Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

doi:10.1152/physiolgenomics.00255.2005

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	Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria
	Zhao, FQ ; Zhang, XW ; Liang, CW ; Wu, JY ; Bao, QY ; Qin, S ; Qin, S, Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China
	2006-02-23
发表期刊	PHYSIOLOGICAL GENOMICS
ISSN	1094-8341
卷号	24 期号:3 页码:181-190
文章类型	Article
摘要	Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.; Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.
关键词	Coevolution Comparative Genomics Horizontal Gene Transfer Molecular Evolution Spirulina Platensis
学科领域	Cell Biology ; Genetics & Heredity ; Physiology
DOI	10.1152/physiolgenomics.00255.2005
URL	查看原文
收录类别	SCI
语种	英语
WOS记录号	WOS:000236722600001
引用统计	被引频次：34[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/1749
专题	实验海洋生物学重点实验室
通讯作者	Qin, S, Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China
作者单位	1.Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China 2.Wenzhou Med Coll, Inst Biomed Informat, Wenzhou, Peoples R China
推荐引用方式 GB/T 7714	Zhao, FQ,Zhang, XW,Liang, CW,et al. Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria[J]. PHYSIOLOGICAL GENOMICS,2006,24(3):181-190.
APA	Zhao, FQ.,Zhang, XW.,Liang, CW.,Wu, JY.,Bao, QY.,...&Qin, S, Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China.(2006).Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria.PHYSIOLOGICAL GENOMICS,24(3),181-190.
MLA	Zhao, FQ,et al."Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria".PHYSIOLOGICAL GENOMICS 24.3(2006):181-190.

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