合成生物学 ›› 2021, Vol. 2 ›› Issue (5): 815-825.DOI: 10.12211/2096-8280.2021-005
张礼文1, MOLNÁR István2, 徐玉泉1
收稿日期:
2021-01-12
修回日期:
2021-04-16
出版日期:
2021-11-19
发布日期:
2021-11-19
通讯作者:
MOLNáR István,徐玉泉
作者简介:
基金资助:
Liwen ZHANG1, István MOLNÀR2, Yuquan XU1
Received:
2021-01-12
Revised:
2021-04-16
Online:
2021-11-19
Published:
2021-11-19
Contact:
István MOLNàR, Yuquan XU
摘要:
肉座菌目虫生真菌合成的非核糖体多肽类天然产物具有抗菌、杀虫、抗癌、调节免疫等生物活性,在临床和农业等领域有重要应用价值。近年来,随着真菌基因组测序数量的迅速增加、注释和分析工具的不断进步,人们发现真菌基因组中存在大量产物未知的天然产物合成基因。准确有效地预测这些基因的功能,筛选最有潜力合成新颖天然产物的基因簇,可以提高天然产物挖掘的效率。本研究选取40株肉座菌目虫生真菌基因组,系统分析了编码非核糖体多肽合成酶的基因及基因簇。基于隐马尔可夫模型,预测了445个模块型非核糖体多肽合成酶和1243个类非核糖体多肽合成酶;通过提取腺苷酰化结构域,构建序列相似性网络,以已知功能的非核糖体多肽合成酶作为标签,利用马尔可夫聚类算法,分析了非核糖体多肽产物的主要类别,发现了可能合成线性多肽、环缩肽、脂多肽、生物碱等新型结构化合物的基因簇。研究结果不仅揭示了肉座菌目虫生真菌合成非核糖体多肽活性产物的巨大潜力,而且为通过激活沉默基因簇挖掘新产物、利用合成生物学手段改造合成途径提供参考。
中图分类号:
张礼文, MOLNÁR István, 徐玉泉. 虫生真菌非核糖体多肽活性产物生物合成潜力预测[J]. 合成生物学, 2021, 2(5): 815-825.
Liwen ZHANG, István MOLNÀR, Yuquan XU. Potential biosynthesis of nonribosomal peptides by hypocrealean entomopathogenic fungi[J]. Synthetic Biology Journal, 2021, 2(5): 815-825.
Description | Function with HMM | Source | Cutoff (Score) | Length | Domains (SwissProt) | Domains (HEF) |
---|---|---|---|---|---|---|
Adenylation domain | AMP-binding | PFAM00501.21 | 55 | 418 | 280 | 2297 |
Condensation domain | Condensation | PFAM00668.13 | 50 | 301 | 255 | 1483 |
Thiolation domain | PP-binding | PFAM0050.20 | 30 | 67 | 312 | 2775 |
表1 非核糖体多肽合成酶结构域注释
Tab. 1 Annotion for NRPS domains in hypocrealean entomopathotenic fungi (HEF)
Description | Function with HMM | Source | Cutoff (Score) | Length | Domains (SwissProt) | Domains (HEF) |
---|---|---|---|---|---|---|
Adenylation domain | AMP-binding | PFAM00501.21 | 55 | 418 | 280 | 2297 |
Condensation domain | Condensation | PFAM00668.13 | 50 | 301 | 255 | 1483 |
Thiolation domain | PP-binding | PFAM0050.20 | 30 | 67 | 312 | 2775 |
Subtype | Definition (Proteins that contain…) | Number(SwissProt) | Number(HEF) |
---|---|---|---|
Multi-modular | more than one A AND C domains | 57 | 280 |
Single-modular | ONE A AND C domains | 21 | 165 |
Pseudo | A OR C domain | 86 | 1243 |
表2 非核糖体多肽合成酶统计信息
Tab. 2 Statistic summary of NRPSs in hypocrealean entomopathotenic fungi (HEF)
Subtype | Definition (Proteins that contain…) | Number(SwissProt) | Number(HEF) |
---|---|---|---|
Multi-modular | more than one A AND C domains | 57 | 280 |
Single-modular | ONE A AND C domains | 21 | 165 |
Pseudo | A OR C domain | 86 | 1243 |
图1 肉座菌目虫生真菌多模块非核糖体多肽合成酶的相似性网络图[其中每个节点代表一个腺苷酰化结构域,连接线粗细与相似性成正比。节点颜色显示非核糖体多肽合成酶的类型,形状表示肉座菌目虫生真菌的种类(科),已知功能的结构域用箭头表示。灰色边框中显示来自同一酶的腺苷酰化结构域的分支(如DtxS1),或由密切相关的结构域分支(如52~64)形成的超级分支(详见正文)。底色显示预测的产物类型。腺苷酰化结构域的亚分支用数字字母组合表示,例如52a]
