链霉菌TRM SA0054 Tubercidin合成基因簇挖掘

doi:10.6048/j.issn.1001-4330.2023.11.024

新疆农业科学 ›› 2023, Vol. 60 ›› Issue (11): 2806-2815.DOI: 10.6048/j.issn.1001-4330.2023.11.024

• 微生物·园艺特产·农产品加工工程 • 上一篇下一篇

链霉菌TRM SA0054 Tubercidin合成基因簇挖掘

张萍(), 罗晓霞, 万传星, 张利莉()

塔里木盆地生物资源保护利用兵团重点实验室/塔里木大学生命科学与技术学院,新疆阿拉尔 843300

收稿日期:2023-01-30 出版日期:2023-11-20 发布日期:2023-12-07
通信作者: 张利莉(1963-),女,新疆人,教授,博士,硕士生/博士生导师,研究方向为微生物资源与利用,(E-mail)zhanglily@taru.edu.cn
作者简介:张萍(1994-),女,河南人,硕士研究生,研究方向为放线菌资源及其次级代谢产物,(E-mail)zhang_ping16@sina.com
基金资助:
国家自然科学基金-新疆联合基金重点项目“塔里木盆地放线菌资源代谢潜力的深度挖掘”(U1703236);新疆生产建设兵团区域发展计划重点项目“基于基因组挖掘的功能成分研究”(2017DB002)

Excavating of synthetic gene cluster of Streptomyces TRM SA0054 Tubercidin

ZHANG Ping(), LUO Xiaoxia, WAN Chuanxing, ZHANG Lili()

The Key Laboratory of the Tarim Basin Biological Resources Conservation and Utilization of XPCC/School of Life Sciences and Technology, Tarim University, Aral Xinjiang 843300,China

Received:2023-01-30 Online:2023-11-20 Published:2023-12-07
Correspondence author: ZHANG Lili (1963-), female, Xinjiang, professor, research field: microbial resources and utilization,(E-mail)zhanglily@taru.edu.cn
Supported by:
National Natural Science Foundation of China "Deep Excavation of the Metabolic Potential of Actinomycetes Resources in Tarim Basin"(U1703236);Key Project of Xinjiang Production and Construction Corps Regional Development Program Project "Research on Functional Components Based on Genome Mining"(2017DB002)

摘要/Abstract

摘要：

【目的】 评估菌株TRM SA0054的代谢潜力,解析其基因组信息研究该菌株次级代谢产物基因资源。【方法】 采用Illumina Hiseq测序平台对菌株TRM SA0054进行全基因组测序,并进行生物信息学分析,采用现代分离纯化方法检测鉴定其代谢产物。【结果】 菌株TRM SA0054基因组大小为7.2 Mb,共有6 410个蛋白编码基因,GC含量为73.16%;预测到26个次级代谢基因簇,其中Region 36.1基因簇与Tubercidin(杀结核菌素)基因簇相似性为81%,菌株TRM SA0054发酵能够产生Tubercidin。【结论】 基于基因组挖掘和LC-MS检测验证菌株TRM SA0054具有产生Tubercidin的能力。

关键词: Streptomyces carminius TRM SA0054; 基因组注释; Tubercidin基因簇

Abstract:

【Objective】 This project aims to evaluate the metabolic potential of strain TRM SA0054 by analyzing the genomic information, thus further studying the secondary metabolite gene resources of the strain.【Methods】 The whole genome of TRM SA0054 was sequenced by Illumina Hiseq sequencing platform, and bioinformatics analysis was conducted. The metabolites were preliminarily detected and identified by modern separation and purification methods. 【Results】 The genome size of strain TRM SA0054 was 7.2 Mb, there were 6,410 protein coding genes, and GC content was 73.16%. AntiSMASH analysis predicted that there were 26 secondary metabolic gene clusters, among which Region 36.1 gene cluster was 81% similar to Tubercidin gene cluster. Fermentation products were detected by LC-MS, the fermentation of strain TRM SA0054 could produce Tubercidin.【Conclusion】 Strain TRM SA0054 has the ability to produce Tubercidin based on genome mining and LC-MS detection.

Key words: Streptomyces carminius TRM SA0054; genome annotation; Tubercidin gene cluster

中图分类号:

Q936
S182

张萍, 罗晓霞, 万传星, 张利莉. 链霉菌TRM SA0054 Tubercidin合成基因簇挖掘[J]. 新疆农业科学, 2023, 60(11): 2806-2815.

