Dormant phages communicate to control exit from lysogeny

Aframian, Nitzan; Bendori, Shira Omer; Hen, Stav; Guler, Polina; Stokar-Avihail, Avigail; Manor, Erica; Msaeed, kholod; Lipsman, Valeria; Grinberg, Ilana; Mahagna, Alaa; Eldar, Avigdor

doi:10.1101/2021.09.20.460909

Cited by 3 publications

(1 citation statement)

References 51 publications

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“…For the Bsub damage PB dataset, cells were grown to mid-log phase in spizizen’s minimal media (SMM) and Mitomycin C (MMC, 0.5 µg/ml final concentration) was added to wildtype B.subtilis (strain 168) as reported by [63]. The Bsub MPA PB data contains B.subtilis cells grown in SMM as described by [64, 65] to mid-log phase and challenged with Mycophenolic acid (MPA, 40 µg/ml final concentration).…”

Section: Star Methodsmentioning

confidence: 99%

BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis

Ostner,

Kirk,

Olayo-Alarcon

et al. 2024

Preprint

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Bacterial single-cell RNA sequencing has the potential to elucidate within-population heterogeneity of prokaryotes, as well as their interaction with host systems. Despite conceptual similarities, the statistical properties of bacterial single-cell datasets are highly dependent on the protocol, making proper processing essential to tap their full potential. We present BacSC, a fully data-driven computational pipeline that processes bacterial single-cell data without requiring manual intervention. BacSC performs data-adaptive quality control and variance stabilization, selects suitable parameters for dimension reduction, neighborhood embedding, and clustering, and provides false discovery rate control in differential gene expression testing. We validated BacSC on a broad selection of bacterial single-cell datasets spanning multiple protocols and species. Here, BacSC detected subpopulations inKlebsiella pneumoniae, found matching structures ofPseudomonas aeruginosaunder regular and low-iron conditions, and better represented subpopulation dynamics ofBacillus subtilis. BacSC thus simplifies statistical processing of bacterial single-cell data and reduces the danger of incorrect processing.

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Section: Star Methodsmentioning

confidence: 99%

BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis

Ostner,

Kirk,

Olayo-Alarcon

et al. 2024

Preprint

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TheBacillusphage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components

Kohm

Floccari

Lutz

et al. 2021

Preprint

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The Bacillus phage SPβ has been known for about 50 years, but only a few strains are avalible. We isolated four new wild type strains of the SPbeta species. Phage vB_BsuS-Goe14 introduces its prophage into the spoVK locus, previously not observed to be used by SPβ-like phages. We could also reveal the SPβ-like phage genome replication strategy, the genome packaging mode, and the phage genome opening point. We extracted 55 SPβ-like prophages from public Bacillus genomes, thereby discovering three more integration loci and one additional type of integrase. The identified prophages resembled four new species clusters and three species orphans in the genus Spbetavirus. The determined core proteome of all SPβ-like prophages consists of 38 proteins. The integration cassette proved to be not conserved even though present in all strains. It consists of distinct integrases. Analysis of SPβ transcriptomes revealed three conserved genes, yopQ, yopR, and yokI, to be transcribed from a dormant prophage. While yopQ and yokI could be deleted from the prophage without activating the prophage, damaging of yopR led to a clear-plaque phenotype. Under the applied laboratory conditions, the yokI mutant showed an elevated virion release implying the YokI protein being a component of the arbitrium system.

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Modern biological methods of processing plant raw materials used to increase its storage capacity

Posokina,

Zakharova

2024

Food systems

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Foodborne illnesses, mainly infectious, are a leading cause of morbidity and mortality worldwide. Pathogenic bacteria are present at virtually every stage of the food production chain, compromising company food safety programs and causing out-breaks of foodborne illnesses in various regions of the world. Finding new solutions that provide adequate microbiological stability to minimally processed foods is key to controlling bacterial pathogens that cause foodborne illnesses. The use of chemical and physical methods of food preservation often leads to a deterioration in their nutritional value, physical and organoleptic properties. Minimally processed foods produced without any radical preservation methods may be at particular risk of developing microorganisms, including pathogens. Low-temperature production processes and refrigerated storage promote the development of psychrophilic microorganisms; another threat is posed by high microbiological contamination of raw materials. To preserve the quality of food products, the most commonly used physicochemical methods include modified atmosphere packaging, membrane methods or ultrasound. Alternatively, biological methods can be used: bacteriophages and phage cocktails, bacteriocins, inactivation of plant tissue degradation enzymes, phytochemicals, edible coatings. Moreover, they can be used either individually to limit the growth of bacteria in the food environment, or in combination with other methods in order to achieve maximum effect. This article discusses the main biological methods of combating pathogenic bacteria most commonly found in the food environment. The purpose of this review was to consider existing biological methods for processing plant objects, as well as to identify the advantages and disadvantages of each method.

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Dormant phages communicate to control exit from lysogeny

Cited by 3 publications

References 51 publications

BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis

BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis

TheBacillusphage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components

Modern biological methods of processing plant raw materials used to increase its storage capacity

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