keyword
https://read.qxmd.com/read/38532498/the-spontaneously-produced-lysogenic-prophage-phi456-promotes-bacterial-resistance-to-adverse-environments-and-enhances-the-colonization-ability-of-avian-pathogenic-escherichia-coli-strain-de456
#1
JOURNAL ARTICLE
Dezhi Li, Wei Liang, Zhiqiang Huang, Wenwen Ma, Qing Liu
In the last decade, prophages that possess the ability of lysogenic transformation have become increasingly significant. Their transfer and subsequent activity in the host have a significant impact on the evolution of bacteria. Here, we investigate the role of prophage phi456 with high spontaneous induction in the bacterial genome of Avian pathogenic Escherichia coli (APEC) DE456. The phage particles, phi456, that were released from DE456 were isolated, purified, and sequenced. Additionally, phage particles were no longer observed either during normal growth or induced by nalidixic acid in DE456Δphi456...
March 26, 2024: Veterinary Research
https://read.qxmd.com/read/38526735/crisprpi-inducing-and-curing-prophage-using-the-crispr-interference
#2
JOURNAL ARTICLE
Jeffrey K Cornuault
We present here a CRISPR-interference-based protocol to trigger prophage induction, even for non-inducible prophages. This method can also be used to cure the prophage from the bacterial host. The method is based on silencing of the phage's repressor transcription, thanks to CRISPR interference. Plasmid electroporation is used to bring the CRISPRi system into the bacteria, specifically on a plasmid carrying spacers targeting the prophage repressor. This method enables prophage induction and curation in a week or two with a high efficiency...
2024: Methods in Molecular Biology
https://read.qxmd.com/read/38440971/integrated-bacterial-transcriptome-and-host-metabolome-analysis-reveals-insights-into-candidatus-liberibacter-asiaticus-population-dynamics-in-the-fruit-pith-of-three-citrus-cultivars-with-different-tolerance
#3
JOURNAL ARTICLE
Yun Li, Ruifeng Ma, Chenying Gao, Ziyi Li, Yongqin Zheng, Fang Fang, Cheng Wang, Guohua Li, Xiaozhen Du, Changbao Xu, Meirong Xu, Rui Liu, Xiaoling Deng, Zheng Zheng
" Candidatus Liberibacter asiaticus" (CLas), the causal agent of citrus Huanglongbing (HLB), is able to multiply to a high abundance in citrus fruit pith. However, little is known about the biological processes and phytochemical substances that are vital for CLas colonization and growth in fruit pith. In this study, CLas-infected fruit pith of three citrus cultivars ("Shatangju" mandarin, "Guanxi" pomelo, and "Shatian" pomelo) exhibiting different tolerance to CLas were collected and used for dual RNA-Seq and untargeted metabolome analysis...
March 5, 2024: Microbiology Spectrum
https://read.qxmd.com/read/38366190/coral-mucus-as-a-reservoir-of-bacteriophages-targeting-vibrio-pathogens
#4
JOURNAL ARTICLE
Esther Rubio-Portillo, Sophia Robertson, Josefa Antón
The increasing trend in sea surface temperature promotes the spread of Vibrio species, which are known to cause diseases in a wide range of marine organisms. Among these pathogens, Vibrio mediterranei has emerged as a significant threat, leading to bleaching in the coral species Oculina patagonica. Bacteriophages, or phages, are viruses that infect bacteria, thereby regulating microbial communities and playing a crucial role in the coral's defense against pathogens. However, our understanding of phages that infect V...
January 31, 2024: ISME Journal
https://read.qxmd.com/read/38251745/understanding-the-impact-of-temperate-bacteriophages-on-their-lysogens-through-transcriptomics
#5
JOURNAL ARTICLE
Revathy Krishnamurthi, Enrique González-Tortuero, Grace Plahe, Ian B Goodhead, Joanne L Fothergill, Chloë E James, Heather E Allison
Temperate phages are found integrated as prophages in the majority of bacterial genomes. Some prophages are cryptic and fixed in the bacterial chromosome, but others are active and can be triggered into a replicative form either spontaneously or by exposure to inducing factors. Prophages are commonly associated with the ability to confer toxin production or other virulence-associated traits on their host cell. More recent studies have shown they can play a much bigger role in altering the physiology of their hosts...
