bioRxiv2025
The Candidate Phyla Radiation, also known as Patescibacteria, represents a vast and diverse division of bacteria that has come to light via culture-independent "omics" technologies. Their limited biosynthetic capacity, along with evidence of their growth as obligate epibionts on other bacteria, suggests a broad reliance on host organisms for their survival. Nevertheless, our understanding of the molecular mechanisms governing their metabolism and lifestyle remains limited. The Type IV Secretion System (T4SS) represents a superfamily of translocation systems with a wide range of functional roles. T4SS genes have been identified in the CPR group Saccharibacteria as essential for their epibiotic growth. In this study, we used a comprehensive bioinformatics approach to investigate the diversity and distribution of T4SS within the Patescibacteria lineage. The phylogenetic analysis of the T4SS signature protein VirB4 suggests that most of these proteins cluster into a distinct monophyletic group with a shared ancestry to the MPFFATA class of T4SS. This class is found in the conjugative elements of Firmicutes, Actinobacteria, Tenericutes, and Archaea, indicating a possible horizontal gene transfer from these monoderm microorganisms to CPR bacteria. We identified additional T4SS components near virB4, particularly those associated with the MPFFATA class, as well as homologs of other T4SS classes, such as VirB2-like pilins, and observed their varied arrangements across different CPR phyla. The absence of a relaxase in most of these T4SS clusters suggests that the system has been co-opted for other functions in CPR bacteria. The proximity of T4SS components to the origin of replication (gene dnaA) in some CPR suggests a potential mechanism for increased expression. The broad ubiquity of a phylogenetically distinct T4SS in CPR, combined with its chromosomal location, underscores the significance of T4SS in the biology of Patescibacteria. Impact statementThe Candidate Phyla Radiation (CPR), or Patescibacteria, represents a highly diverse bacterial group that constitutes a significant fraction of the microbial dark matter. Known for their minimal biosynthetic capabilities and dependence on host bacteria, CPR bacteria exemplify fascinating yet poorly understood lifestyles. Our research sheds light on the molecular strategies underlying their survival by focusing on the Type IV Secretion System (T4SS), a versatile bacterial machinery typically involved in DNA transfer and effector molecule delivery. We revealed that T4SS is not only widespread in CPR but also forms a distinct evolutionary lineage, likely acquired via horizontal gene transfer from Gram-positive bacteria, and we illustrated its gene organization across different CPR phyla. Unlike canonical systems, CPR T4SS lacks key components for conjugation, hinting at a novel functional adaptation. Remarkably, T4SS genes in CPR are often located near the replication origin, suggesting a regulatory role linked to their expression. This research suggests the repurposing of T4SS in CPR to thrive under extreme reliance on other organisms. By unraveling the genomic and evolutionary peculiarities of T4SS in CPR, our work provides valuable insights into their unique biology, broadens our understanding of microbial diversity and innovation, and highlights this system as a strong candidate to sustain their parasitic episymbiotic lifestyle. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.