Characterization of a T7-Like Lytic Bacteriophage (φSG-JL2) of Salmonella enterica Serovar Gallinarum Biovar Gallinarum

ABSTRACT φSG-JL2 is a newly discovered lytic bacteriophage infecting Salmonella enterica serovar Gallinarum biovar Gallinarum but is nonlytic to a rough vaccine strain of serovar Gallinarum biovar Gallinarum (SG-9R), S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Gallinarum biovar Pullorum. The φSG-JL2 genome is 38,815 bp in length (GC content, 50.9%; 230-bp-long direct terminal repeats), and 55 putative genes may be transcribed from the same strand. Functions were assigned to 30 genes based on high amino acid similarity to known proteins. Most of the expected proteins except tail fiber (31.9%) and the overall organization of the genomes were similar to those of yersiniophage φYeO3-12. φSG-JL2 could be classified as a new T7-like virus and represents the first serovar Gallinarum biovar Gallinarum phage genome to be sequenced. On the basis of intraspecific ratios of nonsynonymous to synonymous nucleotide changes (Pi[a]/Pi[s]), gene 2 encoding the host RNA polymerase inhibitor displayed Darwinian positive selection. Pretreatment of chickens with φSG-JL2 before intratracheal challenge with wild-type serovar Gallinarum biovar Gallinarum protected most birds from fowl typhoid. Therefore, φSG-JL2 may be useful for the differentiation of serovar Gallinarum biovar Gallinarum from other Salmonella serotypes, prophylactic application in fowl typhoid control, and understanding of the vertical evolution of T7-like viruses.

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

10.1101/2020.10.05.325894 ◽

2020 ◽

Author(s):

Julie Zaworski ◽

Colleen McClung ◽

Cristian Ruse ◽

Peter R. Weigele ◽

Roger W. Hendrix ◽

...

Keyword(s):

Salmonella Enterica ◽

Cell Envelope ◽

Gc Content ◽

Phase Variation ◽

Trna Genes ◽

Modification System ◽

Restriction Modification System ◽

Serovar Typhimurium ◽

Definition Of ◽

Restriction Modification

ABSTRACTBacteriophage L, a P22-like phage of Salmonella enterica sv Typhimurium LT2, was important for definition of mosaic organization of the lambdoid phage family and for characterization of restriction-modification systems of Salmonella. We report the complete genome sequences of bacteriophage L cI−40 13−am43 and L cII−101; the deduced sequence of wildtype L is 40,633 bp long with a 47.5% GC content. We compare this sequence with those of P22 and ST64T, and predict 71 Coding Sequences, 2 tRNA genes and 14 intergenic rho-independent transcription terminators. The overall genome organization of L agrees with earlier genetic and physical evidence; for example, no secondary immunity region (ImmI: ant, arc) or genes for superinfection exclusion (sieA and sieB) are present. Proteomic analysis confirmed identification of virion proteins, along with low levels of assembly intermediates and host cell envelope proteins. The genome of L is 99.9% identical at the nucleotide level to that reported for phage ST64T, despite isolation on different continents ~35 years apart. DNA modification by the epigenetic regulator Dam is generally incomplete. Dam modification is also selectively missing in one location, corresponding to the P22 phase-variation-sensitive promoter region of the serotype-converting gtrABC operon. The number of sites for SenLTIII (StySA) action may account for stronger restriction of L (13 sites) than of P22 (3 sites).

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Transposition of the Heat-Stable Toxin astA Gene into a Gifsy-2-Related Prophage of Salmonella enterica Serovar Abortusovis

Journal of Bacteriology ◽

10.1128/jb.186.14.4568-4574.2004 ◽

2004 ◽

Vol 186 (14) ◽

pp. 4568-4574 ◽

Cited By ~ 18

Author(s):

Donatella Bacciu ◽

Giovanni Falchi ◽

Alessandra Spazziani ◽

Lionello Bossi ◽

Gavino Marogna ◽

...

