Physiol. Genomics AJP: Regulatory, Integrative and Comparative Physiology
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Physiol. Genomics 24: 181-190, 2006. First published December 20, 2005; doi:10.1152/physiolgenomics.00255.2005
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Received 17 October 2005; accepted in final form 13 December 2005.
Physiological Genomics 24:181-190 (2006)
American Physiological Society © 2006 American Physiological Society

Call For Papers: Comparative Genomics

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

Fangqing Zhao 1, Xiaowen Zhang 1, Chengwei Liang 1, Jinyu Wu 2, Qiyu Bao 2 and Song Qin 1

1 Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
2 Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou, China

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.

coevolution; comparative genomics; horizontal gene transfer; molecular evolution; Spirulina platensis






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