两种蓝细菌中7对毒素-抗毒素系统的分析和鉴定

doi:10.11978/2021144

Abstract

Abstract:

Cyanobacteria are the only oxygenic photosynthetic prokaryotes on Earth, possessing a relatively fast growth rate and prospering in a range of diverse habitats. Toxin-antitoxin (TA) systems are prevalent in prokaryotes, and play important roles in cell physiological activities including maintenance of mobile genetic elements and mediation of stress responses. Previous bioinformatic studies revealed that putative TA systems are widely distributed in the cyanobacteria genomes. However, studies of TA systems in cyanobacteria are limited. In this study, we predicted TA systems in the genomes of Synechocystis sp. PCC6803 and Synechococcus sp. WH7803, the model strains of freshwater and marine environments cyanobacteria, respectively. The toxicity test of five TA systems in PCC6803 and two TA systems in WH7803 were further implemented. We found that the ectopic expression of toxin New ORF7 and BAD01932 lead to growth inhibition in Escherichia coli host. Our study provides vital information for future study of the ecological and biological roles of TA systems in cyanobacteria.

Key words: toxin-antitoxin system, cyanobacteria, Synechocystis sp. PCC6803, Synechococcus sp. WH7803

CLC Number:

Q938

LIN Shituan, WANG Xiaoxue, CHEN Ran. Analysis and identification of seven toxin-antitoxin systems in two cyanobacteria[J].Journal of Tropical Oceanography, 2022, 41(3): 119-134.

Figures/Tables 9

Tab. S1

Primers used in this study"

