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https://read.qxmd.com/read/30809245/bacterial-grounded-prophages-hotspots-for-genetic-renovation-and-innovation
#1
Bhaskar Chandra Mohan Ramisetty, Pavithra Anantharaman Sudhakari
Bacterial genomes are highly plastic allowing the generation of variants through mutations and acquisition of genetic information. The fittest variants are then selected by the econiche thereby allowing the bacterial adaptation and colonization of the habitat. Larger genomes, however, may impose metabolic burden and hence bacterial genomes are optimized by the loss of frivolous genetic information. The activity of temperate bacteriophages has acute consequences on the bacterial population as well as the bacterial genome through lytic and lysogenic cycles...
2019: Frontiers in Genetics
https://read.qxmd.com/read/30800118/prophage-excision-in-streptococcus-pneumoniae-serotype-19a-st320-promote-colonization-insight-into-its-evolution-from-the-ancestral-clone-taiwan-19f-14-st236
#2
Yi-Yin Chen, Jin-Town Wang, Tzu-Lung Lin, Yu-Nong Gong, Ting-Hsuan Li, Ya-Yu Huang, Yu-Chia Hsieh
Streptococcus pneumoniae 19A ST320, a multidrug-resistant strain with high disease severity that notoriously spread before the use of expanded pneumococcal conjugate vaccines, was derived from a capsular switching event between an international strain Taiwan 19F-14 (ST236) and a serotype 19A strain. However, the molecular mechanisms underlying the adaptive evolution of 19F ST236 to 19A ST320 are unknown. In this study, we compared 19A ST320 to its ancestral clone, 19F ST236, in terms of adherence to respiratory epithelial cells, whole transcriptome, and ability to colonize a young mouse model...
2019: Frontiers in Microbiology
https://read.qxmd.com/read/30787917/characterization-of-a-highly-virulent-edwardsiella-anguillarum-strain-isolated-from-greek-aquaculture-and-a-spontaneously-induced-prophage-therein
#3
Pantelis Katharios, Panos G Kalatzis, Constantina Kokkari, Michail Pavlidis, Qiyao Wang
Edwardsiella -associated outbreaks are increasingly reported on both marine and freshwater aquaculture setups, accounting for severe financial and biomass losses. E. tarda, E. ictaluri , and E. hoshinae have been the traditional causative agents of edwardsiellosis in aquaculture, however, intensive studies due to the significance of the disease have just recently revealed two more species, E. piscicida and E. anguillarum . Whole genome sequencing that was conducted on the strain EA011113, isolated from farmed Diplodus puntazzo after an edwardsiellosis outbreak in Greece, confirmed it as a new clinical strain of E...
2019: Frontiers in Microbiology
https://read.qxmd.com/read/30763529/sugar-and-fatty-acids-ack-celerate-prophage-induction
#4
Anushila Chatterjee, Breck A Duerkop
Intestinal cues driving prophage induction in the microbiota are largely unknown. In this issue of Cell Host & Microbe, Oh et al. (2018) reveal that dietary fructose- and microbiota-derived short-chain fatty acids promote AckA-mediated acetic acid biosynthesis, triggering a stress response that facilities phage production.
February 13, 2019: Cell Host & Microbe
https://read.qxmd.com/read/30685209/the-toxin-antidote-model-of-cytoplasmic-incompatibility-genetics-and-evolutionary-implications
#5
REVIEW
John F Beckmann, Manon Bonneau, Hongli Chen, Mark Hochstrasser, Denis Poinsot, Hervé Merçot, Mylène Weill, Mathieu Sicard, Sylvain Charlat
Wolbachia bacteria inhabit the cells of about half of all arthropod species, an unparalleled success stemming in large part from selfish invasive strategies. Cytoplasmic incompatibility (CI), whereby the symbiont makes itself essential to embryo viability, is the most common of these and constitutes a promising weapon against vector-borne diseases. After decades of theoretical and experimental struggle, major recent advances have been made toward a molecular understanding of this phenomenon. As pieces of the puzzle come together, from yeast and Drosophila fly transgenesis to CI diversity patterns in natural mosquito populations, it becomes clearer than ever that the CI induction and rescue stem from a toxin-antidote (TA) system...