Keyword(s):

Salmonella Enterica ◽

Insertion Sequence ◽

Virulence Genes ◽

Systemic Infection ◽

Large Deletion ◽

Tail Fiber ◽

Heat Stable ◽

Serovar Typhimurium ◽

Genes Encoding ◽

Sequence Elements

ABSTRACT The horizontal transfer and acquisition of virulence genes via mobile genetic elements have been a major driving force in the evolution of Salmonella pathogenicity. Serovars of Salmonella enterica carry variable assortments of phage-encoded virulence genes, suggesting that temperate phages play a pivotal role in this process. Epidemic isolates of S. enterica serovar Typhimurium are consistently lysogenic for two lambdoid phages, Gifsy-1 and Gifsy-2, carrying known virulence genes. Other serovars of S. enterica, including serovars Dublin, Gallinarum, Enteritidis, and Hadar, carry distinct prophages with similarity to the Gifsy phages. In this study, we analyzed Gifsy-related loci from S. enterica serovar Abortusovis, a pathogen associated exclusively with ovine infection. A cryptic prophage, closely related to serovar Typhimurium phage Gifsy-2, was identified. This element, named Gifsy-2AO, was shown to contribute to serovar Abortusovis systemic infection in lambs. Sequence analysis of the prophage b region showed a large deletion which covers genes encoding phage tail fiber proteins and putative virulence factors, including type III secreted effector protein SseI (GtgB, SrfH). This deletion was identified in most of the serovar Abortusovis isolates tested and might be dependent on the replicative transposition of an adjacent insertion sequence, IS1414, previously identified in pathogenic Escherichia coli strains. IS1414 encodes heat-stable toxin EAST1 (astA) and showed multiple genomic copies in isolates of serovar Abortusovis. To our knowledge, this is the first evidence of intergeneric transfer of virulence genes via insertion sequence elements in Salmonella. The acquisition of IS1414 (EAST1) and its frequent transposition within the chromosome might improve the fitness of serovar Abortusovis within its narrow ecological niche.

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Genomic Structure of the Salmonella enterica Serovar Typhimurium DT 64 Bacteriophage ST64T: Evidence for Modular Genetic Architecture

Journal of Bacteriology ◽

10.1128/jb.185.11.3473-3475.2003 ◽

2003 ◽

Vol 185 (11) ◽

pp. 3473-3475 ◽

Cited By ~ 34

Author(s):

Princess T. Mmolawa ◽

Horst Schmieger ◽

Carly P. Tucker ◽

Michael W. Heuzenroeder

Keyword(s):

Salmonella Enterica ◽

Salmonella Enterica Serovar Typhimurium ◽

Genomic Sequence ◽

Sequence Similarity ◽

Genomic Structure ◽

Gc Content ◽

Complete Sequence ◽

Serovar Typhimurium ◽

Immunity Genes ◽

High Degree

ABSTRACT The complete sequence of the double-stranded DNA genome of a serotype-converting temperate bacteriophage, ST64T, was determined. The 40,679-bp genomic sequence of ST64T has an overall GC content of 47.5% and was reminiscent of a number of lambdoid phages, in particular, P22. Inferred proteins of ST64T which exhibited a high degree of sequence similarity to P22 proteins (>90%) included the functional serotype conversion cassette, integrase, excisionase, Abc1, Abc2, early antitermination (gp24), NinD, NinH, NinZ, packaging (gp3 and gp2), head (with the exception of gp26, gp7, gp20, and gp16), and tail proteins. The putative immunity genes were highly related to those of Salmonella enterica serotype Typhimurium phage L, whereas the lysis genes were almost identical to those of S. enterica serovar Typhimurium PS3.

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

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa037 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Julie Zaworski ◽

Colleen McClung ◽

Cristian Ruse ◽

Peter R Weigele ◽

Roger W Hendrix ◽

...

