltransferase assembly lines redefined with a central acyl carrier protein[J]. Proteins, 2018, 86(6): 664-675. |
38 | CAFFREY P. Conserved amino acid residues correlating with ketoreductase stereospecificity in modular polyketide synthases[J]. Chembiochem, 2003, 4(7): 654-657. |
39 | VANDER WOOD D A, KEATINGE-CLAY A T. The modules of trans-acyltransferase assembly lines redefined with a central acyl carrier protein[J]. Proteins, 2018, 86(6): 664-675. |
40 | MEDEMA M H, CIMERMANCIC P, SALI A, et al. A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis[J]. PLoS Computational Biology, 2014, 10(12): e1004016. |
41 | RIDLEY C P, LEE H Y, KHOSLA C. Evolution of polyketide synthases in bacteria[J]. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(12): 4595-4600. |
42 | HILLENMEYER M E, VANDOVA G A, BERLEW E E, et al. Evolution of chemical diversity by coordinated gene swaps in typeⅡpolyketide gene clusters[J]. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(45): 13952-13957. |
43 | GABALDÓN T, KOONIN E V. Functional and evolutionary implications of gene orthology[J]. Nature Reviews Genetics, 2013, 14(5): 360-366. |
44 | FRITZSCHE K, ISHIDA K, HERTWECK C. Orchestration of discoid polyketide cyclization in the resistomycin pathway[J]. Journal of the American Chemical Society, 2008, 130(26): 8307-8316. |
45 | FRALEY A E, DIETERICH C L, MABESOONE M F J, et al. Structure of a promiscuous thioesterase domain responsible for branching acylation in polyketide biosynthesis[J]. Angewandte Chemie International Edtion, 2022, 61(39): e202206385. |
46 | SCHWECKE T, APARICIO J F, MOLNÁR I, et al. The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin[J]. Proceedings of the National Academy of Sciences of the United States of America, 1995, 92(17): 7839-7843. |
47 | HAYDOCK S F, APARICIO J F, MOLNÁR I, et al. Divergent sequence motifs correlated with the substrate specificity of (methyl) malonyl-CoA: acyl carrier protein transacylase domains in modular polyketide synthases[J]. FEBS Letters, 1995, 374(2): 246-248. |
48 | APARICIO J F, MOLNÁR I, SCHWECKE T., et al. Organization of the biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus: analysis of the enzymatic domains in the modular polyketide synthase[J]. Gene, 1996, 169(1): 9-16. |
49 | KAKAVAS S J, KATZ L, STASSI D. Identification and characterization of the niddamycin polyketide synthase genes from Streptomyces caelestis [J]. Journal of Bacteriology, 1997, 179(23): 7515-7522. |
50 | KANG H S, BRADY S F. Mining soil metagenomes to better understand the evolution of natural product structural diversity: pentangular polyphenols as a case study[J]. Journal of the American Chemical Society, 2014, 136(52): 18111-18119. |
51 | KANG H S, BRADY S F. Arimetamycin A: improving clinically relevant families of natural products through sequence-guided screening of soil metagenomes[J]. Angewandte Chemie International Edtion, 2013, 52(42): 11063-11067. |
52 | LI L Y, HU Y L, SUN J L, et al. Resistance and phylogeny guided discovery reveals structural novelty of tetracycline antibiotics[J]. Chemical Science, 2022, 13(43): 12892-12898. |
53 | ZIEMERT N, JENSEN P R. Phylogenetic approaches to natural product structure prediction[J]. Methods in Enzymology, 2012, 517: 161-182. |
54 | UEOKA R, URIA A R, REITER S, et al. Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms[J]. Nature Chemical Biology, 2015, 11(9): 705-712. |
55 | HELFRICH E J N, UEOKA R, DOLEV A, et al. Automated structure prediction of trans-acyltransferase polyketide synthase products[J]. Nature Chemical Biology, 2019, 15(8): 813-821. |
