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Scientific Reports Mar 2023Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are...
Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe interactions. In this study, we performed a systematic analysis of prophage elements in 2406 complete actinobacterial genomes. Overall, 2106 prophage elements were predicted to be present in about 50% (1172/2406) of the analyzed datasets. Interestingly, these identified sequences compose a high prevalence of cryptic prophage elements, indicating genetic decay and domestication. Analysis of the sequence relationship of predicted prophages with known actinobacteriophage genomes revealed an exceptional high phylogenetic diversity of prophage elements. As a trend, we observed a higher prevalence of prophage elements in vicinity to the terminus. Analysis of the prophage-encoded gene functions revealed that prophage sequences significantly contribute to the bacterial antiviral immune system, but no biosynthetic gene clusters involved in the synthesis of known antiphage molecules were identified in prophage genomes. Overall, the current study highlights the remarkable diversity of prophages in actinobacterial genomes, with highly divergent prophages in actinobacterial genomes and thus provides an important basis for further investigation of phage-host interactions in this important bacterial phylum.
Topics: Prophages; Phylogeny; Bacteriophages; Genome, Bacterial
PubMed: 36932119
DOI: 10.1038/s41598-023-30829-z -
Nature Communications Nov 2019Bacterial pathogens often carry multiple prophages and other phage-derived elements within their genome, some of which can produce viral particles in response to stress....
Bacterial pathogens often carry multiple prophages and other phage-derived elements within their genome, some of which can produce viral particles in response to stress. Listeria monocytogenes 10403S harbors two phage elements in its chromosome, both of which can trigger bacterial lysis under stress: an active prophage (ϕ10403S) that promotes the virulence of its host and can produce infective virions, and a locus encoding phage tail-like bacteriocins. Here, we show that the two phage elements are co-regulated, with the bacteriocin locus controlling the induction of the prophage and thus its activity as a virulence-associated molecular switch. More specifically, a metalloprotease encoded in the bacteriocin locus is upregulated in response to stress and acts as an anti-repressor for CI-like repressors encoded in each phage element. Our results provide molecular insight into the phenomenon of polylysogeny and its intricate adaptation to complex environments.
Topics: Amino Acid Sequence; Bacteriocins; Bacteriolysis; Bacteriophages; Chromosomes, Bacterial; Genome, Bacterial; Genome, Viral; Host-Pathogen Interactions; Listeria monocytogenes; Lysogeny; Metalloproteases; Prophages; Sequence Homology, Amino Acid; Virus Activation
PubMed: 31754112
DOI: 10.1038/s41467-019-13296-x -
Archives of Razi Institute 2021is a well-known commensal and pathogen agent of many wild and domestic animals. A wide variety of infections can be caused by , from suppurative skin infections to...
is a well-known commensal and pathogen agent of many wild and domestic animals. A wide variety of infections can be caused by , from suppurative skin infections to life-threatening septicemia. This study was conducted to determine the prophage typing and the pattern of antibiotic resistance of isolated from broiler poultry before they have been slaughtered. In this study, 200 nasal and cloacal swab samples from 20 different flocks were collected for bacterial isolation. Staphylococci were identified using biochemical and molecular methods before being examined for gene detections in all samples resistant to oxacillin and cefotaxime. The highest value of antibiotic resistance was observed against ciprofloxacin (94%), and the maximum value of susceptibility was to gentamicin (85%). Twenty-eight (27%) samples were resistant to oxacillin. In methicillin-resistance (MRSA) isolates, 5 prophage types were observed, where the prophage with a frequency of 75% was identified as a dominant prophage; in isolates of susceptible to methicillin, 8 prophage types were observed, where prophage with a frequency about 82% was the dominant prophage. The high prevalence of MRSA isolates can indicate the risk of transmission of these bacteria to the food cycle. Furthermore, existence of various prophages in these isolates can be considered a threat to public health in producing pathogenicity factors in this bacterium while also empowering other bacterial pathogenicity, even other bacterial genera.
Topics: Animals; Chickens; Microbial Sensitivity Tests; Poultry; Prophages; Staphylococcus aureus
PubMed: 34824743
DOI: 10.22092/ari.2020.343199.1498 -
Applied and Environmental Microbiology Oct 2017The prophage-encoded Shiga toxin is a major virulence factor in Stx-producing (STEC). Toxin production and phage production are linked and occur after induction of the...