ZHANG Ping, LUO Xiaoxia, WAN Chuanxing, ZHANG Lili. Excavating of synthetic gene cluster of Streptomyces TRM SA0054 Tubercidin[J]. Xinjiang Agricultural Sciences, 2023, 60(11): 2806-2815.

图/表 9

参考文献 25

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菌株Strain	S.carminius TRM SA0054
基因组总长度 Total length of genome (bp)	7 200 902
CDS基因数 CDS gene number	6 410
CDS平均长度 Average CDS length (bp)	954
G+C%含量 G+C% content (%)	73.15
N50 contig大小 N50 contig size (bp)	300 464
tRNA数目 tRNA number	65
rRNA数目 rRNA number	15

菌株Strain	S.carminius TRM SA0054
基因组总长度 Total length of genome (bp)	7 200 902
CDS基因数 CDS gene number	6 410
CDS平均长度 Average CDS length (bp)	954
G+C%含量 G+C% content (%)	73.15
N50 contig大小 N50 contig size (bp)	300 464
tRNA数目 tRNA number	65
rRNA数目 rRNA number	15

基因簇编号 Cluster	区域 Region	位置 Location (nt)	最相似的已知基因簇 Most similar known cluster	类型 Type	相似性 Similarity (%)
1-407	6.1	1-21641	branched-chain fatty acids(支链脂肪酸)	other	100
2-419	15.1	66732-77136	Ectoine(四氢嘧啶)	other	100
3-475	41.1	25250-66338	Alkylresorcinol (烷基间苯二酚)	Polyketide	100
4-513	65.2	220132-242865	Keywimysin (键维霉素)	RiPP	100
5-513	65.4	637199-659916	SapB	RiPP:Lanthipeptide	100
6-502	54.1	73725-120591	Undecylprodigiosin (十一烷基灵菌红素)	NRP+ Polyketide	95
7-403	4.1	218512-244303	Isorenieratene (异戊二烯)	Terpene	85
8-462	34.1	256788-282579	Isorenieratene (异戊二烯)	Terpene	85
9-464	36.1	13034-33396	Tubercidin (杀结核菌素)	Other	81
10-510	62.2	204780-240191	Lagmysin (拉米霉素)	RiPP	80
11-403	4.2	248350-300464	spore pigmen (孢子色素)	Polyketide	58
12-462	34.2	286626-335712	spore pigmen (孢子色素)	Polyketide	58
13-504	56.1	107039-149217	Diazepinomicin	Terpene	52
14-513	65.3	262275-306630	Melanin (黑色素)	Other	40
15-408	7.1	73518-95460	Hopene (藿烯)	Terpene	30
16-430	19.1	1-23254	Microansamycin (微安霉素)	Polyketide	25
17-513	65.1	175916-206600	Mycosubtilin (抗霉枯草菌素)	NRP + Polyketide	20
18-505	57.1	102245-124388	lankacidin C (兰卡霉素)	NRP+Polyketide	20
19-499	51.1	1-3282	Epepothilone B (埃博霉素B)	NRP+Polyketide	18
20-510	62.1	123308-135233	lipopeptide 8D1-1 / lipopeptide 8D1-2 (脂肽)	NRP	6
21-500	52.1	67269-81582	Ficellomycin (纤维霉素)	NRP	5
22-463	35.1	63166-83705	Kosinostatin(越野他汀)	NRP + Polyketide	4
23-399	1.1	69363-81186	ficellomycin(纤维霉素)	NRP	3
24-492	48.1	69285-89796	7-deoxypactamycin (脱氧帕他霉素)	Polyketide	3
25-515	67.1	1-17298	-	lanthipeptide-class-i	-
26-515	67.2	183303-194151	-	RiPP-like	-

