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Genomic Analysis of Freshwater Cyanophage Pf-WMP3 Infecting Cyanobacterium Phormidium foveolarum: The Conserved Elements for a Phage

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Abstract

Cyanophages are ecologically abundant, genetically diverse in aquatic environments, and affect the population and evolutionary trajectories of their hosts. After reporting the cyanophage Pf-WMP4 genome (Liu et al. in Virology 366:28–39, 2007), we hereby present a related cyanophage, Pf-WMP3, which also infects the freshwater cyanobacterium Phormidium foveolarum. The Pf-WMP3 genome contains 43,249 bp with 234 bp direct terminal repeats. The overall genome organization and core genes of the two phages are comparable to those of the T7 supergroup phages. Compared with Pf-WMP4, cyanophage Pf-WMP3 has diverged extensively at the DNA level; however, they are closely related at the protein level and genome architecture. The left arm genes for the two phages, which mainly encode the DNA replication machinery, are not conserved in the gene order. Whereas the right arm genes of the two phages coding for structural proteins show high similarity in amino acid sequences and modular architecture, indicating that they have retained similar development strategies. The differences in similarity levels between the left and right arm genes suggest that the structural genes are the most conserved elements for a phage.

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Acknowledgments

Our research was supported by the State 863 High Technology R&D Program (grant nos. 2006AA06Z341 and 2004AA214072) and the Beijing Natural Science Foundation (grant no. 5062020).

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Authors and Affiliations

  1. National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, 100871, People’s Republic of China

    Xinyao Liu, Shuanglei Kong, Miao Shi, Liwen Fu, Yin Gao & Chengcai An

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  1. Xinyao Liu
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Correspondence to Chengcai An.

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Table S1

Host-like promoter elements of phages in the T7 supergroup (DOC 75 kb)

Figure S1

Secondary structure prediction of structural proteins of T7 vs Pf-WMP4/3. Helix and beta strands were predicted using the PSIPRED protein secondary structure server [37]. Related proteins of T7 and Pf-WMP4/3 share considerable similarity (JPEG 345 kb)

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Liu, X., Kong, S., Shi, M. et al. Genomic Analysis of Freshwater Cyanophage Pf-WMP3 Infecting Cyanobacterium Phormidium foveolarum: The Conserved Elements for a Phage. Microb Ecol 56, 671–680 (2008). https://doi.org/10.1007/s00248-008-9386-7

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