January 23, 2019: Trends in Genetics: TIG
https://read.qxmd.com/read/30683744/exploiting-prophage-mediated-lysis-for-biotherapeutic-release-by-lactobacillus-reuteri
#6
Laura M Alexander, Jee-Hwan Oh, Donald S Stapleton, Kathryn L Schueler, Mark P Keller, Alan D Attie, Jan-Peter van Pijkeren
Lactobacillus reuteri has the potential to be developed as a microbial therapeutic delivery platform because of an established safety profile, health-promoting properties, and available genome editing tools. Here, we showed that L. reuteri VPL1014 exhibits a low mutation rate compared to other gram-positive bacteria, which we expect will contribute to the stability of genetically modified strains. VPL1014 encodes two biologically active prophages, which are induced during GI transit. We hypothesized that intracellular accumulated recombinant protein can be delivered in situ following bacteriophage-mediated lysis...
January 25, 2019: Applied and Environmental Microbiology
https://read.qxmd.com/read/30630428/transcriptional-profiling-of-pseudomonas-aeruginosa-and-staphylococcus-aureus-during-in-vitro-co-culture
#7
Mikaël Tognon, Thilo Köhler, Alexandre Luscher, Christian van Delden
BACKGROUND: Co-colonization by Pseudomonas aeruginosa and Staphylococcus aureus is frequent in cystic fibrosis patients. Polymicrobial infections involve both detrimental and beneficial interactions between different bacterial species. Such interactions potentially indirectly impact the human host through virulence, antibiosis and immunomodulation. RESULTS: Here we explored the responses triggered by the encounter of these two pathogens to identify early processes that are important for survival when facing a potential competitor...
January 10, 2019: BMC Genomics
https://read.qxmd.com/read/30629725/prophage-induction-but-not-production-of-phage-particles-is-required-for-lethal-disease-in-a-microbiome-replete-murine-model-of-enterohemorrhagic-e-coli-infection
#8
Sowmya Balasubramanian, Marcia S Osburne, Haley BrinJones, Albert K Tai, John M Leong
Enterohemorrhagic Escherichia coli (EHEC) colonize intestinal epithelium by generating characteristic attaching and effacing (AE) lesions. They are lysogenized by prophage that encode Shiga toxin 2 (Stx2), which is responsible for severe clinical manifestations. As a lysogen, prophage genes leading to lytic growth and stx2 expression are repressed, whereas induction of the bacterial SOS response in response to DNA damage leads to lytic phage growth and Stx2 production both in vitro and in germ-free or streptomycin-treated mice...
January 2019: PLoS Pathogens
https://read.qxmd.com/read/30532745/pch-genes-control-biofilm-and-cell-adhesion-in-a-clinical-serotype-o157-h7-isolate
#9
Elisa Andreozzi, Nereus W Gunther, Erin R Reichenberger, Luca Rotundo, Bryan J Cottrell, Alberto Nuñez, Gaylen A Uhlich
In a previous study, induction of the Escherichia coli serotype O157:H7 SOS response decreased csgD expression in the clinical isolate PA20 at 30°C but strongly induced genes in the horizontally transferred-DNA regions (HTR), including many known virulence regulators. To determine the role of HTR regulators in the control of csgD and curli, specific regulators were plasmid-expressed in the wild-type and mutant strains of PA20 and its biofilm-forming derivative, 20R2R. At 30°C, plasmid over-expression of the O157:H7 group 3 perC homolog, pchE , strongly repressed PA20 csgD transcription (>7-fold) while the group 1 homologs, pchA and pchB , resulted in smaller reductions (<2...
2018: Frontiers in Microbiology
https://read.qxmd.com/read/30453470/fighting-fire-with-fire-phage-potential-for-the-treatment-of-e-coli-o157-infection
#10
Cristina Howard-Varona, Dean R Vik, Natalie E Solonenko, Yueh-Fen Li, M Consuelo Gazitua, Lauren Chittick, Jennifer K Samiec, Aubrey E Jensen, Paige Anderson, Adrian Howard-Varona, Anika A Kinkhabwala, Stephen T Abedon, Matthew B Sullivan
Hemolytic⁻uremic syndrome is a life-threating disease most often associated with Shiga toxin-producing microorganisms like Escherichia coli (STEC), including E. coli O157:H7. Shiga toxin is encoded by resident prophages present within this bacterium, and both its production and release depend on the induction of Shiga toxin-encoding prophages. Consequently, treatment of STEC infections tend to be largely supportive rather than antibacterial, in part due to concerns about exacerbating such prophage induction...
