比较基因组学分析弧菌属群体感应通路的分布与进化

doi:10.11978/2021025

热带海洋学报 ›› 2022, Vol. 41 ›› Issue (1): 28-41.doi: 10.11978/2021025CSTR: 32234.14.2021025

比较基因组学分析弧菌属群体感应通路的分布与进化

毛颖津^1,²(), 高贝乐¹()

1. 中国科学院热带海洋生物资源与生态重点实验室, 广东省海洋药物重点实验室, 中国科学院南海海洋研究所, 广东广州, 510301
2. 中国科学院大学, 北京 100049

收稿日期:2021-02-24 修回日期:2021-04-15 出版日期:2022-01-10 发布日期:2021-04-22
通讯作者: 高贝乐
作者简介:毛颖津(1994—), 男, 广东省中山市人, 硕士研究生, 研究方向为微生物功能基因组学研究。email: maoyingjin18@mails.ucas.edu.cn
基金资助:
广州市科技计划项目(201804010437)

Comparative genomic analysis of the distribution and evolution of quorum sensing pathways in the Vibrio genus

MAO Yingjin^1,²(), GAO Beile¹()

1. CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301
2. University of Chinese Academy of Sciences, Beijing 100049

Received:2021-02-24 Revised:2021-04-15 Online:2022-01-10 Published:2021-04-22
Contact: GAO Beile
Supported by:
Science and Technology Program of Guangzhou, China(201804010437)

摘要/Abstract

摘要：

群体感应是一种细菌细胞间的通讯过程, 细菌通过测量细胞外自诱导剂浓度从而感知群体细胞密度变化。群体感应使细菌能够在两种基因表达模式下转换: 在低细胞密度时有利于个体发展, 而在高细胞密度时则有利于群体发展。目前主要有7种群体感应通路, 分别以oligopeptides、AHL(Acylated Homoserine Lactones)、AI-2(Autoinducer-2)、CAI-1(Cholera Autoinducer-1)、PQS(Pseudomonas Quinolone Signal)、AI-3(Autoinducer-3)以及DSF(Diffusible Signal Factor)作为各群体感应通路的信号分子; 其中oligopeptides存在于革兰氏阳性细菌中, 其余6种信号分子存在于革兰氏阴性细菌中。弧菌是导致人类感染和水产品污染的主要病原菌, 传统的抗生素治疗弧菌感染具有很强的选择压力, 导致越来越多耐药弧菌出现。面对愈发严峻的弧菌耐药性问题, 目前群体感应淬灭被认为是治疗弧菌感染的重要替代手段之一, 因而有必要调查弧菌属细菌不同群体感应通路的分布情况, 为针对弧菌的群体感应淬灭剂研发提供重要参考信息。通过比较基因组学分析, 发现全基因组测序的46株弧菌存在AHL、AI-2以及CAI-1这3种信号分子通路, 其中5株弧菌均含有上述3种信号分子通路, 共有30株弧菌只含有AI-2和CAI-1两种信号分子通路; 而46株弧菌都不存在PQS、AI-3以及DSF群体感应通路。此外, 弧菌群体感应通路的分布与物种进化有关, 含有同种群体感应信号分子通路的弧菌, 其亲缘关系较近, 说明该通路的基因进化自它们的共同祖先。本研究表明开发针对弧菌的群体感应淬灭剂应以AI-2和CAI-1两种信号分子介导的通路作为靶点。

关键词: 比较基因组学, 弧菌, 群体感应, 信号分子, 物种进化, 群体感应淬灭剂

Abstract:

Quorum sensing (QS) is a process of bacterial cell-cell communication in which bacteria can monitor their population density by detection of extracellular autoinducer. QS allows the bacteria to switch between two kinds of gene expression modes: The program is suitable for individual development at low cell density, while favoring community at high cell density. Presently, there are mainly seven kinds of QS signaling molecules, including oligopeptides, AHL (Acylated Homoserine Lactones), AI-2 (Autoinducer-2), CAI-1 (Cholera Autoinducer-1), PQS (Pseudomonas Quinolone Signal), AI-3 (Autoinducer-3), and DSF (Diffusible Signal Factor). Among them, oligopeptides mainly exist in gram-positive bacteria, and the others are commonly found in gram-negative bacteria. Species of the Vibrio genus are important pathogens for human and aquaculture. Since traditional antibiotic treatment has a strong selection pressure leading to increasing number of drug-resistant Vibrio and increasing serious problems, QS quenching is believed as one alternative strategy of the most potential to combat bacterial infection. Thus, it is necessary to investigate the distribution of QS pathways among the Vibrio genus. Among the 46 whole genome sequenced Vibrio species, we found that only three pathways exist in Vibrio species, including AHL, AI-2 and CAI-1 pathways. Specifically, five Vibrio species contain the above three pathways, and 30 strains contain both AI-2 and CAI-1 pathways. However, none of the 46 Vibrio species have the PQS, AI-3 and DSF pathways. In addition, the distribution of QS pathways in Vibrio is related to their phylogeny, suggesting that species with the same QS pathway(s) are close relatives, which indicates that the genes of this pathway evolved from their common ancestor. This study provides useful information for QS quenching against Vibrio pathogens by targeting the AI-2 and CAI-1 QS pathways.

Key words: comparative genomics, vibrio genera, quorum sensing, signaling molecules, species evolution, quorum quenching

中图分类号:

P735.51

毛颖津, 高贝乐. 比较基因组学分析弧菌属群体感应通路的分布与进化[J]. 热带海洋学报, 2022, 41(1): 28-41.