56 | HELFRICH E J N, UEOKA R, CHEVRETTE M G, et al. Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria[J]. Nature Communications, 2021, 12(1): 1422. |
57 | GUO J, RAN H M, ZENG J, et al. Tafuketide, a phylogeny-guided discovery of a new polyketide from Talaromyces funiculosus Salicorn 58[J]. Applied Microbiology and Biotechnology, 2016, 100(12): 5323-5338. |
58 | SHEN B, HINDRA, YAN X H, et al. Enediynes: exploration of microbial genomics to discover new anticancer drug leads[J]. Bioorganic and Medicinal Chemistry Letters, 2015, 25(1): 9-15 |
59 | YAN X H, GE H M, HUANG T T, et al. Strain prioritization and genome mining for enediyne natural products[J]. mBio, 2016, 7(6): e02104-e02116. |
60 | WEISSMAN K J. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology[J]. Natural Product Reports, 2016, 33(2): 203-230. |
61 | 曹晨凯, 李佳隆, 张科春. 人工代谢途径合成有机醇有机酸的研究进展[J]. 合成生物学, 2021, 2(6): 902-919. |
CAO C K, LI J L, ZHANG K C. Progress in artificial metabolic pathways for biosynthesis of organic alcohols & acids[J]. Synthetic Biology Journal, 2021, 2(6): 902-919. | |
62 | BOOTH T J, BOZHÜYÜK K A J, LISTON J D, et al. Bifurcation drives the evolution of assembly-line biosynthesis[J]. Nature Communications, 2022, 13(1): 3498. |
63 | HIRSCH M, FITZGERALD B J, KEATINGE-CLAY A T. How cis-acyltransferase assembly-line ketosynthases gatekeep for processed polyketide intermediates[J]. ACS Chemical Biology, 2021, 16(11): 2515-2526. |
64 | MIYAZAWA T, HIRSCH M, ZHANG Z C, et al. An in vitro platform for engineering and harnessing modular polyketide synthases[J]. Nature Communications, 2020, 11(1): 80. |
65 | MIYAZAWA T, FITZGERALD B J, KEATINGE-CLAY A T. Preparative production of an enantiomeric pair by engineered polyketide synthases[J]. Chemical Communications, 2021, 57(70): 8762-8765. |
66 | PENG H Y, ISHIDA K, SUGIMOTO Y, et al. Emulating evolutionary processes to morph aureothin-type modular polyketide synthases and associated oxygenases[J]. Nature Communications, 2019, 10(1): 3918. |
67 | YUZAWA S, DENG K, WANG G, et al. Comprehensive in vitro analysis of acyltransferase domain exchanges in modular polyketide synthases and its application for short-chain ketone production[J]. ACS Synthetic Biology, 2017, 6(1): 139-147. |
68 | YUZAWA S, MIRSIAGHI M, JOCIC R, et al. Short-chain ketone production by engineered polyketide synthases in streptomyces albus[J]. Nature Communications, 2018, 9: 4569. |
69 | ZARGAR A, VALENCIA L, WANG J, et al. A bimodular PKS platform that expands the biological design space[J]. Metabolic Engineering, 2020, 61: 389-396. |
70 | ENG C H, YUZAWA S, WANG G, et al. Alteration of polyketide stereochemistry from anti to syn by a ketoreductase domain exchange in a typeⅠmodular polyketide synthase subunit[J]. Biochemistry, 2016, 55(12): 1677-1680. |
71 | HAGEN A, POUST S, DE ROND T, et al. Engineering a polyketide synthase for in vitro production of adipic acid[J]. ACS Synthetic Biology, 2016, 5(1): 21-27. |
72 | ZARGAR A, LAL R, VALENCIA L, et al. Chemoinformatic-guided engineering of polyketide synthases[J]. Journal of the American Chemical Society, 2020, 142(22): 9896-9901. |
73 | MUSIOL-KROLL E M, WOHLLEBEN W. Acyltransferases as tools for polyketide synthase engineering[J]. Antibiotics, 2018, 7(3): 62. |
74 | KWAN D H, TOSIN M, SCHLÄGER N, et al. Insights into the stereospecificity of ketoreduction in a modular polyketide synthase[J]. Organic & Biomolecular Chemistry, 2011, 9(7): 2053-2056. |
75 | BAGDE S R, MATHEWS I I, FROMME J C, et al. Modular polyketide synthase contains two reaction chambers that operate asynchronously[J]. Science, 2021, 374(6568): 723-729. |
