基于比较基因组学分析海洋聚球藻对铁限制的适应机制

doi:10.11978/2023036

Abstract

Abstract:

Low solubility and limited source of iron in seawater are the main growth limiting factors for phytoplankton in 40%of the global ocean. Marine Synechococcus is a picocyanobacteria with global distribution and is one of the most important contributors to marine prime productivity. Affected by the source and concentration of iron in coastal and oceanic environments, marine Synechococcus has different adaptive mechanisms to iron limitation. In this study, we performed a comparative genomic analysis of 29 whole genome sequenced marine Synechococcus. The results showed that marine Synechococcus had high genetic diversity and belonged to four genera of Cyanobiaceae under the GTDB (Genome Taxonomy Database) taxonomy, and these four genera corresponded well to the subtype under NCBI (National Center for Biotechnology Information) taxonomy. The results of functional annotation showed that the number and types of unique genes differed between coastal and oceanic Synechococcus, and unique gene of coastal strains are more involved in inorganic ion transport and metabolism. Further analysis of iron limitation-related genes in marine Synechococcus revealed that the coastal strain had stronger abilities of iron uptake, homeostasis regulation and storage than the oceanic strains, and had a better ability to sense and respond to environmental changes. In this study, we reviewed the evolutionary relationships and taxonomic positions of marine Synechococcus using comparative genomics, and identified the differences in the genome and adaptive mechanisms of coastal and oceanic strains in response to iron limitation, to provide a basis for better understanding of the environmental adaptation of marine Synechococcus.

Key words: Comparative genomics, marine Synechococcus, iron limitation, adaptive mechanisms

MU Rong, ZHU Zhu, ZHANG Ruifeng. Adaptive mechanisms of iron limitation on the marine Synechococcus based on comparative genomics[J].Journal of Tropical Oceanography, 2023, 42(6): 89-100.

Figures/Tables 9

Tab. 1

Fig. 1

Fig. 2

Fig. 3

Tab. 2

Genome features of the 29 analyzed marine Synechococcus strains"

分离地点		基因组编号	类型	基因组大小/bp	GC含量/%	完整度/%	污染度/%
大西洋马尾藻海	WH8102	GCA_000195975.1	大洋	2434428	59.4	99.46	0
	WH7803	GCA_000063505.1	大洋	2366980	60.2	99.18	0
	WH8103	GCA_001182765.1	大洋	2429688	59.5	99.73	0.27
	UW69	GCA_900474185.1	大洋	2372121	58.7	100	0
	UW140	GCA_900474295.1	大洋	2704142	57.8	99.73	0
	UW105	GCA_900473935.1	大洋	2659417	57.5	99.46	0
	UW106	GCA_900474015.1	大洋	2479535	58	99.73	0.27
	WH8109	GCA_000161795.2	大洋	2111515	60.1	99.46	0
赤道太平洋	UW179A	GCA_900473965.1	大洋	3057835	54.5	100	0.41
	MITS9508	GCA_001632165.1	大洋	2502434	56.1	100	0.27
	MITS9509	GCA_001631935.1	大洋	3087928	55.4	99.18	0.82
	MITS9504	GCA_001632105.1	大洋	3087293	55.4	99.73	1.09
东太平洋加利福尼亚海流	CC9605	GCA_000012625.1	近岸	2510659	59.2	99.73	0
	CC9311	GCA_000014585.1	近岸	2606748	52.5	99.73	0
	CC9902	GCA_000012505.1	近岸	2234828	54.2	99.46	0
中国东海	KORDI-52	GCA_000737595.1	近岸	2572069	59.1	100	0
中国东海	KORDI-49	GCA_000737575.1	近岸	2585813	61.4	99.37	0
地中海	RCC307	GCA_000063525.1	近岸	2224914	60.8	99.64	0
地中海	BL107	GCA_000153805.1	近岸	2285034	54.2	99.46	0
红海亚喀巴湾	RS9916	GCA_000153825.1	近岸	2664873	59.8	99.73	0
红海亚喀巴湾	RS9917	GCA_000153065.1	近岸	2584918	64.5	99.46	0
波多黎马格耶斯岛	PCC7002	GCA_000019485	近岸	3409935	49.2	100	0
西太平洋	KORDI-100	GCA_000737535.1	大洋	2789000	57.5	99.46	0
新英格兰大陆架	WH8020	GCA_001040845.1	近岸	2661166	53.1	99.73	0.27
伍兹霍尔沿海海水	WH8101	GCA_004209775.1	近岸	2630292	63.3	100	0.82
北大西洋潮间带	WH8016	GCA_000230675.2	近岸	2694843	54.1	99.18	0
北大西洋	WH7805	GCA_000153285.1	大洋	2627046	57.6	99.73	0
北大西洋长岛海峡	WH5701	GCA_000153045	近岸	3280236	65.4	99.18	7.84
东太平洋	CC9616	GCA_000515235.1	大洋	2645910	56.6	99.46	0.27

Tab. 2

Fig. 4

Fig. 5

Fig. 6

Tab. 3

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基因分类		基因	基因描述	KEGG 编号
铁吸收	铁载体相关基因	TonB sidero	TonB dependent receptor	K02014
	孔蛋白基因	Porin	Outer membrane protein insertion porin family	K07277
	Fe³⁺转运基因	idiA/FutA	Iron deﬁciency induced protein A / iron(Ⅲ) transport system substrate-binding protein	K02012
		idiB/FutB	ABC-type Fe³⁺transport system permease component / iron(Ⅲ) transport system permease protein	K02011
		idiC/FutC	ATP binding component / iron(Ⅲ) transport system ATP-binding protein	K02010
	二价金属转运基因	NRAMP	Natural resistance associated macrophage protein, Nramp	K03322
		FTR1	FTR1 family iron permease	K07243
		ZIP	ZRT / IRT-like Protein	K14709
	Fe²⁺转运基因	FeoA	Ferrous iron transport protein A	K04758
	Fe²⁺转运基因	FeoB	Ferrous iron transport protein B	K04759
铁稳态	—	Fur	Ferric uptake regulator	K03711
		FecR	Periplasmic ferric-dicitrate binding protein FerR	K07165
		CRP	Cyclic AMP receptor protein	K10914
铁储存	铁储存蛋白	Dps	DNA-binding stress protein	K04047
		Bfr	Bacterioferritin	K03594
		Ftn	Ferritins	K02217

	相关基因/蛋白	海洋聚球藻
	相关基因/蛋白	近岸株	大洋株
铁吸收	铁载体	合成和利用铁载体的能力较强	合成和利用铁载体的能力较弱
	孔蛋白	存在	存在
	Fe(Ⅲ)转运蛋白	存在, 基因表达量相对较低	存在, 基因表达量相对较高
	Fe(Ⅱ)特异性转运蛋白	普遍存在	除生态型CRD1中不存在
铁稳态	Fur家族(FurA、Zur、PerR)	存在, 具有更复杂的调节能力	存在
	FecR	存在	仅在生态型CRD1中广泛分布
	CRP	存在	存在
铁储存	Ftn	拷贝数较多	仅在生态型CRD1中拥有多拷贝数
	Bfr	存在	不存在
	Dps	存在	存在

Adaptive mechanisms of iron limitation on the marine Synechococcus based on comparative genomics

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