MAO Yingjin, GAO Beile. Comparative genomic analysis of the distribution and evolution of quorum sensing pathways in the Vibrio genus[J]. Journal of Tropical Oceanography, 2022, 41(1): 28-41.

图/表 8

图1

表1

表2

菌株信息"

物种名称	菌株	基因组编号	基因组大小/Mb	编码序列数目/个
Vibrio alfacsensis	CAIM 1831	GCA_003544875.1	4.91	3830
Vibrio alginolyticus	FA2	GCA_011801435.1	5.25	4598
Vibrio anguillarum	VIB12	GCA_002310335.1	4.90	4091
Vibrio antiquarius	EX25	GCA_000024825.1	5.09	4451
Vibrio aphrogenes	CA-1004	GCA_002157735.2	3.38	2881
Vibrio astriarenae	HN897	GCA_010587385.1	4.80	4176
Vibrio breoganii	FF50	GCA_001677275.1	4.49	3978
Vibrio campbellii	BoB-90	GCA_002906455.1	6.17	5407
Vibrio casei	DSM 22364	GCA_002218025.2	4.14	3601
Vibrio chagasii	ECSMB14107	GCA_004022545.1	5.55	4448
物种名称	菌株	基因组编号	基因组大小/Mb	编码序列数目/个
Vibrio cholerae	10432-62	GCA_000969265.1	4.08	3546
Vibrio cidicii	2756-81	GCA_009763805.1	4.75	3492
Vibrio cincinnatiensis	2070-81	GCA_009763705.1	3.81	3284
Vibrio coralliilyticus	RE22	GCA_003391375.1	5.78	5064
Vibrio cyclitrophicus	ECSMB14105	GCA_005144905.1	5.07	4283
Vibrio diabolicus	FA3	GCA_011801455.1	5.11	4501
Vibrio europaeus	NPI-1	GCA_013154935.1	5.45	4782
Vibrio fluvialis	FDAARGOS_104	GCA_001558415.2	4.83	4338
Vibrio furnissii	FDAARGOS_777	GCA_006364355.1	4.99	4466
Vibrio gazogenes	ATCC 43942	GCA_002196515.1	4.79	4070
Vibrio harveyi	ATCC 33843	GCA_000770115.2	5.88	5166
Vibrio hyugaensis	090810a	GCA_002906655.1	5.61	4845
Vibrio jasicida	090810c	GCA_002887615.1	5.99	5188
Vibrio mediterranei	QT6D1	GCA_002214345.1	5.81	5146
Vibrio metoecus	08-2459	GCA_009665275.1	3.99	3518
Vibrio metschnikovii	9502-00	GCA_009763765.1	3.62	3118
Vibrio mimicus	SCCF01	GCA_001767355.1	4.48	3925
Vibrio natriegens	CCUG 16371	GCA_001680045.1	5.16	4451
Vibrio navarrensis	2462-79	GCA_009763725.1	4.78	4093
Vibrio nigripulchritudo	SFn1	GCA_000801275.1	6.32	5545
Vibrio owensii	XSBZ03	GCA_002021755.1	5.89	5112
Vibrio panuliri	JCM 19500	GCA_009938205.1	4.86	4235
Vibrio ponticus	DSM 16217	GCA_009938225.1	4.80	4098
Vibrio parahaemolyticus	VPD14	GCA_004006515.1	5.17	4531
Vibrio qinghaiensis	Q67	GCA_002257545.1	4.02	3373
Vibrio rotiferianus	B64D1	GCA_002214395.1	5.28	4593
Vibrio rumoiensis	FERM P-14531	GCA_002218045.2	4.21	3605
Vibrio scophthalmi	VS-12	GCA_001685465.1	4.93	4206
Vibrio sp	2521-89	GCA_002216685.1	4.12	3539
Vibrio splendidus	BST398	GCA_003345295.1	5.51	4582
Vibrio taketomensis	C4III291	GCA_009938185.1	4.36	3526
Vibrio tapetis	CECT4600	GCA_900233005.1	5.73	4800
Vibrio tasmaniensis	LGP32	GCA_000091465.1	4.97	4169
Vibrio tritonius	JCM 16456	GCA_001547935.1	5.22	4549
Vibrio tubiashii	ATCC 19109	GCA_000772105.1	5.54	4946
Vibrio vulnificus	07-2444	GCA_009764115.1	5.23	4554

表2

表3

图2

表4

表5

表6

参考文献 53

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合成酶	信号分子	受体蛋白	模式菌株	参考文献
LuxI	AHL	LuxR	费氏弧菌 Aliivibrio fischeri	Eberhard et al, 1981
LuxS	AI-2	LuxPQ/LsrB/RbsB	霍乱弧菌 Vibrio cholerae	Bassler et al, 1993
CqsA	CAI-1	CqsS	霍乱弧菌 Vibrio cholerae	Miller et al, 2002
PqsA/B/C/D/E/H	PQS	PqsR	铜绿假单胞菌 Pseudomonas aeruginosa	Pesci et al, 1999
LuxS	AI-3	QseBC/QseEF	大肠杆菌 Escherichia coli O157:H7	Sperandio et al, 2003
RpfF	DSF	RpfCG/RpfR	野油菜黄单胞菌 Xanthomonas campestris	Barber et al, 1997

比较基因组学分析弧菌属群体感应通路的分布与进化

Comparative genomic analysis of the distribution and evolution of quorum sensing pathways in the Vibrio genus

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