Characterization of Pseudomonas aeruginosa phage K5 genome and identification of its receptor related genes

Quorum sensing gene lasR promotes phage vB_Pae_PLY infection in Pseudomonas aeruginosa

BACKGROUND

Quorum sensing (QS) is a cell density-based intercellular communication system that controls virulence gene expression and biofilm formation. In Pseudomonas aeruginosa (P. aeruginosa), the LasR system sits at the top of the QS hierarchy and coordinates the expression of a series of important traits. However, the role of lasR in phage infection remains unclear. This study aims to investigate the role of lasR QS in phage infection.

METHODS

The P. aeruginosa phage was isolated from sewage, and its biological characteristics and whole genome were analyzed. The adsorption receptor was identified via a phage adsorption assay. Following lasR gene knockout, the adsorption rate and bactericidal activity of phage were analyzed. Finally, real-time quantitative polymerase chain reaction (RT-qPCR) was conducted to explore how lasR promoting phage infection.

RESULTS

The lytic phage vB_Pae_PLY was isolated and lipopolysaccharide (LPS) was identified as its adsorption receptor. The adsorption rate and bactericidal activity of vB_Pae_PLY were reduced after lasR knockout. RT-qPCR results showed that the expression of galU, a key gene involved in LPS synthesis, was down-regulated, and several genes related to type IV pili (T4P) were also down-regulated in the lasR mutant PaΔlasR.

CONCLUSIONS

The study showed that QS lasR may promote phage vB_Pae_PLY infection by involving in the synthesis of LPS and T4P. This study provides an example of QS in promoting phage infection and deepens the understanding of phage-bacteria interactions.

Phage resistance of Salmonella enterica obtained by transposon Tn5-mediated SefR gene silent mutation

Salmonella enterica contamination is a primary cause of global food poisoning. Using phages as bactericidal alternatives to antibiotics could confront the issue of drug resistance. However, the problem of phage resistance, especially mutant strains with multiple phage resistance, is a critical barrier to the practical application of phages. In this study, a library of EZ-Tn5 transposable mutants of susceptible host S. enterica B3-6 was constructed. After the infestation pressure of a broad-spectrum phage TP1, a mutant strain with resistance to eight phages was obtained. Analysis of the genome resequencing results revealed that the SefR gene was disrupted in the mutant strain. The mutant strain displayed a reduced adsorption rate of 42% and a significant decrease in swimming and swarming motility, as well as a significantly reduced expression of the flagellar-related FliL and FliO genes to 17% and 36%, respectively. An uninterrupted form of the SefR gene was cloned into vector pET-21a (+) and used for complementation of the mutant strain. The complemented mutant exhibited similar adsorption and motility as the wild-type control. These results suggest that the disrupted flagellar-mediated SefR gene causes an adsorption inhibition, which is responsible for the phage-resistant phenotype of the S. enterica transposition mutant.

A Novel XRE-Type Regulator Mediates Phage Lytic Development and Multiple Host Metabolic Processes in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, the leading cause of acute and chronic infections in immunocompromised patients, frequently with high morbidity and mortality rates. The xenobiotic response element (XRE) family proteins are the second most common transcriptional regulators (TRs) in P. aeruginosa. However, only a few XRE-like TRs have been reported to regulate multiple bacterial cellular processes, encompassing virulence, metabolism, antibiotic synthesis or resistance, stress responses, and phage infection, etc. Our understanding of what roles these XRE-like small regulatory proteins play in P. aeruginosa remains limited. Here, we aimed to decipher the role of a putative XRE-type transcriptional regulator (designated LfsT) from a prophage region on the chromosome of a clinical P. aeruginosa isolate, P8W. Southern blot and reverse transcription quantitative PCR (RT-qPCR) assays demonstrated that LfsT controlled host sensitivity to the phage PP9W2 and was essential for efficient phage replication. In addition, electrophoretic mobility shift assays (EMSAs) and transcriptional lacZ fusion analyses indicated that LfsT repressed the lysogenic development and promoted the lytic cycle of phage PP9W2 by binding to the promoter regions of the gp71 gene (encoding a CI-like repressor) and several vital phage genes. Combined with RNA-seq and a series of phenotypic validation tests, our results showed that LfsT bound to the flexible palindromic sites within the promoters upstream of several genes in the bacterial genome, regulating fatty acid (FA) metabolism, spermidine (SPD) transport, as well as the type III secretion system (T3SS). Overall, this study reveals novel regulatory roles of LfsT in P. aeruginosa, improving our understanding of the molecular mechanisms behind bacterium-phage interactions. IMPORTANCE This work elucidates the novel roles of a putative XRE family TR, LfsT, in the intricate regulatory systems of P. aeruginosa. We found that LfsT bound directly to the core promoter regions upstream of the start codons of numerous genes involved in various processes, including phage infection, FA metabolism, SPD transport, and the T3SS, regulating as the repressor or activator. The identified partial palindromic motif NAACN(5,8)GTTN recognized by LfsT suggests extensive effects of LfsT on gene expression by maintaining preferential binding to nucleotide sites under evolutionary pressure. In summary, these findings indicate that LfsT enhances metabolic activity in P. aeruginosa, while it reduces host resistance to the phage. This study helps us better understand the coevolution of bacteria and phages (e.g., survival comes at a cost) and provides clues for designing novel antimicrobials against P. aeruginosa infections.