November 16, 2018: Antibiotics
https://read.qxmd.com/read/30425253/mobilisation-mechanism-of-pathogenicity-islands-by-endogenous-phages-in-staphylococcus-aureus-clinical-strains
#11
Mercedes Cervera-Alamar, Katerina Guzmán-Markevitch, Miglė Žiemytė, Leticia Ortí, Patricia Bernabé-Quispe, Antonio Pineda-Lucena, Javier Pemán, María Ángeles Tormo-Mas
Staphylococcus aureus pathogenicity islands (SaPIs) are a type of mobile genetic element that play a significant role in the pathogenesis and virulence of this microorganism. SaPIs are integrated in the chromosome under the control of the master repressor Stl, but they can be horizontally transferred at a high frequency due to certain bacteriophages. Thus, a phage protein can bind to the SaPI Stl and induce the SaPI cycle, spreading the SaPI virulence factors to other bacterial populations. We report the dissemination mechanism of SaPIs mediated by endogenous prophages in S...
November 13, 2018: Scientific Reports
https://read.qxmd.com/read/30418590/brex-system-of-escherichia-coli-distinguishes-self-from-non-self-by-methylation-of-a-specific-dna-site
#12
Julia Gordeeva, Natalya Morozova, Nicolas Sierro, Artem Isaev, Tomas Sinkunas, Ksenia Tsvetkova, Mikhail Matlashov, Lidija Truncaite, Richard D Morgan, Nikolai V Ivanov, Virgis Siksnys, Lanying Zeng, Konstantin Severinov
Prokaryotes evolved numerous systems that defend against predation by bacteriophages. In addition to well-known restriction-modification and CRISPR-Cas immunity systems, many poorly characterized systems exist. One class of such systems, named BREX, consists of a putative phosphatase, a methyltransferase and four other proteins. A Bacillus cereus BREX system provides resistance to several unrelated phages and leads to modification of specific motif in host DNA. Here, we study the action of BREX system from a natural Escherichia coli isolate...
November 12, 2018: Nucleic Acids Research
https://read.qxmd.com/read/30384416/comparative-genomics-and-characterization-of-the-late-promoter-p-r-from-shiga-toxin-prophages-in-escherichia-coli
#13
Ling Xiao Zhang, David J Simpson, Lynn M McMullen, Michael G Gänzle
Shiga-toxin producing Escherichia coli (STEC) causes human illness ranging from mild diarrhea to death. The bacteriophage encoded stx genes are located in the late transcription region, downstream of the antiterminator Q. The transcription of the stx genes is directly under the control of the late promoter p R', thus the sequence diversity of the region between Q and stx , here termed the pR' region, may affect Stx toxin production. Here, we compared the gene structure of the p R' region and the stx subtypes of nineteen STECs...
October 31, 2018: Viruses
https://read.qxmd.com/read/30314296/roles-of-orf60a-and-orf61-in-development-of-bacteriophages-%C3%AE-and-%C3%AE-24-b
#14
Aleksandra Dydecka, Bożena Nejman-Faleńczyk, Sylwia Bloch, Gracja Topka, Agnieszka Necel, Logan W Donaldson, Grzegorz Węgrzyn, Alicja Węgrzyn
The exo-xis region of lambdoid bacteriophage genomes contains several established and potential genes that are evolutionarily conserved, but not essential for phage propagation under laboratory conditions. Nevertheless, deletion or overexpression of either the whole exo-xis region and important regulatory elements can significantly influence the regulation of phage development. This report defines specific roles for orf60a and orf61 in bacteriophage λ and Φ24B , a specific Shiga toxin-converting phage with clinical relevance...
October 11, 2018: Viruses
https://read.qxmd.com/read/30291266/cytometry-meets-next-generation-sequencing-rna-seq-of-sorted-subpopulations-reveals-regional-replication-and-iron-triggered-prophage-induction-in-corynebacterium-glutamicum
#15
Raphael Freiherr von Boeselager, Eugen Pfeifer, Julia Frunzke
Phenotypic diversification is key to microbial adaptation. Currently, advanced technological approaches offer insights into cell-to-cell variation of bacterial populations at a spatiotemporal resolution. However, the underlying molecular causes or consequences often remain obscure. In this study, we developed a workflow combining fluorescence-activated cell sorting and RNA-sequencing, thereby allowing transcriptomic analysis of 106 bacterial cells. As a proof of concept, the workflow was applied to study prophage induction in a subpopulation of Corynebacterium glutamicum...
