Comparative genomics of the DNA damage‐inducible network in the Patescibacteria

Abstract

Metagenomics provide unprecedented insights into the genetic diversity of uncultivated bacteria inhabiting natural environments. Recent surveys have uncovered a major radiation of candidate phyla encompassing the Patescibacteria superphylum. Patescibacteria have small genomes and a presumed symbiotic or parasitic lifestyle, but the difficulty in culturing representative members constrains the characterization of behavioural and adaptive traits. Here we combine in silico and in vitro approaches to characterize the SOS transcriptional response to DNA damage in the Patescibacteria superphylum. Leveraging comparative genomics methods, we identify and experimentally define a novel binding motif for the SOS transcriptional repressor LexA, and we use this motif to characterize the conserved elements of the SOS regulatory network in Patescibacteria. The Patescibacteria LexA-binding motif has unusual direct-repeat structure, and comparative analyses reveal sequence and structural similarities with the distant Acidobacteria LexA protein. Our results reveal a shared core SOS network, complemented by varying degrees of LexA regulation of other core SOS functions. This work illustrates how the combination of computational and experimental methods can leverage metagenomic data to characterize transcriptional responses in uncultivated bacteria. The report of an operational SOS response in presumed symbiotic and parasitic bacteria hints at an intermediate step in the process of genome reduction.

Genomic signatures and co‐occurrence patterns of the ultra‐small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle

“…Last, the literature also provides an indication that several CPR/ Patescibacteria representatives might have symbiotic lifestyles (Anantharaman et al, 2016;Nelson & Stegen, 2015;Sánchez-Osuna, Barbé, & Erill, 2017). For example, He et al (2015) cultivated the first Saccharimonadia, TM7x, and suggested that this organism lives in an obligate symbiotic association with Actinomyces odontolyticus in the human oral cavity.…”

Diversity of Pelagic and Benthic Bacterial Assemblages in the Western Pacific Ocean

“…Patescibacteria are part of the Candidate Phyla Radiation with ultra-small genomes and have a presumed symbiotic or parasitic lifestyle ( Sánchez-Osuna et al, 2017 ; Lemos et al, 2019 ). Members of Patecibacteria were found to be enriched in the disease lesions of coral species from Thailand ( Roder et al, 2014 ) and the Florida Reef Tract ( Meyer et al, 2019 ).…”

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

“…In our study, the four strongest increasing phyla, i.e., Verrucomicrobia, Actinobacteria, Cyanobacteria, and Bacteroidetes, are all considered typical freshwater bacteria ( Newton et al, 2011 ) and have also been found previously in freshwater by Iliev et al (2017) and Kim et al (2018) and others. Patescibacteria were first reported in groundwater and sediments of anoxic environments ( Elshahed et al, 2005 ; Youssef et al, 2011 ; Wrighton et al, 2012 ), but showed to be widespread in most semiaquatic habitats ( Sánchez-Osuna et al, 2017 ). Rokubacteria, also found in groundwater samples, are most closely related to the phylum Nitrospira.…”