引物名称	序列(5'—3')	描述
pBAD-01933-F	GGGCTAACAGGAGGAATTAACATGACCCAGATCACCAAGTCCA	过表达
pBAD-01933-R	GTTTTTGTTCTACGTAAGCTTTCAATTTTTAACACCATCAATCTCTATT	过表达
pBAD-01932-F	GGGCTAACAGGAGGAATTAACATGGTGTTAAAAATTGAACTTCTTGATA	过表达
pBAD-01932-R	GTTTTTGTTCTACGTAAGCTTCTAAAAGAGTCTTTCCACCGATTTC	过表达
Pet28apsp-01933-F	GGGCTAACAGGAGGAATTAACATG GTGTTAAAAATTGAACTTCT	蛋白表达
Pet28apsp-01933-R	GGTGGTGGTGGTGGTGCTCGAG CTAAAAGAGTCTTTCCACCG	蛋白表达
Pet28apsp-01932-F	GGGCTAACAGGAGGAATTAACATG ACCCAGATCACCAAGTCCAA	蛋白表达
Pet28apsp-01932-R	GGTGGTGGTGGTGGTGCTCGAG TCAATTTTTAACACCATCAA	蛋白表达
pBAD-New ORF7-F	ACAGGAGGAATTAACCATGGAT ATGTTACCTGAAATTAATATTT	过表达
pBAD-New ORF7-R	GTTTTTGTTCTACGTAAGCTT CTATTTTTTCTCGATAATTTCA	过表达
pBAD-BAA18559-F	ACAGGAGGAATTAACCATGGAT ATGAATTATCCAATTGTTATTT	过表达
pBAD-BAA18559-R	GTTTTTGTTCTACGTAAGCTT CTATGCGGCACTCAACATCTTA	过表达
Pet28apsp-New ORF7-NdeI-F	TCTGTTCCAGGGGCCCCATATG TTACCTGAAATTAATATTTGCC	蛋白表达
Pet28apsp-New ORF7-NdeI-R	GGTGGTGGTGGTGGTGCTCGAG CTATGCGGCACTCAACATCTTA	蛋白表达
Pet28apsp-BAA18559-F	TTAAGAAGGAGATATACATATG TTACCTGAAATTAATATTTGCC	蛋白表达
Pet28apsp-BAA18559-R	GGTGGTGGTGGTGGTGCTCGAG TGCGGCACTCAACATCTTAATT	蛋白表达
pBAD-01997-F	GGGCTAACAGGAGGAATTAACATGACATCTGTTTTTCACGTTCTAATC	过表达
pBAD-01997-R	GTTTTTGTTCTACGTAAGCTTTTAGTTTTTCCACTGACTTCTTAGCTG	过表达
pBAD-01998-F	GGGCTAACAGGAGGAATTAACATGAGATATAAAAATAATTGTCGAATCAAT	过表达
pBAD-01998-R	GTTTTTGTTCTACGTAAGCTTTTATCTTAAAACCTGTAGATGAAGTTCTTC	过表达
pBAD-01871-F	TAACAGGAGGAATTAACATGCGAAGACGCAGACCTACC	过表达
pBAD-01871-R	GTTTTTGTTCTACGTAAGCTTCTAGACATGCTCAAACTTAACGTATTTG	过表达
pBAD-01872 -F	TAACAGGAGGAATTAACATGTCTAGCACCCTGGCAATCA	过表达
pBAD-01872 -R	GTTTTTGTTCTACGTAAGCTTTTAAATCCGCCAGACCAAAGC	过表达
pBAD-BAA17887-1-58-F	GGGCTAACAGGAGGAATTAACATGAAGGTTAAAGTAATCCTCAAAATCT	过表达
pBAD-BAA17887-1-58-R	GTTTTTGTTCTACGTAAGCTTTCAAGATTGCTTGAGAATACTGGC	过表达
pBAD-BAA17887-59-136-F	GGGCTAACAGGAGGAATTAACATGTCTCAAGCAATCAGGTATTACTTTA	过表达
pBAD-BAA17887-59-136-R	GTTTTTGTTCTACGTAAGCTTTTAAGCCGCAACTGTTACGTAGG	过表达
pBAD-SynWH7803_1122- F	GGGCTAACAGGAGGAATTAACATGGTGGCGGCTGATCATC	过表达
pBAD-SynWH7803_1122- R	GTTTTTGTTCTACGTAAGCTTTCACAGCGGAACGGCCTG	过表达
pBAD-SynWH7803_1121- F	GGGCTAACAGGAGGAATTAACATGACCCATCTCAAGCCATCC	过表达
pBAD-SynWH7803_1121- R	GTTTTTGTTCTACGTAAGCTTCACCACAGCTGCAGTTTCAGG	过表达
pBAD-SynWH7803_1701 -F	GGGCTAACAGGAGGAATTAACATGATCCCTGTTCTCTCTGGGTT	过表达
pBAD-SynWH7803_1701- R	GTTTTTGTTCTACGTAAGCTTTCAACCTGTTGCAGTTGATCGG	过表达
pBAD-SynWH7803_1700- F	GGGCTAACAGGAGGAATTAACATGGGATTTCAGGCTGTGCC	过表达
pBAD-SynWH7803_1700- R	GTTTTTGTTCTACGTAAGCTTTCAGGAATGCGGCGGTTG	过表达
pBAD-01933-F	GGGCTAACAGGAGGAATTAACATGACCCAGATCACCAAGTCCA	过表达
pBAD-01933-R	GTTTTTGTTCTACGTAAGCTTTCAATTTTTAACACCATCAATCTCTATT	过表达
pUC19-pro-BAD1932-1933-f	GAAAAAGAAGAATTGATGATGT	质粒稳定性
pUC19-pro-BAD1932-1933-r	CTAAAAGAGTCTTTCCACCGAT	质粒稳定性
M13-f	CGCCAGGGTTTTCCCAGTCACGAC	质粒稳定性
M13-r	AGCGGATAACAATTTCACACAGGA	质粒稳定性

Tab. S1

Fig. 1

Tab. S2

Prediction information of toxin-antitoxin systems in Synechocystis sp. PCC6803"