76 | COGAN D P, ZHANG K M, LI X Y, et al. Mapping the catalytic conformations of an assembly-line polyketide synthase module[J]. Science, 2021, 374(6568): 729-734. |
77 | HERBST D A, JAKOB R P, ZÄHRINGER F, et al. Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases[J]. Nature, 2016, 531(7595): 533-537 |
78 | ZHENG J T, GAY D C, DEMELER B, et al. Divergence of multimodular polyketide synthases revealed by a didomain structure[J]. Nature Chemical Biology, 2012, 8(7): 615-621. |
79 | GAY D, YOU Y O, KEATINGE-CLAY A, et al. Structure and stereospecificity of the dehydratase domain from the terminal module of the rifamycin polyketide synthase[J]. Biochemistry, 2013, 52(49): 8916-8928. |
80 | DUTTA S, WHICHER J R, HANSEN D A, et al. Structure of a modular polyketide synthase[J]. Nature, 2014, 510(7506): 512-517. |
81 | WHICHER J R, DUTTA S, HANSEN D A, et al. Structural rearrangements of a polyketide synthase module during its catalytic cycle[J]. Nature, 2014, 510(7506): 560-564. |
82 | FELNAGLE E A, JACKSON E E, CHAN Y A, et al. Nonribosomal peptide synthetases involved in the production of medically relevant natural products[J]. Molecular Pharmaceutics, 2008, 5(2): 191-211. |
83 | SIEBER S A, MARAHIEL M A. Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics[J]. Chemical Reviews, 2005, 105(2): 715-738. |
84 | SÜSSMUTH R D, MAINZ A. Nonribosomal peptide synthesis-principles and prospects[J]. Angewandte Chemie International Edtion, 2017, 56(14): 3770-3821. |
85 | JAREMKO M J, DAVIS T D, CORPUZ J C, et al. TypeⅡnon-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions[J]. Natural Product Reports, 2020, 37(3): 355-379. |
86 | CALCOTT M J, OWEN J G, ACKERLEY D F. Efficient rational modification of non-ribosomal peptides by adenylation domain substitution[J]. Nature Communications, 2020, 11(1): 4554. |
87 | BAUNACH M, CHOWDHURY S, STALLFORTH P, et al. The landscape of recombination events that create nonribosomal peptide diversity[J]. Molecular Biology and Evolution, 2021, 38(5): 2116-2130. |
88 | RAUSCH C, HOOF I, WEBER T, et al. Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution[J]. BMC Ecology and Evolution, 2007, 7: 78. |
89 | WHEADON M J, TOWNSEND C A. Evolutionary and functional analysis of an NRPS condensation domain integrates β-lactam, ᴅ-amino acid, and dehydroamino acid synthesis[J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(17): e2026017118. |
90 | STACHELHAUS T, MOOTZ H D, MARAHIEL M A. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases[J]. Chemistry & Biology, 1999, 6(8): 493-505. |
91 | RÖTTIG M, MEDEMA M H, BLIN K, et al. NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity[J]. Nucleic Acids Research, 2011, 39(): W362-W367. |
92 | CHEVRETTE M G, AICHELER F, KOHLBACHER O, et al. SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria[J]. Bioinformatics, 2017, 33(20): 3202-3210. |
93 | ZIEMERT N, LECHNER A, WIETZ M, et al. Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora [J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(12): E1130-E1139. |
94 | PATTESON J B, FORTINEZ C M, PUTZ A T, et al. Structure and function of a dehydrating condensation domain in nonribosomal peptide biosynthesis[J]. Journal of the American Chemical Society, 2022, 144(31): 14057-14070. |
95 | HOVER B M, KIM S H, KATZ M, et al. Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens[J]. Nature Microbiology, 2018, 3(4): 415-422. |
96 | CULP E J, WAGLECHNER N, WANG W L, et al. Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling[J]. Nature, 2020, 578(7796): 582-587. |
97 | XU M, WANG W L, WAGLECHNER N, et al. Phylogeny-informed synthetic biology reveals unprecedented structural novelty in type Ⅴ glycopeptide antibiotics[J]. ACS Central Science, 2022, 8(5): 615-626. |
