Abstract
Cyanophage genomes frequently possess the psbA gene, encoding the D1 polypeptide of photosystem II. This protein is believed to maintain host photosynthetic capacity during infection and enhance phage fitness under high-light conditions. Although the first documented cyanophage-encoded psbA gene contained a group I intron, this feature has not been widely reported since, despite a plethora of new sequences becoming available. In this study, we show that in cyanophage S-PM2, this intron is spliced during the entire infection cycle. Furthermore, we report the widespread occurrence of psbA introns in marine metagenomic libraries, and with psbA often adjacent to a homing endonuclease (HE). Bioinformatic analysis of the intergenic region between psbA and the adjacent HE gene F-CphI in S-PM2 showed the presence of an antisense RNA (asRNA) connecting these two separate genetic elements. The asRNA is co-regulated with psbA and F-CphI, suggesting its involvement with their expression. Analysis of scaffolds from global ocean survey datasets shows this asRNA to be commonly associated with the 3′ end of cyanophage psbA genes, implying that this potential mechanism of regulating marine ‘viral’ photosynthesis is evolutionarily conserved. Although antisense transcription is commonly found in eukaryotic and increasingly also in prokaryotic organisms, there has been no indication for asRNAs in lytic phages so far. We propose that this asRNA also provides a means of preventing the formation of mobile group I introns within cyanophage psbA genes.
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Acknowledgements
We acknowledge Michael Zuker and Nicholas Markham for UNAFOLD. DJE was supported by grants from the Medical Research Council and the Wellcome Trust; WRH was supported by the DFG Focus program ‘Sensory and regulatory RNAs in Prokaryotes’ SPP1258 (project HE 2544/4–2) and the BMBF—Freiburg Initiative in Systems Biology—Grant no. 0313921; ADM was funded by Leverhulme Trust grant F/00215/AL to DJS.
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Millard, A., Gierga, G., Clokie, M. et al. An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease. ISME J 4, 1121–1135 (2010). https://doi.org/10.1038/ismej.2010.43
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DOI: https://doi.org/10.1038/ismej.2010.43
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