基因簇编号 Cluster	区域 Region	位置 Location (nt)	最相似的已知基因簇 Most similar known cluster	类型 Type	相似性 Similarity (%)
1-407	6.1	1-21641	branched-chain fatty acids(支链脂肪酸)	other	100
2-419	15.1	66732-77136	Ectoine(四氢嘧啶)	other	100
3-475	41.1	25250-66338	Alkylresorcinol (烷基间苯二酚)	Polyketide	100
4-513	65.2	220132-242865	Keywimysin (键维霉素)	RiPP	100
5-513	65.4	637199-659916	SapB	RiPP:Lanthipeptide	100
6-502	54.1	73725-120591	Undecylprodigiosin (十一烷基灵菌红素)	NRP+ Polyketide	95
7-403	4.1	218512-244303	Isorenieratene (异戊二烯)	Terpene	85
8-462	34.1	256788-282579	Isorenieratene (异戊二烯)	Terpene	85
9-464	36.1	13034-33396	Tubercidin (杀结核菌素)	Other	81
10-510	62.2	204780-240191	Lagmysin (拉米霉素)	RiPP	80
11-403	4.2	248350-300464	spore pigmen (孢子色素)	Polyketide	58
12-462	34.2	286626-335712	spore pigmen (孢子色素)	Polyketide	58
13-504	56.1	107039-149217	Diazepinomicin	Terpene	52
14-513	65.3	262275-306630	Melanin (黑色素)	Other	40
15-408	7.1	73518-95460	Hopene (藿烯)	Terpene	30
16-430	19.1	1-23254	Microansamycin (微安霉素)	Polyketide	25
17-513	65.1	175916-206600	Mycosubtilin (抗霉枯草菌素)	NRP + Polyketide	20
18-505	57.1	102245-124388	lankacidin C (兰卡霉素)	NRP+Polyketide	20
19-499	51.1	1-3282	Epepothilone B (埃博霉素B)	NRP+Polyketide	18
20-510	62.1	123308-135233	lipopeptide 8D1-1 / lipopeptide 8D1-2 (脂肽)	NRP	6
21-500	52.1	67269-81582	Ficellomycin (纤维霉素)	NRP	5
22-463	35.1	63166-83705	Kosinostatin(越野他汀)	NRP + Polyketide	4
23-399	1.1	69363-81186	ficellomycin(纤维霉素)	NRP	3
24-492	48.1	69285-89796	7-deoxypactamycin (脱氧帕他霉素)	Polyketide	3
25-515	67.1	1-17298	-	lanthipeptide-class-i	-
26-515	67.2	183303-194151	-	RiPP-like	-

位点 Locus tag	氨基酸 Amino acids	功能预测 Proposed function	一致性 Identify(%)	登录号 Accession No.
1-ctg36_17	319	glucosyl-3-phosphoglycerate (葡萄糖基-3-磷酸甘油酸酯)	92.16	WP_101256758.1
2-ctg36_18	489	trehalose-6-phosphate synthase (6-磷酸海藻糖合酶)	86.71	WP_093658899.1
3-ctg36_19	290	trehalose-phosphatase(海藻糖磷酸酶)	91.29	WP_031509476.1
4-ctg36_20	240	hypothetical protein	62.18	WP_031509478.1
5-ctg36_21	755	hypothetical protein	69.15	WP_155070928.1
6-ctg36_22	170	hypothetical protein	69.41	WP_1155070929.1
7-ctg36_23	86	DUF3263 domain-containing protein (DUF3263结构域的蛋白 )	82.67	WP_030218603.1
8-ctg36_24	120	6carboxytetrahydropterin synthase (6-羧基四氢蝶呤合酶)	74.17	AVW83009.1
9-ctg36_25	181	7carboxy7deazaguanine synthase QueE/radical SAM family protein (7-羧基-7-脱氮鸟嘌呤合酶 QueE/ 自由基 SAM 家族蛋白)	72.66	AVW83010.1
10-ctg36_26	199	GTP cyclohydrolase I (GCHI)(GTP环水解酶ⅰ)	78.28	AVW83011.1
11-ctg36_27	385	IMP dehydrogenase ( IMP 脱氢酶)	78.59	WP_159742672.1
12-ctg36_28	195	Phosphoribosylpyrophosphate transferase(磷酸核糖转移酶)	68.51	WP_159742671.1
13-ctg36_29	422	UbiD family decarboxylase (UbiD 家族脱羧酶 )	78.01	WP_159742670.1
14-ctg36_30	168	NUDIX domaincontaining protein (NUDIX结构域的蛋白质) 水解酶	79.76	WP_159742669.1
15-ctg36_31	327	Carbohydrate kinase family protein (碳水化合物激酶家族蛋白)	51.95	WP_159742668.1
16-ctg36_32	429	MFS (Major facilitator superfamily) transporter (主要促进者超家族转运蛋白)	68.39	WP_159742667.1
17-ctg36_33	249	HAD family hydrolase	67.52	WP_057574898.1
18-ctg36_34	395	hypothetical protein	46.22	WP_155070927.1

链霉菌TRM SA0054 Tubercidin合成基因簇挖掘

Excavating of synthetic gene cluster of Streptomyces TRM SA0054 Tubercidin

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