Scientists have isolated* a number of previously undescribed bacteriophages from various sources. These phages are unusually large in size and have a large genome encoding variants of the bacterial immune system CRISPR-Cas. The authors suggest that phages use CRISPR-Cas to combat competing phages.

As is known, scientists can cultivate a relatively limited number of bacterial species in the laboratory. Consequently, phages specific to these bacteria are primarily available for research. Furthermore, when studying natural phages, they are typically separated from bacteria and eukaryotic cells using filters with pores of 100-200 nm in diameter, although larger phages are known to exist. To expand beyond these limitations, microbiologists from the University of California, Berkeley, USA, collected DNA samples from various sources: bodies of water, soil, bottom sediments, hot springs, and human and animal feces. After DNA analysis, all fragments that were definitely not from archaea, bacteria, eukaryotes, or eukaryotic viruses were classified as phage DNA. From this DNA, 35 complete phage genomes and several dozen more partial ones were assembled. Four of the 35 complete genomes were longer than 630 kbp, 34 kbp longer than the largest known phage genome.

Interestingly, the DNA of giant phages contained genes encoding transcription and translation factors, transfer RNA, and ribosomal proteins. Phages are known to be unable to synthesize these molecules themselves, and therefore rely on them in the bacterial host cell. Why giant phages acquired their own protein biosynthesis components remains unclear. Perhaps this helps them more efficiently reorganize the bacterial protein-synthesizing system for their own needs.

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An equally unusual discovery for phages is the presence of components of the CRISPR-Cas system, which bacteria use to defend themselves against phages. Phage CRISPR-Cas differs from bacterial CRISPR-Cas. Scientists believe that phages use this system to destroy competing phages attempting to infect the same bacteria.

The work of the Berkeley scientists not only opens new horizons in the study of phage diversity and ecology, but also has practical applications – the new variant of CRISPR-Cas could be useful as a genome editing tool.

* Al-Shayeb, B., Sachdeva, R., Chen, L. et al. Treasures of huge phages from across Earth's ecosystems. Nature, 2020, Published 12 February 2020. https://doi.org/10.1038/s41586-020-2007-4