Influence of Staphylococcus aureus Strain Background on Sa3int Phage Life Cycle Switches

Abstract

Staphylococcus aureus asymptomatically colonizes the nasal cavity of mammals, but it is also a leading cause of life-threatening infections. Most human nasal isolates carry Sa3 phages, which integrate into the bacterial hlb gene encoding a sphingomyelinase. The virulence factor-encoding genes carried by the Sa3-phages are highly human-specific, and most animal strains are Sa3 negative. Thus, both insertion and excision of the prophage could potentially confer a fitness advantage to S. aureus. Here, we analyzed the phage life cycle of two Sa3 phages, Φ13 and ΦN315, in different phage-cured S. aureus strains. Based on phage transfer experiments, strains could be classified into low (8325-4, SH1000, and USA300c) and high (MW2c and Newman-c) transfer strains. High-transfer strains promoted the replication of phages, whereas phage adsorption, integration, excision, or recA transcription was not significantly different between strains. RNASeq analyses of replication-deficient lysogens revealed no strain-specific differences in the CI/Mor regulatory switch. However, lytic genes were significantly upregulated in the high transfer strain MW2c Φ13 compared to strain 8325-4 Φ13. By transcriptional start site prediction, new promoter regions within the lytic modules were identified, which are likely targeted by specific host factors. Such host-phage interaction probably accounts for the strain-specific differences in phage replication and transfer frequency. Thus, the genetic makeup of the host strains may determine the rate of phage mobilization, a feature that might impact the speed at which certain strains can achieve host adaptation.

(p)ppGpp-mediated GTP homeostasis ensures the survival and antibiotic tolerance ofStaphylococcus aureusduring starvation by preserving the proton motive force

“…Expression of rRNA is controlled by the concentration of the transcription-initiating nucleotide (iNTP) within the promoter 11 . Analysis of potential transcriptional start sites upstream of qoxABCD predict an ATP as the transcription-initiating nucleotide (based on data from 32 )(Fig. 7).…”

CI:Mor interactions in the lysogeny switches of Lactococcus lactis TP901-1 and Staphylococcus aureus φ13 bacteriophages

“…Recent work has shown that in addition to the interplay between CI, Mor, and RecA, host-specific factors and additional phage regulatory genes are also involved in determining the mobility of φ13 and other S. aureus phages [ 37 ] . This opens new possibilities for discovering important regulatory mechanisms beyond the CI:Mor switch.…”

“…AlphaFold2 (AF2) models for individual φ13 proteins were either from the Alphafold database (Q2FWP6 and Q2FWP7, model version 4) [35] or constructed using the Colab version of Alphafold2 [36] using default parameters. TP901-1 CI-NTD was modeled using the full-length TP901-1 CI wild-type sequence with no templates.…”

Noncontiguous operon atlas for the Staphylococcus aureus genome

“…Importantly, NcOs identification may allow to uncover functional relationships between neighbouring genes that would otherwise go unnoticed. After the first description of the NcO architecture in Staphylococcus aureus (Sáenz-Lahoya et al 2019 ), gene arrangements consistent with an NcO structure have been detected in Bacillus subtilis (Johnson et al 2020 ), the phytopathogenic bacterium Dickeya dadantii (Forquet et al 2022 ), a temperate phage of the Siphoviridae family from S. aureus (Rohmer et al 2022 ) and large DNA viruses such as varicella, Epstein–barr, and Baculovirus (Prazsák et al 2018 , Fülöp et al 2022 , Torma et al 2022 ). Altogether, these examples support the idea that NcOs are not exclusive to bacteria and are also present in the genomes of phages and viruses.…”