Genome analysis of <i>Salmonella enterica</i> serovar Typhimurium bacteriophage L, indicator for StySA (StyLT2III) restriction-modification system action

Zaworski, Julie; McClung, Colleen; Ruse, Cristian; Weigele, Peter; Hendrix, Roger W.; Ko, Ching-Chung; Edgar, Robert H.; Hatfull, Graham F.; Casjens, Sherwood; Raleigh, Elisabeth A.

doi:10.1093/g3journal/jkaa037

Cited by 7 publications

(7 citation statements)

References 79 publications

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“…casei system [ 32 ], and is also apparent with StySA. Phage L has 13 sites [ 83 ] and yields 100-fold restriction, while P22, with 3 sites, was so poorly restricted (~2 fold) that we did not collect EOP data systematically. Thus, the much or all of the unmodified target must be available for scanning inside the cell.…”

Section: Discussionmentioning

confidence: 99%

“…R + , R - : restriction phenotype, measured by reduction in plaque formation of bacteriophage L when grown on a StySA M - host [ 83 ].…”

Section: Methodsmentioning

confidence: 99%

“…Bacteriophage L, with 13 sites for StySA [ 83 ] was used to test for StySA restriction, following the practice of the Colson and Ryu laboratories [ 44 , 92 ]. Bacterial strains were grown in RB with antibiotic overnight at 37°C with agitation.…”

Section: Methodsmentioning

confidence: 99%

“…After a first QC step to assess the quality of the reads, they were trimmed using TrimGalore (Version 0.4.3) with parameters: -q 20 -s 3 -e 0.1 –length 20 and then a second QC steps was performed to verify the read quality after trimming. The trimmed reads were mapped with bowtie2 (with default parameters except–fr for upstream/downstream mate orientations) to the ER3625 genome (NCBI CP067091-CP067092 and [ 83 , 99 ]. The alignment was then used to count the number of fragments mapped to CDS and rRNA features using in parallel Featurecounts [ 99 ] (parameters: -s stranded (reverse)) and htseq (Version 0.9.1) with parameters:--mode Union–stranded reverse–minaqual 10 --idattr locus_tag–nonunique no.…”

Section: Methodsmentioning

confidence: 99%

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Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

et al. 2022

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Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX (BacteRiophage EXclusion) systems. These RM-like activities employ host protection by DNA modification, but immediate replication arrest occurs without evident of nuclease action on unmodified phage DNA. Here we show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a variant BREX system. A laboratory strain disabled for both the restriction and methylation activity of StySA nevertheless has wild type sequence in brxX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations (μ) in their C-terminal domains. We further investigate this system in situ, replacing the mutated pglZμ and brxCμ genes with the WT counterpart. PglZ-WT supports methylation in the presence of either BrxCμ or BrxC-WT but not in the presence of a deletion/insertion allele, ΔbrxC::cat. Restriction requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. These results suggests that while BrxC, PglZ and BrxX are principal components of the BREX modification activity, BrxL is required for restriction only. Furthermore, we show that a partial disruption of brxL disrupts transcription globally.

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Section: Discussionmentioning

confidence: 99%

“…R + , R - : restriction phenotype, measured by reduction in plaque formation of bacteriophage L when grown on a StySA M - host [ 83 ].…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

et al. 2022

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“…Genome sequences are available for LT2 ( McClelland et al 2001 ) and LT7 ( Zaworski et al 2021 ), but none within this hybrid lineage.…”

Section: Introductionmentioning

confidence: 99%

Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium

Zaworski

Dagva

Kingston

et al. 2021

G3 Genes|Genomes|Genetics

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The Salmonella research community has used strains and bacteriophages over decades, exchanging useful new isolates among laboratories for study of cell surface antigens, metabolic pathways and restriction-modification studies. Here we present the sequences of two laboratory Salmonella strains (STK005, an isolate of LB5000; and its descendant ER3625). In the ancestry of LB5000, segments of ∼15 and ∼42 kb were introduced from Salmonella enterica sv Abony 103 into Salmonella enterica sv Typhimurium LT2, forming strain SD14; this strain is thus a hybrid of S. enterica isolates. Strains in the SD14 lineage were used to define flagellar antigens from the 1950s to the 1970s, and to define three restriction-modification systems from the 1960s to the 1980s. LB5000 was also used as host in phage typing systems used by epidemiologists. In the age of cheaper and easier sequencing, this resource will provide access to the sequence that underlies the extensive literature.

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Genomic analysis of Anderson typing phages of Salmonella Typhimrium: towards understanding the basis of bacteria-phage interaction

Mohammed

Casjens

Millard

et al. 2023

Sci Rep

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The Anderson phage typing scheme has been successfully used worldwide for epidemiological surveillance of Salmonella enterica serovar Typhimurium. Although the scheme is being replaced by whole genome sequence subtyping methods, it can provide a valuable model system for study of phage-host interaction. The phage typing scheme distinguishes more than 300 definitive types of Salmonella Typhimurium based on their patterns of lysis to a unique collection of 30 specific Salmonella phages. In this study, we sequenced the genomes of 28 Anderson typing phages of Salmonella Typhimurium to begin to characterize the genetic determinants that are responsible for the differences in these phage type profiles. Genomic analysis of typing phages reveals that Anderson phages can be classified into three different groups, the P22-like, ES18-like and SETP3-like clusters. Most Anderson phages are short tailed P22-like viruses (genus Lederbergvirus); but phages STMP8 and STMP18 are very closely related to the lambdoid long tailed phage ES18, and phages STMP12 and STMP13 are related to the long noncontractile tailed, virulent phage SETP3. Most of these typing phages have complex genome relationships, but interestingly, two phage pairs STMP5 and STMP16 as well as STMP12 and STMP13 differ by a single nucleotide. The former affects a P22-like protein involved in DNA passage through the periplasm during its injection, and the latter affects a gene whose function is unknown. Using the Anderson phage typing scheme would provide insights into phage biology and the development of phage therapy for the treatment of antibiotic resistant bacterial infections.

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Genome analysis of Salmonella enterica serovar Typhimurium bacteriophage L, indicator for StySA (StyLT2III) restriction-modification system action

Cited by 7 publications

References 79 publications

Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium

Genomic analysis of Anderson typing phages of Salmonella Typhimrium: towards understanding the basis of bacteria-phage interaction

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