The Role of Pseudomonas aeruginosa Lipopolysaccharide in Bacterial Pathogenesis and Physiology

The major constituent of the outer membrane of Gram-negative bacteria is lipopolysaccharide (LPS), which is comprised of lipid A, core oligosaccharide, and O antigen, which is a long polysaccharide chain extending into the extracellular environment. Due to the localization of LPS, it is a key molecule on the bacterial cell wall that is recognized by the host to deploy an immune defence in order to neutralize invading pathogens. However, LPS also promotes bacterial survival in a host environment by protecting the bacteria from these threats. This review explores the relationship between the different LPS glycoforms of the opportunistic pathogen Pseudomonas aeruginosa and the ability of this organism to cause persistent infections, especially in the genetic disease cystic fibrosis. We also discuss the role of LPS in facilitating biofilm formation, antibiotic resistance, and how LPS may be targeted by new antimicrobial therapies.

Identification of Brevibacterium flavum genes related to receptors involved in bacteriophage BFK20 adsorption

Phage infection of bacterial cells is a process requiring the interaction between phage receptor binding proteins and receptors on the bacterial cell surface. We prepared a Brevibacterium flavum CCM 251 EZ-Tn5 transposon insertional library and isolated phage-resistant mutants. Analysis of the DNA fragments produced by single-primer PCR was used to determine the EZ-Tn5 transposon insertion sites in the genomes of phage-resistant B. flavum mutants. Seven disrupted genes were identified in forty B. flavum mutants. The phage resistance of these mutants was demonstrated by cultivation analysis in the presence of BFK20, and the adsorption rate of BFK20 to these mutants was tested. B. flavum mutants displayed significantly reduced adsorption rates; the lowest rate was observed for mutants containing interrupted major facilitator superfamily (MFS) protein and glycosyltransferase genes. Uninterrupted forms of these genes were cloned into corynebacterial vector pJUP06 and used for in trans complementation of the corresponding B. flavum mutants. The growth of these complemented mutants when infected with BFK20 closely resembled that of wild-type B. flavum. These complemented mutants also exhibited similar BFK20 adsorption as the wild-type control. We infer that the disrupted MFS protein and glycosyltransferase genes are responsible for the phage-resistant phenotype of these B. flavum transposition mutants.

A putative LysR-type transcriptional regulator inhibits biofilm synthesis in Pseudomonas aeruginosa

Biofilm formation is an important virulence factor which is controlled by complex regulatory circuits in Pseudomonas aeruginosa. In this work, a biofilm hyper-producing strain, P2-7, was selected from a collection of transposon insertion mutants in which the PA2121 gene was disrupted. PA2121 was predicted as a putative LysR-type regulator. Analyses showed that it was involved in early biofilm formation, mature biofilm development, and colony morphology. Quantitative measurements revealed that PA2121 repressed biosynthesis of extracellular polysaccharides (alginate, psl and pel). Furthermore, it was observed that PA2121 was self-regulated, highly expressed in the early phase of biofilm development, and subject to the negative regulation by a biofilm synthesis regulator SrpA that binds directly to the PA2121 gene promoter. Collectively, this study proposes that PA2121 is a novel biofilm synthesis repressor (BsrA) in P. aeruginosa.

vB_EcoS_IME347 a novel T1-like Escherichia coli bacteriophage

Advances in phage therapy and its application require more information on phage genome characteristics and host-phage interaction mechanisms. In this study, a so far unknown T1-like Escherichia coli phage was identified and named vB_EcoS_IME347 (IME347). The genome length of phage IME347 is 50,048 bp with a G + C content of 49.7%. BLASTn alignment showed that the phage has its highest homology (identity 78%, query cover 72%) with phage SRT8 (GenBank: MF996376). Electron microscopy showed that phage IME347 has an icosahedral head and a long non-contractiled tail, features of the family Siphoviridae. Phylogenetic analysis of the large subunit of the terminal enzyme and tail fiber protein revealed that phage IME347 is a novel member of the T1 virus. Furthermore, through comparative genomics, silencing mutation, phage spotting assay, and phage adsorption assay, an E. coli BL21 TonB-dependent receptor YncD was identified to be responsible for phage IME347 adsorption and entry. The identification of the phage receptor YncD enriches the phage receptor database and provides a theoretical basis for bacteriophage therapy.