October 5, 2018: Scientific Reports
https://read.qxmd.com/read/30249194/spontaneously-induced-prophages-are-abundant-in-a-naturally-evolved-bacterial-starter-culture-and-deliver-competitive-advantage-to-the-host
#16
Svetlana Alexeeva, Jesús Adrián Guerra Martínez, Maciej Spus, Eddy J Smid
BACKGROUND: In complex microbial ecosystems such as the marine environment, the gastrointestinal tract, but also in mixed culture fermentations, bacteriophages are frequently found to be a part of the microbial community. Moreover, prophages or prophage-like elements are frequently identified in sequenced bacterial genomes. The mixed undefined starter cultures represent an ecosystem which is shaped by long term evolution under relatively defined environmental conditions and provides an interesting model to study co-evolution of phages and their hosts as well as the impact of diversity on microbial community stability...
September 24, 2018: BMC Microbiology
https://read.qxmd.com/read/30143740/characterization-and-induction-of-prophages-in-human-gut-associated-bifidobacterium-hosts
#17
Travis N Mavrich, Eoghan Casey, Joana Oliveira, Francesca Bottacini, Kieran James, Charles M A P Franz, Gabriele Andrea Lugli, Horst Neve, Marco Ventura, Graham F Hatfull, Jennifer Mahony, Douwe van Sinderen
In the current report, we describe the identification of three genetically distinct groups of prophages integrated into three different chromosomal sites of human gut-associated Bifidobacterium breve and Bifidobacterium longum strains. These bifidobacterial prophages are distantly related to temperate actinobacteriophages of several hosts. Some prophages, integrated within the dnaJ2 gene, are competent for induction, excision, replication, assembly and lysis, suggesting that they are fully functional and can generate infectious particles, even though permissive hosts have not yet been identified...
August 24, 2018: Scientific Reports
https://read.qxmd.com/read/29915115/a-linear-plasmid-like-prophage-of-actinomyces-odontolyticus-promotes-biofilm-assembly
#18
Mengyu Shen, Yuhui Yang, Wei Shen, Lujia Cen, Jeffrey S McLean, Wenyuan Shi, Shuai Le, Xuesong He
The human oral cavity is home to a large number of bacteria and bacteriophages (phages). However, the biology of oral phages as members of the human microbiome is not well understood. Recently, we isolated Actinomyces odontolyticus subsp. actinosynbacter strain XH001 from the human oral cavity, and genomic analysis revealed the presence of an intact prophage named xhp1. Here, we demonstrated that xhp1 is a linear plasmid-like prophage, which is a newly identified phage of A. odontolyticus The prophage xhp1 genome is a 35-kb linear double-stranded DNA with 10-bp single-stranded, 3' cohesive ends...
September 1, 2018: Applied and Environmental Microbiology
https://read.qxmd.com/read/29875435/phage-inducible-chromosomal-islands-are-ubiquitous-within-the-bacterial-universe
#19
Alfred Fillol-Salom, Roser Martínez-Rubio, Rezheen F Abdulrahman, John Chen, Robert Davies, José R Penadés
Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies...
September 2018: ISME Journal
https://read.qxmd.com/read/29797432/comparative-genomic-analysis-of-myroides-odoratimimus-isolates
#20
Shaohua Hu, Lin Cao, Yiyin Wu, Yajun Zhou, Tao Jiang, Liqiang Wang, Qiujing Wang, Desong Ming, Shicheng Chen, Mingxi Wang
Myroides odoratimimus is an important nosocomial pathogen. Management of M. odoratimimus infection is difficult owing to the multidrug resistance and the unknown pathogenesis mechanisms. Based on our previous genomic sequencing data of M. odoratimimus PR63039 (isolated from a patient with the urinary tract infection), in this study, we further performed comparative genomic analysis for 10 selected Myroides strains. Our results showed that these Myroides genome contexts were very similar and phylogenetically related...
May 23, 2018: MicrobiologyOpen
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