Fig. 1 Network for the subgroups of multi-modular NRPSs in Hypocrealean Entomopathogenic fungi(Nodes in the network represent A domains, and the line boldness is proportional to the identity. The nodes are colored according to the domain composition of NRPS. Referenced A domains from voucher NRPSs with known products are indicated by arrowheads. The predicted products/functions of the enzymes are listed below the clades. Boxed groups show A domains from the group of enzymes that also contain DtxS1, or superclades that are formed by closely related A domain clades such as clades #52~64 (see text for details). Sub-clades of A domains are indicated with a number-letter combination, for example 52a. NRPSs of the BGCs that contain the voucher A domains include: #27a~32a, destruxin synthetase DtxS1[9]; #32b, cyclosporine synthetase[29]; #33~39, serinocyclin synthetase[13-14]; #44~45, ACVS: N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthetase in penicillin/cephalosporin biosynthesis; #46~51, Tex1: a peptaibol synthetase from Trichoderma virens[30]; #75~76, beauvericin and bassianolide synthetase[11-12].)
图3 肉座菌目虫生真菌单模块和双模块非核糖体多肽合成酶的相似性网络图[其中每个节点代表一个腺苷酰化结构域,连接线粗细与相似性成正比。节点颜色显示非核糖体多肽合成酶的类型,形状表示肉座菌目虫生真菌的种类(科),已知功能的结构域用箭头表示。绿色阴影标注产物未知的非核糖体多肽合成酶腺苷酰化结构域。括号中的数字表示腺苷酰化结构域在标签非核糖体多肽合成酶中的位置,例如(1/3)表示该结构域是一个具有3个模块的非核糖体多肽合成酶的第1个腺苷酰化结构域。AAR—L-氨基己二酸半醛脱氢酶[24];LpsC和LpsB—D-麦角酰肽合成酶亚基1和2,参与麦角生物碱的生物合成[32];ChNPS10—参与真菌形态发育[33-34];NPS2/SidC[35-36]和SidI[37]—胞内铁载体合成酶;SidN[38]和NPS6[39]:胞外铁载体合成酶]
Fig. 3 Overview of the A domain distance network for monomodular, bimodular or siderophore-like NRPSs in Hypocrealean entomopathogenic fungal species(Nodes in the network represent A domains, and the line boldness is proportional to the identity. Nodes are colored according to the domain composition of NRPS. Referenced A domains from voucher NRPSs with known products are indicated by arrowheads. The predicted products/functions of the enzymes are listed below the clades. NRPSs that contain the voucher A domains include: AAR, L-aminoadipate-semialdehyde dehydrogenase[24]; LpsC and LpsB: D-lysergyl-peptide synthetase subunit 1 and 2, respectively, involved in ergot alkaloid biosynthesis[32]; ChNPS10[33-34]: an NRPS-like protein involved in morphological development; NPS2/SidC[35-36] and SidI[37]: synthetases for intracellular siderophores; SidN[38] and NPS6[39]: synthetases for extracellular siderophores. Numbers in parentheses indicate the position of the A domain in the voucher NRPS, for example (1/3) indicates the first A domain out of the three housed in the NRPS.)
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