Adaptation of Pseudomonas aeruginosa to Phage PaP1 Predation via O-Antigen Polymerase Mutation

Adaptation of bacteria to phage predation poses a major obstacle for phage therapy. Bacteria adopt multiple mechanisms, such as inhibition of phage adsorption and CRISPR/Cas systems, to resist phage infection. Here, a phage-resistant mutant of Pseudomonas aeruginosa strain PA1 under the infection of lytic phage PaP1 was selected for further study. The PaP1-resistant variant, termed PA1RG, showed decreased adsorption to PaP1 and was devoid of long chain O-antigen on its cell envelope. Whole genome sequencing and comparative analysis revealed a single nucleotide mutation in the gene PA1S_08510, which encodes the O-antigen polymerase Wzy that is involved in lipopolysaccharide (LPS) biosynthesis. PA1_Wzy was classified into the O6 serotype based on sequence homology analysis and adopts a transmembrane topology similar to that seem with P. aeruginosa strain PAO1. Complementation of gene wzy in trans enabled the mutant PA1RG to produce the normal LPS pattern with long chain O-antigen and restored the susceptibility of PA1RG to phage PaP1 infection. While wzy mutation did not affect bacterial growth, mutant PA1RG exhibited decreased biofilm production, suggesting a fitness cost of PA1 associated with resistance of phage PaP1 predation. This study uncovered the mechanism responsible for PA1RG resistance to phage PaP1 via wzy mutation and revealed the role of phages in regulating bacterial behavior.

Characterization of a novel lytic podovirus O4 of Pseudomonas aeruginosa

Phage O4 of Pseudomonas aeruginosa was previously visualized as a short-tailed virus using a transmission electron microscope. In this work, the O4 genome was characterized to be a linear dsDNA molecule comprising 50509 bp with 76 predicted genes located in five clusters. Mass spectrometry showed that the O4 virion contains 6 putative structural proteins, 2 putative enzymes, and 7 hypothetical proteins. By analyzing a Tn5G transposon mutation library, eight genes, wbpR, wbpV, wbpO, wbpT, wbpS, wbpL,  galU, and wzy, were identified and confirmed responsible for the phage-resistant phenotype; all of them are related to the synthesis of O-specific antigen (OSA) of lipopolysaccharide (LPS), indicating that OSA is the receptor for the adsorption of phage O4. Comparative genomic analysis revealed that the phage O4 genome shares little similarity to any known podovirus, indicating that phage O4 is classifiable as a novel member of the Podoviridae family.

Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa

Our understanding of the molecular mechanisms behind bacteria-phage interactions remains limited. Here we report that a small protein, SrpA, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa. We show that SrpA is essential for efficient genome replication of phage K5, and controls transcription by binding to a palindromic sequence upstream of the phage RNA polymerase gene. We identify potential SrpA-binding sites in 66 promoter regions across the P. aeruginosa genome, and experimentally validate direct binding of SrpA to some of these sites. Using transcriptomics and further experiments, we show that SrpA, directly or indirectly, regulates many cellular processes including cell motility, chemotaxis, biofilm formation, pyocyanin synthesis and protein secretion, as well as virulence in a Caenorhabditis elegans model of infection. Further research on SrpA and similar proteins, which are widely present in many other bacteria, is warranted.

You et al. show that SrpA, a small protein widely conserved among bacteria, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa, including cell motility, chemotaxis, biofilm formation, and virulence.

Characterization of Pseudomonas aeruginosa Phage C11 and Identification of Host Genes Required for Virion Maturation

The underlying mechanisms of phage-host interactions largely remained to be elucidated. In this work, Pseudomonas aeruginosa phage C11 was first characterized as a Myoviridae virus having a linear dsDNA molecule of 94109 bp with 1173 bp identical terminal direct repeats (TDR). Then the mutants resistant to phage C11 were screened in a Tn5G transposon mutant library of P. aeruginosa PAK, including two mutants with decreased adsorption rates (DAR) and five mutants with wild-type adsorption rates (WAR). When the WAR mutants were incubated with phage C11, their growth rates were significantly inhibited; the replication of the phage genomic DNA was detected in all the WAR mutants with the real-time quantitative PCR analysis; and the synthesized phage genomic DNA was processed into monomers for packaging evidenced by the southern blot analysis. Moreover, with strain PAK as indicator, small quantities of phage C11 were synthesized in the WAR mutants. Taken together, these data suggested the identified genes of the WAR mutants are necessary for efficient synthesis of the infectious phage particles. Finally, the WAR mutants were detected sensitive to two other Pseudomonas phages closely related with C11, further implying the evolved diversity and complexity of the phage-host interactions in both sides.