The prophage-encoded Shiga toxin is a major virulence factor in Stx-producing (STEC). Toxin production and phage production are linked and occur after induction of the RecA-dependent SOS response. However, food-related stress and Stx-prophage induction have not been studied at the single-cell level. This study investigated the effects of abiotic environmental stress on expression by single-cell quantification of gene expression in STEC O104:H4 Δ:::: In addition, the effect of stress on production of phage particles was determined. The lethality of stressors, including heat, HCl, lactic acid, hydrogen peroxide, and high hydrostatic pressure, was selected to reduce cell counts by 1 to 2 log CFU/ml. The integrity of the bacterial membrane after exposure to stress was measured by propidium iodide (PI). The fluorescent signals of green fluorescent protein (GFP) and PI were quantified by flow cytometry. The mechanism of prophage induction by stress was evaluated by relative gene expression of and cell morphology. Acid (pH < 3.5) and HO (2.5 mM) induced the expression of in about 18% and 3% of the population, respectively. The mechanism of prophage induction by acid differs from that of induction by HO HO induction but not acid induction corresponded to production of infectious phage particles, upregulation of , and cell filamentation. Pressure (200 MPa) or heat did not induce the Stx2-encoding prophage (Stx2-prophage). Overall, the quantification method developed in this study allowed investigation of prophage induction and physiological properties at the single-cell level. HO and acids mediate different pathways to induce Stx2-prophage. Induction of the Stx-prophage in STEC results in production of phage particles and Stx and thus relates to virulence as well as the transduction of virulence genes. This study developed a method for a detection of the induction of Stx-prophages at the single-cell level; membrane permeability and an indication of SOS response to environmental stress were additionally assessed. HO and mitomycin C induced expression of the prophage and activated a SOS response. In contrast, HCl and lactic acid induced the Stx-prophage but not the SOS response. The lifestyle of STEC exposes the organism to intestinal and extraintestinal environments that impose oxidative and acid stress. A more thorough understanding of the influence of food processing-related stressors on Stx-prophage expression thus facilitates control of STEC in food systems by minimizing prophage induction during food production and storage.
Topics: Acids; Hydrogen Peroxide; Prophages; Shiga Toxin 2; Shiga-Toxigenic Escherichia coli; Virulence; Virus Activation
PubMed: 28778890
DOI: 10.1128/AEM.01378-17 -
BMC Microbiology Jan 2019Group A Streptococcus (GAS) is a major human pathogen, which is associated with a wide spectrum of invasive diseases, such as pharyngitis, scarlet fever, rheumatic...
BACKGROUND
Group A Streptococcus (GAS) is a major human pathogen, which is associated with a wide spectrum of invasive diseases, such as pharyngitis, scarlet fever, rheumatic fever, and streptococcal toxic shock syndrome (STSS). It is hypothesized that differences in GAS pathogenicity are related to the acquisition of diverse bacteriophages (phages). Nevertheless, the GAS genome also harbors clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes, which play an important role in eliminating foreign DNA, including those of phages. However, the structure of prophages in GAS strains is mosaic, and the phylogenetic relationship between prophages and CRISPR is not clear. In this study, we analyzed CRISPR and prophage structure using 118 complete genome sequences of GAS strains to elucidate the relationship between two genomic elements. Additionally, phylogenetic and M-type analyses were performed.
RESULTS
Of the 118 GAS strains, 80 harbored type I-C and/or II-A CRISPR/cas loci. A total of 553 spacer sequences were identified from CRISPR/cas loci and sorted into 229 patterns. We identified and classified 373 prophages into 14 groups. Some prophage groups shared a common integration site, and were related to M-type. We further investigated the correlation between spacer sequences and prophages. Of the 229 spacer sequence patterns, 203 were similar to that of other GAS prophages. No spacer showed similarity with that of a specific prophage group with mutL integration site. Moreover, the average number of prophages in strains with type II-A CRISPR was significantly less than that in type I-C CRISPR and non-CRISPR strains. However, there was no statistical difference between the average number of prophages in type I-C strains and that in non-CRISPR strains.
CONCLUSIONS
Our results indicated that type II-A CRISPR may play an important role in eliminating phages and that the prophage integration site may be an important criterion for the acceptance of foreign DNA by GAS. M type, spacer sequence, and prophage group data were correlated with the phylogenetic relationships of GAS. Therefore, we hypothesize that genetic characteristics and/or phylogenetic relationships of GAS may be estimated by analyzing its spacer sequences.
Topics: Clustered Regularly Interspaced Short Palindromic Repeats; Evolution, Molecular; Genome, Bacterial; Phylogeny; Prophages; Streptococcus pyogenes; Virus Integration
PubMed: 30691408
DOI: 10.1186/s12866-019-1393-y -
MSystems Jun 2022The genus includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. species frequently exchange DNA with one another,...