January 5, 2024: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/38224456/single-cell-evidence-for-plasmid-addiction-mediated-by-toxin-antitoxin-systems
#6
JOURNAL ARTICLE
Nathan Fraikin, Laurence Van Melderen
Toxin-antitoxin (TA) systems are small selfish genetic modules that increase vertical stability of their replicons. They have long been thought to stabilize plasmids by killing cells that fail to inherit a plasmid copy through a phenomenon called post-segregational killing (PSK) or addiction. While this model has been widely accepted, no direct observation of PSK was reported in the literature. Here, we devised a system that enables visualization of plasmid loss and PSK at the single-cell level using meganuclease-driven plasmid curing...
January 15, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38153127/lethal-perturbation-of-an-escherichia-coli-regulatory-network-is-triggered-by-a-restriction-modification-system-s-regulator-and-can-be-mitigated-by-excision-of-the-cryptic-prophage-rac
#7
JOURNAL ARTICLE
Katarzyna Gucwa, Ewa Wons, Aleksandra Wisniewska, Marcin Jakalski, Zuzanna Dubiak, Lukasz Pawel Kozlowski, Iwona Mruk
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level...
December 28, 2023: Nucleic Acids Research
https://read.qxmd.com/read/38117844/bacteriophage-encoded-24b_1-molecule-resembles-herpesviral-micrornas-and-plays-a-crucial-role-in-the-development-of-both-the-virus-and-its-host
#8
JOURNAL ARTICLE
Sylwia Bloch, Natalia Lewandowska, Joanna Zwolenkiewicz, Paulina Mach, Aleksandra Łukasiak, Mikołaj Olejniczak, Logan W Donaldson, Grzegorz Węgrzyn, Bożena Nejman-Faleńczyk
The 24B_1 small non-coding RNA molecule has been identified in Escherichia coli after induction of Shiga toxin-converting bacteriophage Φ24B. In this work, we focused on its direct role during phage and bacterial host development. We observed that in many aspects, this phage sRNA resembles herpesviral microRNAs. Similar to microRNAs, the mature 24B_1 is a short molecule, consisting of just 20 nucleotides. It is generated by cleaving the 80-nt long precursor transcript, and likely it undergoes a multi-step maturation process in which the Hfq protein plays an important role, as confirmed by demonstration of its binding to the 24B_1 precursor, but not to the 24B_1 mature form...
2023: PloS One
https://read.qxmd.com/read/38084945/seasonal-trends-in-lysogeny-in-an-appalachian-oak-hickory-forest-soil
#9
JOURNAL ARTICLE
Melaina L Jacoby, Graham D Hogg, Madeleine R Assaad, Kurt E Williamson
Lysogeny is a relationship in which certain viruses that infect bacteria (phages) may exist within their bacterial host cell as a segment of nucleic acid. In this state, the phage genome is protected from environmental damage and retains the potential to generate progeny particles in the future. It is thought that lysogeny provides a mechanism for long-term persistence for phages when host density is low or hosts are starved-two conditions likely to be found in soils. In the present study, we provide the first known evidence for a seasonal trend in lysogeny in a forest soil...
December 12, 2023: Applied and Environmental Microbiology
https://read.qxmd.com/read/38084890/a-prophage-encoded-ribosomal-rna-methyltransferase-regulates-the-virulence-of-shiga-toxin-producing-escherichia-coli-stec
#10
JOURNAL ARTICLE
Chen Gong, Dolonchapa Chakraborty, Gerald B Koudelka
Shiga toxin (Stx) released by Shiga toxin producing Escherichia coli (STEC) causes life-threatening illness. Its production and release require induction of Stx-encoding prophage resident within the STEC genome. We identified two different STEC strains, PA2 and PA8, bearing Stx-encoding prophage whose sequences primarily differ by the position of an IS629 insertion element, yet differ in their abilities to kill eukaryotic cells and whose prophages differ in their spontaneous induction frequencies. The IS629 element in ϕPA2, disrupts an ORF predicted to encode a DNA adenine methyltransferase, whereas in ϕPA8, this element lies in an intergenic region...
December 12, 2023: Nucleic Acids Research
https://read.qxmd.com/read/38073204/unusual-modifications-of-protein-biomarkers-expressed-by-plasmid-prophage-and-bacterial-host-of-pathogenic-escherichia-coli-identified-using-top-down-proteomic-analysis
#11
JOURNAL ARTICLE
Clifton K Fagerquist, Yanlin Shi, Jihyun Park
RATIONALE: Pathogenic bacteria often carry prophage (bacterial viruses) and plasmids (small circular pieces of DNA) that may harbor toxin, antibacterial, and antibiotic resistance genes. Proteomic characterization of pathogenic bacteria should include the identification of host proteins and proteins produced by prophage and plasmid genomes. METHODS: Protein biomarkers of two strains of Shiga toxin-producing Escherichia coli (STEC) were identified using antibiotic induction, matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) with post-source decay (PSD), top-down proteomic (TDP) analysis, and plasmid sequencing...
