Biosynthesis of alkyne moiety in natural products and application of alkyne biosynthetic machineries

doi:10.12211/2096-8280.2021-056

Abstract

Abstract:

Alkyne is a biologically significant moiety in many drugs and natural products, which is also a versatile building block in modern chemistry. Therefore, it is of great importance to efficiently synthesize alkyne-containing products in the fields of medicinal chemistry, organic chemistry, chemical biology and so on. Generally, alkyne-containing products are obtained via chemical synthesis, but this strategy often suffers from high cost, low efficiency and harsh reaction conditions. Alternatively, microbial biotransformation can be performed through feeding alkyne-containing precursors, but it is still challenging since these precursors are not easily accessible. Inspired by the advancement of synthetic biology, de novo biosynthesis is expected to be a promising approach for producing acetylenic products, which is environmentally friendly and industrially tractable. Great efforts have thus been devoted to elucidating the biosynthetic machinery of alkyne moiety in natural products so as to provide efficient enzymatic tools for the de novo biosynthesis of acetylenic products. In this review, we comment recent progress in biosynthesis of alkynes in different natural products. In unsaturated fatty acids, a special family of desaturases serve as acetylenases, converting olefinic bonds to triple bonds via O₂-dependent dehydrogenation with the use of a diiron active site. In polyketides, although lots of work has been done in revealing the biosynthetic routes of enediyne antibiotics, the genetic basis for synthesizing acetylenic bonds in their core backbones remains enigmatic. In polyketide-non ribosomal peptide hybrid molecules, the three-gene cassette encoding the ligase, acyl carrier protein (ACP) and acetylenase is responsible for the formation of the terminal alkyne-labeled fatty acyl-ACP, which is then used as the starting unit to be incorporated into the assembly line. In amino acids, the halogenase catalyzes the side-chain halogenation followed by the oxidase-mediated side-chain cleavage, and then the lyase catalyzes the elimination reaction to convert resulted alkene to the terminal triple bond. In meroterpenoids, the cytochrome P450 oxidase can consecutively catalyze two rounds of dehydrogenation to provide the internal alkyne in the prenyl chain. Moreover, we also introduce de novo biosynthesis of the terminal-alkyne tagged polyketides and proteins on the basis of the characterized biosynthetic machineries of alkynes. Despite the great progress in alkyne biosynthesis, it needs to be further strengthened in exploring the types of alkyne synthases as well as expanding their substrate specificity, so as to provide more enzymatic tools for the de novo biosynthesis of alkyne-containing products.

Key words: alkyne, de novo biosynthesis, acetylenase, pyridoxal phosphate-dependent lyase, cytochrome P450 oxidase

摘要：

炔基是许多药物、活性天然产物以及功能材料等的重要官能团，因此，开发高效的炔类化合物合成策略具有重要意义。传统的合成策略包括通过化学反应直接制备，或以简单的炔类前体为底物，通过生物转化获得。随着合成生物学技术的飞速发展，从头生物合成有望成为炔类化合物合成的新策略。该策略绿色环保，易于操作，是对传统化学合成以及生物转化策略的有效补充。炔类化合物从头生物合成的关键是阐明天然产物中炔基的生物合成机制，获得炔基合成酶。本文重点总结了不同天然产物中炔基的生物合成研究进展，包括脂肪酸、聚酮、聚酮-非核糖体肽杂合体、氨基酸以及杂萜，并介绍了炔基合成酶在炔类化合物从头生物合成中的应用。尽管炔基的生物合成研究近年来取得了长足发展，但在炔基合成酶的种类挖掘及其底物特异性拓展方面还有待进一步加强，从而为炔类化合物的从头生物合成提供更多可供选择的酶工具。

关键词: 炔基, 从头生物合成, 乙炔酶, 磷酸吡哆醛依赖的裂解酶, 细胞色素P450氧化酶

CLC Number:

Jianming LYU, Huan ZHAO, Dan HU, Hao GAO. Biosynthesis of alkyne moiety in natural products and application of alkyne biosynthetic machineries[J]. Synthetic Biology Journal, 2021, 2(5): 734-750.

吕建明, 赵欢, 胡丹, 高昊. 天然产物中炔基的生物合成机制研究及其应用[J]. 合成生物学, 2021, 2(5): 734-750.

Figures/Tables 15

Fig. 1 Two hypotheses for the biosynthesis of acetylenic bonds in fatty acids

Fig. 2 Crep1-mediated formation of acetylenic bond in crepenynate

Tab. 1 Acetylenases identified for the biosynthesis of acetylenic fatty acids

序号		来源	乙炔酶名称与NCBI登录号	产物	文献
1	植物	Crepis alpina	Crep1 (CAA76158)		[39-40]
2		Petroselinum crispum	PcACET (AAB80697)		[41]
3		Hedera helix	HhACET (AAO38031)		[41]
4		Helianthus annuus	HaACET (AAO38032)		[41]
5		Calendula officinalis	CoACET (CAB64256)		[41]
6		Daucus carota	DCAR_013552 (XP_017247320)		[42]
7		Daucus carota	DCAR_017011 (XP_017253817)		[42]
8		Daucus carota	DCAR_013548 (XP_017246930)		[42]
9		Solanum lycopersicum	ACET1a/b		[43]
10		Ceratodon purpureus	CpAcet6 (Q9LEN0)		[44]
11		Bidens pilosa	BPFAA (MF318525)	未知	[45-46]
12	昆虫	Thaumetopoea pityocampa	Tpi-PGFAD (ABO43722)		[47]
13		Chauliognathus lugubris	CL10 (AFJ66832)		[48]
14		Chauliognathus lugubris	CL2-1 (AFJ66828)		[48]
15		Chauliognathus lugubris	CL2-2 (AFJ66829)		[48]
16	微生物	Cantharellus formosus	CfACET (ADK24720)		[49]
17		Burkholderia caryophylli	CayB (AIG53817)	未知	[50]
18		Burkholderia caryophylli	CayC (AIG53820)	未知	[50]

Fig. 3 Sequence alignment of acetylenases with SCD1

Fig. 4 Proposed catalytic mechanism for acetylenases

Fig. 5 Chemical structures of typical enediyne antibiotics

Fig. 6 Proposed routes for biosynthesizing 9-membered and 10-membered enediyne antibiotics

Fig. 7 Chemical structures of typical terminal alkyne tagged PKS-NRPS hybrids

Fig. 8 Biosynthetic pathway of terminal alkyne in jamaicamide B

Fig. 9 The biosynthetic pathway of L-β-ethynylserine

Fig. 10 Mechanism for the biosynthesis of terminal alkyne catalyzed by BesB

Fig. 11 Routes for the biosynthesis of acetylenic meroterpenoids biscognienyne B and asperpentyn

Fig. 12 Functional analysis of BisI and AtyI

Fig. 13 Mechanism of alkyne biosynthesis in acetylenic meroterpenoids catalyzed by BisI or AtyI

Fig. 14 De novo biosynthesis of non-natural acetylenic polyketides

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