RT Journal Article
SR Electronic
T1 Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.11.22.517103
DO 10.1101/2022.11.22.517103
A1 Jett Liu
A1 Alexander L. Jaffe
A1 LinXing Chen
A1 Batbileg Bor
A1 Jillian F. Banfield
YR 2022
UL http://biorxiv.org/content/early/2022/11/23/2022.11.22.517103.abstract
AB Within human microbiomes, Gracilibacteria, Absconditabacteria, and Saccharibacteria, members of Candidate Phyla Radiation (CPR), are increasingly correlated with human oral health and disease. We profiled the diversity of CRISPR-Cas systems in the genomes of these bacteria and sought phages that are capable of infecting them by comparing their spacer inventories to large phage sequence databases. Gracilibacteria and Absconditabacteria recode the typical TGA stop codon to glycine and are infected by phages that share their host’s alternate genetic code. Unexpectedly, however, other predicted phages of Gracilibacteria and Absconditabacteria do not use an alternative genetic code. Some of these phages are predicted to infect both alternatively coded CPR bacteria and standard coded bacteria. These phages rely on other stop codons besides TGA, and thus should be capable of producing viable gene products in either bacterial host type. Interestingly, we predict that phages of Saccharibacteria can replicate in Actinobacteria, which have been shown to act as episymbiotic hosts for Saccharibacteria. Overall, the broad host range of some CPR phages may be advantageous for the production of these phages for microscopic characterization or use as therapy agents, given the current difficulty of CPR cultivation. Absconditabacteria phages and Gracilibacteria phages may have avoided acquisition of in-frame stop codons to increase the diversity of bacteria in which they can replicate.Competing Interest StatementJFB is a co-founder of Metagenomi.