January 15, 2024: Rapid Communications in Mass Spectrometry: RCM
https://read.qxmd.com/read/38071361/genotoxic-stress-stimulates-edna-release-via-explosive-cell-lysis-and-thereby-promotes-streamer-formation-of-burkholderia-cenocepacia-h111-cultured-in-a-microfluidic-device
#12
JOURNAL ARTICLE
Zaira Heredia-Ponce, Eleonora Secchi, Masanori Toyofuku, Gabriela Marinova, Giovanni Savorana, Leo Eberl
DNA is a component of biofilms, but the triggers of DNA release during biofilm formation and how DNA contributes to biofilm development are poorly investigated. One key mechanism involved in DNA release is explosive cell lysis, which is a consequence of prophage induction. In this article, the role of explosive cell lysis in biofilm formation was investigated in the opportunistic human pathogen Burkholderia cenocepacia H111 (H111). Biofilm streamers, flow-suspended biofilm filaments, were used as a biofilm model in this study, as DNA is an essential component of their matrix...
December 9, 2023: NPJ Biofilms and Microbiomes
https://read.qxmd.com/read/38059344/crispr-cas-immunity-is-repressed-by-the-lysr-type-transcriptional-regulator-pigu
#13
JOURNAL ARTICLE
Leah M Smith, Hannah G Hampton, Mariya S Yevstigneyeva, Marina Mahler, Zacharie S M Paquet, Peter C Fineran
Bacteria protect themselves from infection by bacteriophages (phages) using different defence systems, such as CRISPR-Cas. Although CRISPR-Cas provides phage resistance, fitness costs are incurred, such as through autoimmunity. CRISPR-Cas regulation can optimise defence and minimise these costs. We recently developed a genome-wide functional genomics approach (SorTn-seq) for high-throughput discovery of regulators of bacterial gene expression. Here, we applied SorTn-seq to identify loci influencing expression of the two type III-A Serratia CRISPR arrays...
December 7, 2023: Nucleic Acids Research
https://read.qxmd.com/read/38045928/distribution-inducibility-and-characteristics-of-latilactobacillus-curvatus-temperate-phages
#14
JOURNAL ARTICLE
Conrad L Ambros, Matthias A Ehrmann
Aim: Temperate phages are known to heavily impact the growth of their host, be it in a positive way, e.g., when beneficial genes are provided by the phage, or negatively when lysis occurs after prophage induction. This study provides an in-depth look into the distribution and variety of prophages in Latilactobacillus curvatus ( L. curvatus ). This species is found in a wide variety of ecological niches and is routinely used as a meat starter culture. Methods: Fourty five L. curvatus genomes were screened for prophages...
2023: Microbiome Res Rep
https://read.qxmd.com/read/38038061/inhibition-of-pqs-signaling-by-the-pf-bacteriophage-protein-pfse-enhances-viral-replication-in-pseudomonas-aeruginosa
#15
JOURNAL ARTICLE
Caleb M Schwartzkopf, Véronique L Taylor, Marie-Christine Groleau, Dominick R Faith, Amelia K Schmidt, Tyrza L Lamma, Diane M Brooks, Eric Déziel, Karen L Maxwell, Patrick R Secor
Quorum sensing, a bacterial signaling system that coordinates group behaviors as a function of cell density, plays an important role in regulating viral (phage) defense mechanisms in bacteria. The opportunistic pathogen Pseudomonas aeruginosa is a model system for the study of quorum sensing. P. aeruginosa is also frequently infected by Pf prophages that integrate into the host chromosome. Upon induction, Pf phages suppress host quorum sensing systems; however, the physiological relevance and mechanism of suppression are unknown...