	起始位点	终止位点	蛋白长度(氨基酸)	正负链	基因功能描述	蛋白家族编号	蛋白家族描述	xtalpred 软件分析结果	毒素/抗毒素
BAA10220	2516150	2516527	125	-	未知蛋白 Cag_0280	PF01850	PIN 结构域	VpaC	毒素
New ORF1	2516528	2516749	73	-	New ORF	/	/	VapB	抗毒素
BAA10330	2631207	2631608	133	-	毒力相关蛋白毒力相关蛋白C	PF01850	PIN 结构域	VpaC	毒素
BAA10331	2631611	2631868	85	-	PEMI-样蛋白	/	/	VapB	抗毒素
BAA10426	2738712	2738915	67	-	未知蛋白 AM1_C0132	/	/	HicB	抗毒素
New ORF2	2738918	2739133	71	-	New ORF	/	/	HicA	毒素
BAA10766	3121193	3121687	164	-	未知蛋白 sll0658	PF11848	未知功能结构域 (DUF3368)	VpaC	毒素
BAA10767	3121684	3121953	89	-	未知蛋白 ssl1255	PF03683	未表征蛋白家族 (UPF0175)	VapB	抗毒素
BAA10878	3262064	3262459	131	-	未知蛋白 sll0525	PF01850	PIN 结构域	VpaC	毒素
BAA10879	3262471	3262749	92	-	未知蛋白 ssl1004	/	/	VapB	抗毒素
BAA16615	48067	48408	113	-	未知蛋白 sll1400	PF18480	未知功能结构域 (DUF5615)	VpaC	毒素
BAA16616	48405	48635	76	-	未知蛋白 ssl2733	PF04255	未知功能蛋白 (DUF433)	VapB	抗毒素
BAA16671	110392	110724	110	+	PrlF	PF15937	毒素蛋白YhaV的抗毒素PrlF _	PrlF_抗毒素	抗毒素
BAA16672	110808	111224	138	+	未知蛋白 slr0725	PF11663	具有核酸内切酶活性的毒素	YhaV	毒素
BAA16930	382392	382646	84	+	未知蛋白 ssr1765	PF15919	HicB样抗毒素	HicB	抗毒素
BAA16931	382643	382873	76	+	未知蛋白 ssr1766	PF07927	HicA	HicA	毒素
BAA17012	473953	474204	83	-	毒力相关蛋白 C	PF01850	PIN结构域	VpaC	毒素
BAA17013	474205	474432	75	-	毒力相关蛋白 B	/	/	VapB	抗毒素
New ORF3	474504	474785	93	-	New ORF	/	/	HigB_毒素	毒素
BAA17014	474789	475007	72	-	未知蛋白 MAE_61720	/	/	HigA_抗毒素	抗毒素
BAA17015	475110	475445	111	-	未知蛋白 sll1505	PF01934	未知功能蛋白 DUF86	HEPN	毒素
BAA17016	475435	475743	102	-	未知蛋白 sll1504	PF01909	核苷酸转移酶结构域	MNT	抗毒素
BAA17065	545029	545253	74	+	未知蛋白 SYNGTS_0489	PF04255	未知功能蛋白 (DUF433)	VapB	抗毒素
BAA17066	545250	545588	112	+	未知蛋白 SYNGTS_0490	PF18480	未知功能结构域 (DUF5615)	VapC	毒素
BAA17191	679690	680178	162	+	未知蛋白 Ppha_2119	PF01850	PIN结构域	VapC	毒素
BAA17192	680096	680368	90	+	未知蛋白 Ppha_2120	/	/	VapB	抗毒素
BAA17278	775687	776061	124	-	未知蛋白 sll1912	PF13470	PIN结构域	VapC	毒素