The genus includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect species. We also identified similar predicted prophages in genomes of different species. Additionally, we examined CRISPR-Cas targeting of each genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel prophages, several of which may infect multiple species. These findings have important implications for understanding horizontal gene transfer between members of this genus. Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
Topics: Humans; Prophages; Neisseria; Host Specificity; Bacteriophages; Genomics; Neisseria gonorrhoeae; Neisseria meningitidis
PubMed: 35418239
DOI: 10.1128/msystems.00083-22 -
The Journal of Antimicrobial... Oct 2019To investigate the presence and transfer of the oxazolidinone/phenicol resistance gene optrA and identify the genetic elements involved in the horizontal transfer of the...
OBJECTIVES
To investigate the presence and transfer of the oxazolidinone/phenicol resistance gene optrA and identify the genetic elements involved in the horizontal transfer of the optrA gene in Streptococcus suis.
METHODS
A total of 237 S. suis isolates were screened for the presence of the optrA gene by PCR. Whole-genome DNA of three optrA-positive strains was completely sequenced using the Illumina MiSeq and Pacbio RSII platforms. MICs were determined by broth microdilution. Transferability of the optrA gene in S. suis was investigated by conjugation. The presence of circular intermediates was examined by inverse PCR.
RESULTS
The optrA gene was present in 11.8% (28/237) of the S. suis strains. In three strains, the optrA gene was flanked by two copies of IS1216 elements in the same orientation, located either on a prophage or on ICESa2603-family integrative and conjugative elements (ICEs), including one tandem ICE. In one isolate, the optrA-carrying ICE transferred with a frequency of 2.1 × 10-8. After the transfer, the transconjugant displayed elevated MICs of the respective antimicrobial agents. Inverse PCRs revealed that circular intermediates of different sizes were formed in the three optrA-carrying strains, containing one copy of the IS1216E element and the optrA gene alone or in combination with other resistance genes.
CONCLUSIONS
A prophage and two ICESa2603-family ICEs (including one tandem ICE) associated with the optrA gene were identified in S. suis. The association of the optrA gene with the IS1216E elements and its location on either a prophage or ICEs will aid its horizontal transfer.
Topics: Animals; Anti-Bacterial Agents; Chloramphenicol; Conjugation, Genetic; Drug Resistance, Bacterial; Gene Transfer, Horizontal; Genes, Bacterial; Interspersed Repetitive Sequences; Microbial Sensitivity Tests; Oxazolidinones; Polymerase Chain Reaction; Prophages; Streptococcal Infections; Streptococcus suis; Swine; Swine Diseases; Whole Genome Sequencing
PubMed: 31314095
DOI: 10.1093/jac/dkz309 -
Nucleic Acids Research Dec 2016DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but...
DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction.
Topics: AT Rich Sequence; Actinobacteria; Corynebacterium glutamicum; DNA, Viral; Gene Silencing; Gene Transfer, Horizontal; Genome, Bacterial; Genome-Wide Association Study; Prophages; Sequence Homology, Amino Acid; Viral Proteins
PubMed: 27492287
DOI: 10.1093/nar/gkw692 -
Journal of Biomolecular Structure &... 2016Mycobacterium tuberculosis complex (MTBC) is notorious for causing diseases, such as tuberculosis. Tuberculosis caused by M. tuberculosis remains a global public health...
Mycobacterium tuberculosis complex (MTBC) is notorious for causing diseases, such as tuberculosis. Tuberculosis caused by M. tuberculosis remains a global public health concern. Two prophages, phiRv1 and phiRv2, can be found among most MTBC genomes. However, no precise functions have been assigned for the two prophages. In this paper, to find out the function of these two prophages, the distribution and function of phiRv1 and phiRv2 in MTBC genomes were analyzed from multiple omics data. We found that complex insertion, deletion, and reorganization appeared on the locus of two prophages in MTBC genomes; some genes of the two prophages can be translated and are functional from proteomic data; the expression of other prophage genes, such as Rv1577c, Rv2650c, Rv2652c, Rv2659c, and Rv2658c, can vary with environmental stresses and might enhance the fitness of MTBC. These data will facilitate our in-depth understanding of their function.
Topics: Gene Expression Regulation, Bacterial; Genome, Bacterial; Mycobacterium tuberculosis; Oxidative Phosphorylation; Prophages; Proteomics; Stress, Physiological; Transcriptome
PubMed: 25855385
DOI: 10.1080/07391102.2015.1022602 -
BMC Genomics Jun 2024Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding...
BACKGROUND
Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage.
RESULTS
We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes.
CONCLUSIONS
In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.
Topics: Prophages; Phylogeny; Treponema; Genomics; Genome, Bacterial; Computational Biology; Genome, Viral; Bacteriophages
PubMed: 38824509
DOI: 10.1186/s12864-024-10461-5