December 1, 2023: Molecular Microbiology
https://read.qxmd.com/read/37999503/characteristics-of-shiga-toxin-producing-escherichia-coli-circulating-in-asymptomatic-food-handlers
#16
JOURNAL ARTICLE
Xinxia Sui, Xi Yang, Ming Luo, Hua Wang, Qian Liu, Hui Sun, Yujuan Jin, Yannong Wu, Xiangning Bai, Yanwen Xiong
Shiga toxin-producing Escherichia coli (STEC) is a foodborne zoonotic pathogen that causes diarrhea, hemorrhagic colitis (HC), and hemolytic uremic syndrome (HUS) worldwide. Since the infection can be asymptomatic, the circulation of STEC in some asymptomatic carriers, especially in healthy-food-related professionals, is not yet well understood. In this study, a total of 3987 anal swab samples from asymptomatic food handlers were collected, and ten swabs recovered STEC strains (0.251%). Of the ten STEC isolates, seven serotypes and eight sequence types (ST) were determined using whole genome sequencing (WGS)...
November 2, 2023: Toxins
https://read.qxmd.com/read/37981215/appelmans-protocol-a-directed-in-vitro-evolution-enables-induction-and-recombination-of-prophages-with-expanded-host-range
#17
JOURNAL ARTICLE
Thao Nguyen Vu, Justin Ryan Clark, Eris Jang, Roshan D'Souza, Le Phuong Nguyen, Naina Adren Pinto, Seongjun Yoo, Ricardo Enrique Abadie Saenz, Anthony William Maresso, Dongeun Yong
Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) present significant healthcare challenges due to limited treatment options. Bacteriophage (phage) therapy offers potential as an alternative treatment. However, the high host specificity of phages poses challenges for their therapeutic application. To broaden the phage spectrum, laboratory-based phage training using the Appelmans protocol was employed in this study. As a result, the protocol successfully expanded the host range of a phage cocktail targeting CRAB...
November 17, 2023: Virus Research
https://read.qxmd.com/read/37968427/complex-effects-of-the-exo-xis-region-of-the-shiga-toxin-converting-bacteriophage-%C3%AE-24-b-genome-on-the-phage-development-and-the-escherichia-coli-host-physiology
#18
JOURNAL ARTICLE
Sylwia Bloch, Bożena Nejman-Faleńczyk, Katarzyna Licznerska, Aleksandra Dydecka, Gracja Topka-Bielecka, Agnieszka Necel, Alicja Węgrzyn, Grzegorz Węgrzyn
Lambdoid bacteriophages are excellent models in studies on molecular aspects of virus-host interactions. However, some of them carry genes encoding toxins which are responsible for virulence of pathogenic strains of bacteria. Shiga toxin-converting bacteriophages (Stx phages) encode Shiga toxins that cause virulence of enterohemorrhagic Escherichia coli (EHEC), and their effective production depends on Stx prophage induction. The exo-xis region of the lambdoid phage genome consists of genes which are dispensable for the phage multiplication under laboratory conditions; however, they might modulate the virus development...
November 16, 2023: Journal of Applied Genetics
https://read.qxmd.com/read/37919394/widespread-and-largely-unknown-prophage-activity-diversity-and-function-in-two-genera-of-wheat-phyllosphere-bacteria
#19
JOURNAL ARTICLE
Peter Erdmann Dougherty, Tue Kjærgaard Nielsen, Leise Riber, Helen Helgå Lading, Laura Milena Forero-Junco, Witold Kot, Jos M Raaijmakers, Lars Hestbjerg Hansen
Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 108  virions/mL in overnight cultures, with significant induction also observed in planta...
November 2, 2023: ISME Journal
https://read.qxmd.com/read/37914998/evolution-of-wolbachia-reproductive-and-nutritional-mutualism-insights-from-the-genomes-of-two-novel-strains-that-double-infect-the-pollinator-of-dioecious-ficus-hirta
#20
JOURNAL ARTICLE
Wanzhen Liu, Xue Xia, Ary A Hoffmann, Yamei Ding, Ji-Chao Fang, Hui Yu
Wolbachia is a genus of maternally inherited endosymbionts that can affect reproduction of their hosts and influence metabolic processes. The pollinator, Valisia javana, is common in the male syconium of the dioecious fig Ficus hirta. Based on a high-quality chromosome-level V. javana genome with PacBio long-read and Illumina short-read sequencing, we discovered a sizeable proportion of Wolbachia sequences and used these to assemble two novel Wolbachia strains belonging to supergroup A. We explored its phylogenetic relationship with described Wolbachia strains based on MLST sequences and the possibility of induction of CI (cytoplasmic incompatibility) in this strain by examining the presence of cif genes known to be responsible for CI in other insects...
November 1, 2023: BMC Genomics
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