BAA17279	776058	776342	94	-	未知蛋白 ssl3615	/	/	VapB	抗毒素
BAA17391	893261	893590	109	+	未知蛋白 slr1209	PF04255	未知功能蛋白 (DUF433)	VapB	抗毒素
BAA17392	893583	893972	129	+	未知蛋白 slr1210	PF18480	未知功能结构域 (DUF5615)	VapC	毒素
BAA17455	968487	968960	157	-	未知蛋白 sll1715	PF01850	PIN结构域结构域	VapC	毒素
BAA17456	968893	969294	133	-	未知蛋白 sll1714	/	/	VapB	抗毒素
BAA17528	1048406	1048753	115	-	未知蛋白 sll1130	PF02452	PemK-样毒素	MazF	毒素
BAA17529	1048750	1049016	88	-	未知蛋白 ssl2245	/	/	MazE	抗毒素
BAA17539	1056714	1056944	76	+	HicB	/	/	HicB	抗毒素
New ORF4	1056487	1056717	76	+	New ORF	/	/	HicA	毒素
BAA17886	1444115	1445392	425	+	未知蛋白 slr1998	PF01494	FAD 结合结构域	未知	未知
BAA17887	1445425	1445835	136	+	未知蛋白 Gura_0600	PF07927	HicA	N-HicA,C-HicB	抗毒素
BAA18037	1617376	1617813	145	-	未知蛋白 sll1411	PF01934	未知功能蛋白 DUF86	HEPN	毒素
BAA18038	1617806	1618096	96	-	未知蛋白 ssl2749	PF01909	核苷酸转移酶结构域结构域	MNT	抗毒素
BAA18040	1620037	1620222	61	+	未知蛋白 ssr3570	/	/	YoeB	毒素
BAA18041	1620276	1620539	87	+	prevent-host-death family protein	PF02604	Phd_YefM抗毒素	YefM	抗毒素
	起始位点	终止位点	蛋白长度(氨基酸)	正负链	基因功能描述	蛋白家族编号	蛋白家族描述	xtalpred 软件分析结果	毒素/抗毒素
BAA18080	1660069	1660287	72	+	未知蛋白 ssr2201	/	/	VapB	抗毒素
BAA18081	1660277	1660711	144	+	未知蛋白 slr1327	PF13470	PIN结构域	VapC	毒素
BAA18337	1933468	1933854	128	-	未知蛋白 SYNGTS_1762	PF01850	PIN结构域	VapC	毒素
BAA18338	1933854	1934060	68	-	未知蛋白 SYNGTS_1763	PF10047	未知功能蛋白 (DUF2281)	VapB	抗毒素
New ORF5	2084922	2085206	94	+	New ORF	/	/	BrnT	毒素
New ORF6	2085136	2085417	93	+	New ORF	PF07927	HicA	BrnA	抗毒素
BAA18559	2193591	2193812	73	-	未知蛋白 MAE_17890	PF15919	HicB样抗毒素	HicB	抗毒素
New ORF7	2193813	2194157	114	-	New ORF	PF07927	HicA,	HicA	毒素
New ORF8	3341880	3342128	82	-	New ORF	/	/	HicB	抗毒素
BAA18682	3342125	3342442	105	-	未知蛋白 MAE_13550	PF13470	PIN结构域	VapC	毒素
BAA18687	3347941	3348201	86	+	未知蛋白 SYNGTS_2983	/	/	VapB	抗毒素
BAA18688	3348191	3348553	120	+	未知蛋白 SYNGTS_2984	PF06296	RelE / RelB系统毒素	RelE	毒素