98 | WANG Z Q, KOIRALA B, HERNANDEZ Y, et al. Bioinformatic prospecting and synthesis of a bifunctional lipopeptide antibiotic that evades resistance[J]. Science, 2022, 376(6596): 991-996. |
99 | CALCOTT M J, OWEN J G, LAMONT I L, et al. Biosynthesis of novel Pyoverdines by domain substitution in a nonribosomal peptide synthetase of Pseudomonas aeruginosa [J]. Applied and Environmental Microbiology, 2014, 80(18): 5723-5731. |
100 | THIRLWAY J, LEWIS R, NUNNS L, et al. Introduction of a non-natural amino acid into a nonribosomal peptide antibiotic by modification of adenylation domain specificity[J]. Angewandte Chemie International Edition, 2012, 51(29): 7181-7184. |
101 | KRIES H, WACHTEL R, PABST A, et al. Reprogramming nonribosomal peptide synthetases for clickable amino acids[J]. Angewandte Chemie International Edition, 2014, 53(38): 10105-10108. |
102 | NGUYEN K T, RITZ D, GU J Q, et al. Combinatorial biosynthesis of novel antibiotics related to daptomycin[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(46): 17462-17467. |
103 | CRÜSEMANN M, KOHLHAAS C, PIEL J. Evolution-guided engineering of nonribosomal peptide synthetase adenylation domains[J]. Chemical Science, 2013, 4(3): 1041-1045. |
104 | KRIES H, NIQUILLE D L, HILVERT D. A subdomain swap strategy for reengineering nonribosomal peptides[J]. Chemistry & Biology, 2015, 22(5): 640-648. |
105 | BOZHÜYÜK K A J, LINCK A, TIETZE A, et al. Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains[J]. Nature Chemistry, 2019, 11(7): 653-661. |
106 | BOZHÜYÜK K A J, WATZEL J, ABBOOD N, et al. Synthetic zippers as an enabling tool for engineering of non-ribosomal peptide synthetases[J]. Angewandte Chemie International Edtion, 2021, 60(32): 17531-17538. |
107 | KRANZ J, WENSKI S L, DICHTER A A, et al. Influence of condensation domains on activity and specificity of adenylation domains[EB/OL]. bioRxiv, 2021, DOI: 10.1101/2021.08.23.457306[2023-02-01]. . |
108 | BOZHÜYÜK K A J, FLEISCHHACKER F, LINCK A, et al. De novo design and engineering of non-ribosomal peptide synthetases[J]. Nature Chemistry, 2018, 10(3): 275-281. |
109 | MINAMI A, UGAI T, OZAKI T, et al. Predicting the chemical space of fungal polyketides by phylogeny-based bioinformatics analysis of polyketide synthase-nonribosomal peptide synthetase and its modification enzymes[J]. Scientific Reports, 2020, 10: 13556. |
110 | AWAKAWA T, FUJIOKA T, ZHANG L H, et al. Reprogramming of the antimycin NRPS-PKS assembly lines inspired by gene evolution[J]. Nature Communications, 2018, 9: 3534. |
111 | SANTOS-ABERTURAS J, CHANDRA G, FRATTARUOLO L, et al. Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool[J]. Nucleic Acids Research, 2019, 47(9): 4624-4637. |
112 | 吕靖伟, 邓子新, 张琪, 等. 基于深度学习识别RiPPs前体肽及裂解位点[J]. 合成生物学, 2022, 3(6), 1262-1276. |
LYU J W, DENG Z X, ZHANG Q, et al. Identification of RiPPs precursor peptides and cleavage sites based on deep learning[J]. Synthetic Biology Journal, 2022, 3(6), 1262-1276. | |
113 | MEDEMA M H, TAKANO E, BREITLING R. Detecting sequence homology at the gene cluster level with MultiGeneBlast[J]. Molecular Biology and Evolution, 2013, 30(5): 1218-1223. |
114 | TIETZ J I, SCHWALEN C J, PATEL P S, et al. A new genome-mining tool redefines the lasso peptide biosynthetic landscape[J]. Nature Chemical Biology, 2017, 13(5): 470-478. |
115 | MERWIN N J, MOUSA W K, DEJONG C A, et al. DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(1): 371-380. |
116 | MARTÍN-SÁNCHEZ L, SINGH K S, AVALOS M, et al. Phylogenomic analyses and distribution of terpene synthases among Streptomyces [J]. Beilstein Journal of Organic Chemistry, 2019, 15: 1181-1193. |
