Prophage SOS-dependency Predictor (PSOSP)

A novel bioinformatics tool to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding to target DNA.

Abstract

Prophages are ubiquitously present in bacterial genomes, significantly influencing their physiological and ecological functions. This study developed a novel bioinformatics tool, the Prophage SOS-dependency Predictor (PSOSP), to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding to target DNA, classifying prophages into SOS-dependent (SdPs) and SOS-independent (SiPs).

PSOSP was experimentally validated to accurately distinguish SdPs from SiPs. We found that SiPs are broadly dispersed in bacterial genomes, particularly prevalent in Gammaproteobacteria, and exhibit distinct genomic features compared to SdPs, including smaller genomes, higher GC content, and greater protein-coding density. This study systematically reveals the widespread distribution of SOS-independent prophages and their unique genomic and host characteristics, providing novel insights into the lysogenic-lytic switch of temperate phages.

The Principle of PSOSP

Temperate phages integrate into the bacterial host genome as prophages. Under normal conditions, the LexA protein binds to the SOS box within the prophage, repressing the expression of phage-related genes and maintaining the lysogenic state. Upon external stimuli (such as exposure to DNA-damaging agents), the RecA protein is activated, leading the self-cleavage of LexA and its dissociation from the SOS box. This relieves the prophage repression, triggering the temperate phage to enter the lytic cycle and thereby facilitating its proliferation.

PSOSP Theory Diagram

PSOSP Workflow

The PSOSP workflow consists of four main steps, leading to a detailed output:

  • LexA & Canonical SOS Box (CBS) Identification : Scanning the host genome to identify LexA protein and canonical SOS boxes (CSBs) located upstream of the lexA gene.
  • Heterology Index (HI) Calculation: Identifying potential SOS boxes (PSBs) across bacterial genomes, calculating the Heterology Index (HI) for each PSB and establishing classification thresholds (HIc1 and HIc2) via Mean Shift clustering results.
  • PSB scan in prophage: Scanning PSBs within prophage promoter regions and determining of the minimum HI (HImin).
  • Prophage categoriation : Evaluating the ability of LexA binding to prophage promoter regions by comparing HImin with thresholds
    • HImin ≤ HIc1 → SdP (SOS-dependent Prophage)
    • HImin ≥ HIc2 → SiP (SOS-independent Prophage)
    • HIc1 < HImin < HIc2 → SuP (SOS-uncertain Prophage)
PSOSP Workflow Diagram

All Experimentally Validated Prophages

Distribution of HI values for all experimentally validated prophages:

  • SW1 in Shewanella piezotolerans WP3
  • SP1,SP2,SP3 in Shewanella psychrophila WP2
  • P22, Fels1 and Fels2 in Salmonella typhimurium LT2
  • ФЕСО1 in Escherichia coli HS
  • ST2-8624 in Escherichia coli O157:H7
  • VALG_phi6 in Vibrio alginolyticus K01M1
  • B3 in Pseudomonas aeruginosa PAO1
  • vB_SspM_BZS1, vB_SspS_OS31 in Serratia sp.OS31
  • yong1 in Hafnia paralvei LY-23
Experimental Validation Results

References

  • M. Zünd et al., High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains. Microbiome 9, 77 (2021).
  • H. Nilsson, C. Cardoso-Palacios, E. Haggård-Ljungquist, A. S. Nilsson, Phylogenetic structure and evolution of regulatory genes and integrases of P2-like phages. Bacteriophage 1, 207-218 (2011).
  • J. M. Łoś, M. Łoś, A. Węgrzyn, G. Węgrzyn, Hydrogen peroxide-mediated induction of the Shiga toxin-converting lambdoid prophage ST2-8624 in Escherichia coli O157:H7. FEMS Immunol. Med. Microbiol. 58, 322-329 (2010).
  • C. M. Chibani, R. Hertel, M. Hoppert, H. Liesegang, C. Charlotte Wendling, Closely Related Vibrio alginolyticus Strains Encode an Identical Repertoire of Caudovirales-Like Regions and Filamentous Phages. Viruses 12, 1359 (2020).
  • M. D. Braid, J. L. Silhavy, C. L. Kitts, R. J. Cano, M. M. Howe, Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa. J. Bacteriol. 186, 6560-6574 (2004).
  • Bujak, K., Decewicz, P., Kaminski, J. and Radlinska, M. Identification, characterization, and genomic analysis of novel Serratia temperate phages from a gold mine. International Journal of Molecular Sciences, 21(18), p.6709 (2020).
  • Pan, L., Li, D., Tong, Y., Lin, W., Qin, W., Xu, L., & Zhan, P. Induction and genomic analysis of a lysogenic phage of Hafnia paralvei. Current Microbiology, 79(2), 50 (2022).