BAA18757	3428962	3429171	69	+	未知蛋白 MAE_40070	PF15919	HicB样抗毒素	HicB	抗毒素
New ORF9	3429171	3429398	75	+	New ORF	/	/	HicA	毒素
BAB61866	2074694	2074957	87	+	prevent-host-death family protein (plasmid)	PF02604	Phd_YefM类抗毒素	YefM 抗毒素	抗毒素
BAB61867	2085826	2086110	94	+	prevent-host-death family protein	PF02604	Phd_YefM类抗毒素	YefM 抗毒素	抗毒素
BAD01773	1136	1540	134	-	未知蛋白 sll5003 (plasmid)	PF18480	未知功能结构域 (DUF5615)	VapC	毒素
BAD01774	1515	1826	103	-	未知蛋白 sll5004 (plasmid)	PF04255	未知功能蛋白 (DUF433)	VapB	抗毒素
BAD01790	24181	24462	93	+	未知蛋白 ssr5020 (plasmid)	PF05015	RelE 样毒素	HigB-like_毒素	毒素
BAD01791	24473	24787	104	+	未知蛋白 slr5021	PF01381	螺旋-转角-螺旋	HigA_抗毒素	抗毒素
BAD01835	67163	67378	71	-	未知蛋白 ssl5065	/	/	ParD_抗毒素	抗毒素
BAD01836	67362	67976	204	-	ParA 家族	PF01656	CobQ/CobB/MinD/ParA 核苷酸结合结构域	ParA_毒素	毒素
BAD01864	92805	93236	143	-	质粒稳定蛋白	PF01850	PIN结构域	VapC	毒素
BAD01865	93233	93520	95	-	未知蛋白 ssl5095	PF02604	Phd_YefM类抗毒素	VapB	抗毒素
BAD01871	96124	96561	145	+	未知蛋白 Ajs_1570	/	/	未知	未知
BAD01872	96554	97156	200	+	未知蛋白 BURPS1106A_2452	PF08843	核苷酸转移酶 AbiEii毒素	AbiEii 毒素	毒素
BAD01886	107105	107527	140	+	未知蛋白 slr5116 (plasmid)	PF13470	PIN结构域	VapC	毒素
BAD01887	107531	107746	71	+	未知蛋白 ssr5117	PF05534	HicB 家族	VapB	抗毒素
BAD01905	1399	1827	142	-	质粒稳定蛋白	PF01850	PIN结构域	VapC	毒素
BAD01906	1799	2032	77	-	未知蛋白 MYO_450	/	/	VapB	抗毒素
BAD01908	3041	3364	107	-	未知蛋白 sll7006	PF05534	HicB 家族	HicB	抗毒素
BAD01909	3367	3591	74	-	未知蛋白 ssl7007	/	/	VapC	毒素
BAD01932	28850	29353	167	-	未知蛋白 sll7030	PF13508	乙酰基转移酶(GNAT)结构域	GNAT 毒素	毒素
BAD01933	29337	29639	100	-	未知蛋白 sll7031	PF08681	未知功能蛋白 (DUF1778)	GNAT 抗毒素	抗毒素
BAD01940	35891	36178	95	-	未知蛋白 ssl7038	/	/	HigA 抗毒素	抗毒素
BAD01941	36189	36479	96	-	未知蛋白 ssl7039	PF05973	噬菌体衍生蛋白 Gp49 样(DUF891)	HigB 毒素	毒素
BAD01942	36597	36848	83	+	未知蛋白 ssr7040	PF04014	MazE抗毒素	MazE	抗毒素
BAD01943	36839	37201	120	+	未知蛋白 slr7041	PF02452	PemK-样, MazF-样毒素	MazF	毒素
BAD01947	40013	40234	73	-	未知蛋白 ssl7045	/	/	未知	未知