117 | JIA Q D, CHEN X L, KÖLLNER T G, et al. Terpene synthase genes originated from bacteria through horizontal gene transfer contribute to terpenoid diversity in fungi[J]. Scientific Reports, 2019, 9: 9223. |
118 | AVALOS M, GARBEVA P, VADER L, et al. Biosynthesis, evolution and ecology of microbial terpenoids[J]. Natural Product Reports, 2022, 39(2): 249-272. |
119 | YANG Y L, ZHANG S S, MA K, et al. Discovery and characterization of a new family of diterpene cyclases in bacteria and fungi[J]. Angewandte Chemie International Edtion, 2017, 56(17): 4749-4752. |
120 | CHEN R, JIA Q D, MU X, et al. Systematic mining of fungal chimeric terpene synthases using an efficient precursor-providing yeast chassis[J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(29): e2023247118. |
121 | TAO H, LAUTERBACH L, BIAN G K, et al. Discovery of non-squalene triterpenes[J]. Nature, 2022, 606(7913): 414-419. |
122 | JIANG C G, KIM S Y, SUH D Y. Divergent evolution of the thiolase superfamily and chalcone synthase family[J]. Molecular Phylogenetics and Evolution, 2008, 49(3): 691-701. |
123 | TAN Z G, CLOMBURG J M, CHEONG S, et al. A polyketoacyl-CoA thiolase-dependent pathway for the synthesis of polyketide backbones[J]. Nature Catalysis, 2020, 3(7): 593-603. |
124 | SHANKLIN J, GUY J E, MISHRA G, et al. Desaturases: emerging models for understanding functional diversification of diiron-containing enzymes[J]. Journal of Biological Chemistry, 2009, 284(28): 18559-18563. |
125 | ZHU X J, LIU J, ZHANG W J. De novo biosynthesis of terminal alkyne-labeled natural products[J]. Nature Chemical Biology, 2015, 11(2): 115-120. |
126 | ZHU X J, SU M, MANICKAM K, et al. Bacterial genome mining of enzymatic tools for alkyne biosynthesis[J]. ACS Chemical Biology, 2015, 10(12): 2785-2793. |
127 | CHANG F Y, BRADY S F. Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(7): 2478-2483. |
128 | CHANG F Y, TERNEI M A, CALLE P Y, et al. Targeted metagenomics: finding rare tryptophan dimer natural products in the environment[J]. Journal of the American Chemical Society, 2015, 137(18): 6044-6052. |
129 | CIMERMANCIC P, MEDEMA M H, CLAESEN J., et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters[J]. Cell, 2014, 158(2): 412-421. |
130 | O'NEILL E C, SCHORN M, LARSON C B, et al. Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining[J]. Critical Reviews in Microbiology, 2019, 45(3): 255-277. |
131 | YAN Y, LIU N, TANG Y. Recent developments in self-resistance gene directed natural product discovery[J]. Natural Product Reports, 2020, 37(7): 879-892. |
132 | BERNHARDSGRÜTTER I, SCHELL K, PETER D M, et al. Awakening the sleeping carboxylase function of enzymes: engineering the natural CO2-binding potential of reductases[J]. Journal of the American Chemical Society, 2019, 141(25): 9778-9782. |
133 | SIKOSEK T. Computational methods in protein evolution[M]// Methods in molecular biology. New York: Humana Press, 2019: 1064-3745. |
134 | HARMS M J, THORNTON J W. Analyzing protein structure and function using ancestral gene reconstruction[J]. Current Opinion in Structural Biology, 2010, 20(3): 360-366. |
135 | CECH N B, MEDEMA M H, CLARDY J. Benefiting from big data in natural products: importance of preserving foundational skills and prioritizing data quality[J]. Natural Product Reports, 2021, 38(11): 1947-1953. |
136 | JEON J, KANG S, KIM H U. Predicting biochemical and physiological effects of natural products from molecular structures using machine learning[J]. Natural Product Reports, 2021, 38(11): 1954-1966. |
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