Tab. S2

Tab. S3

Prediction information of toxin-antitoxin systems in Synechococcus sp. WH7803"

基因编号(ensembl数据库)		起始位点	终止位点	蛋白长度(氨基酸)	正负链	基因功能描述	蛋白家族编号	蛋白家族描述	xtalpred 软件分析结果	毒素/抗毒素
SynWH7803_0100	102513	102677	54	+	NTP_transf_2 结构域蛋白	/	未知	未知	毒素
SynWH7803_0101	102623	102820	65	+	RelA 和 Spot 样 ppGpp 合成酶和水解酶	/	NT_Pol-β-样超家族	MNT	抗毒素
SynWH7803_0976	902407	902246	53	+	未表征的膜蛋白	/	PIN	未知	抗毒素
SynWH7803_0977	902875	902492	127	+	保守的假定蛋白保守的假定蛋白	PF11964	SpoIIAA-样	SpoIIAA-样蛋白	未知
SynWH7803_1086	996599	995259	446	-	保守的假定蛋白保守的假定蛋白	PF14403	Circularly permuted ATP-grasp type 2	谷胱甘肽精氨酸合酶	未知
SynWH7803_1087	997032	996586	148	-	保守的假定蛋白保守的假定蛋白	/	/	未知	抗毒素
SynWH7803_1088	997508	997032	158	-	分泌的五肽重复蛋白	PF00805	五肽重复序列 (8 份)	未知	未知
SynWH7803_1121	1027292	1026795	165	-	预测的 rRNA 甲基化酶	PF00588	SpoU rRNA 甲基化酶家族	RNA甲基化酶	毒素
SynWH7803_1122	1027843	1027289	184	-	双功能腺苷钴胺生物合成蛋白	PF02283	甲酰胺激酶	腺苷钴酰胺激酶/腺苷钴酰胺磷酸鸟苷转移酶	未知
SynWH7803_1603	1475142	1474984	52	+	假定蛋白	/	/	ATP依赖性RNA解旋酶	未知
SynWH7803_1604	1475671	1475198	157	+	未表征的保守分泌蛋白	/	Gp49	未知	毒素
SynWH7803_1605	1476140	1475679	153	+	SufE 样蛋白, 可能参与 Fe-S 中心组装	PF02657	Fe-S代谢相关域	Cpta_toxin	毒素
基因编号(ensembl数据库)		起始位点	终止位点	蛋白长度(氨基酸)	正负链	基因功能描述	蛋白家族编号	蛋白家族描述	xtalpred 软件分析结果	毒素/抗毒素
SynWH7803_1606	1477492	1476176	438	+	高丝氨酸脱氢酶	PF03447	高丝氨酸脱氢酶, NAD 结合结构域	高丝氨酸脱氢酶	未知
SynWH7803_1700	1554939	1554607	110	-	假定蛋白	PF13469	磺基转移酶家族	磺基转移酶家族	未知
SynWH7803_1701	1555576	1554899	225	-	假定蛋白	PF13469	磺基转移酶家族	磺基转移酶家族	毒素
SynWH7803_1762	1616798	1615596	400	+	整合膜蛋白(PIN 域超家族)	/	PIN_5	VapC	毒素
SynWH7803_1763	1617500	1616829	223	+	ATP 依赖性 Clp 蛋白酶的蛋白酶亚基	PF00574	Clp 蛋白酶	Clp 蛋白酶	未知
SynWH7803_1944	1778918	1779145	75	+	假定蛋白SynWH7803_1944	PF02604	Phd YefM抗毒素	Phd YefM_超家族抗毒素	抗毒素
SynWH7803_1945	1779145	1779555	136	+	假定蛋白 SynWH7803_1945	PF01850	PIN 结构域	VapC	毒素
SynWH7803_2509	2341171	2340317	284	-	甲酰基四氢叶酸去甲酰基酶	PF00551	甲酰基转移酶	甲酰基转移酶	未知
SynWH7803_2510	2341482	2341222	86	-	预测的转录调节因子	PF02195	ParB 样核酸酶结构域	ParBc	抗毒素

Tab. S3

Tab. 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

References 42

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Analysis and identification of seven toxin-antitoxin systems in two cyanobacteria

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菌株名称	基因编号	起始位置	终止位置	蛋白长度/aa	TA信息	TA 类型预测
集胞藻PCC6803	BAD01871	96124	96561	145	x
	BAD01872	96554	97156	200	T	AbiEii家族毒素
	BAD01932	28850	29353	167	x	GNAT家族毒素
	BAD01933	29337	29639	100	A	GNAT家族抗毒素
	BAD01997	93673	94188	171	T	NTP水解酶家族毒素
	BAD01998	94198	94611	137	x
	BAA17887	1445425	1445835	136	A	HicA和HicB融合蛋白
	New ORF 7	2193818	2194157	114	T	HicAB家族毒素
	BAA18559	2193591	2193812	73	A	HicAB家族抗毒素
聚球藻WH7803	SynWH7803_1121	1026795	1027292	165	T	甲基转移酶
	SynWH7803_1122	1027289	1027843	184	x
	SynWH7803_1700	1554607	1554939	110	x	硫转移酶家族
	SynWH7803_1701	1554899	1555576	225	T	硫转移酶家族

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