Keyword(s):

Salmonella Enterica ◽

Cell Envelope ◽

Gc Content ◽

Phase Variation ◽

Trna Genes ◽

Modification System ◽

Restriction Modification System ◽

Serovar Typhimurium ◽

Definition Of ◽

Restriction Modification

Abstract Bacteriophage L, a P22-like phage of Salmonella enterica sv Typhimurium LT2, was important for definition of mosaic organization of the lambdoid phage family and for characterization of restriction-modification systems of Salmonella. We report the complete genome sequences of bacteriophage L cI–40 13–am43 and L cII–101; the deduced sequence of wildtype L is 40,633 bp long with a 47.5% GC content. We compare this sequence with those of P22 and ST64T, and predict 72 Coding Sequences, 2 tRNA genes and 14 intergenic rho-independent transcription terminators. The overall genome organization of L agrees with earlier genetic and physical evidence; for example, no secondary immunity region (immI: ant, arc) or known genes for superinfection exclusion (sieA and sieB) are present. Proteomic analysis confirmed identification of virion proteins, along with low levels of assembly intermediates and host cell envelope proteins. The genome of L is 99.9% identical at the nucleotide level to that reported for phage ST64T, despite isolation on different continents ∼35 years apart. DNA modification by the epigenetic regulator Dam is generally incomplete. Dam modification is also selectively missing in one location, corresponding to the P22 phase-variation-sensitive promoter region of the serotype-converting gtrABC operon. The number of sites for SenLTIII (StySA) action may account for stronger restriction of L (13 sites) than of P22 (3 sites).

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Complete Genome Sequence of Salmonella enterica Lytic Bacteriophage LPST10, Isolated in China

Genome Announcements ◽

10.1128/genomea.00427-17 ◽

2017 ◽

Vol 5 (35) ◽

Cited By ~ 1

Author(s):

Xingxing Dong ◽

Chenxi Huang ◽

Mohamed Khairy Morsy ◽

Zhi Li ◽

Yang Zhou ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Salmonella Enterica ◽

Complete Genome ◽

Lytic Activity ◽

Lytic Bacteriophage ◽

Coding Sequences ◽

Content Type ◽

Double Stranded Dna ◽

Serovar Typhimurium

ABSTRACT Bacteriophage LPST10 was isolated from Wuhan, China. Lytic activity was demonstrated against multiple Salmonella enterica serovars, including Salmonella enterica serovar Typhimurium strains. This bacteriophage has a 47,657-bp double-stranded DNA genome encoding 87 putative coding sequences.

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Crystal Structure of the Salmonella enterica Serovar Typhimurium Virulence Factor SrfJ, a Glycoside Hydrolase Family Enzyme

Journal of Bacteriology ◽

10.1128/jb.00641-09 ◽

2009 ◽

Vol 191 (21) ◽

pp. 6550-6554 ◽

Cited By ~ 9

Author(s):

Yeon-Gil Kim ◽

Jin-Hong Kim ◽

Kyung-Jin Kim

Keyword(s):

Crystal Structure ◽

Active Site ◽

Salmonella Enterica ◽

Glycoside Hydrolase ◽

Catalytic Domain ◽

Membrane Lipids ◽

Glycoside Hydrolase Family ◽

Secretion Systems ◽

High Amino Acid ◽

Serovar Typhimurium

ABSTRACT To cause infection, Salmonella enterica serovar Typhimurium uses type III secretion systems, which are encoded on two Salmonella pathogenicity islands, SPI-1 and SPI-2, the latter of which is thought to play a crucial role in bacterial proliferation in Salmonella-containing vacuoles (SCVs) after invading cells. S. Typhimurium SrfJ, located outside SPI-2, is also known to be involved in Salmonella pathogenicity and has high amino acid sequence homology with human lysosomal glucosylceramidase (GlcCerase). We present the first crystal structure of SrfJ at a resolution of 1.8 Å. The overall fold of SrfJ shares high structure similarities with that of human GlcCerase, comprising two distinctive domains: a (β/α)8-barrel catalytic domain and a β-sandwich domain. As in human GlcCerase, the pocket-shaped active site of SrfJ is located on the C-terminal side of the barrel, and two conserved glutamic acid residues are used for the enzyme catalysis. Moreover, a glycerol-bound form of SrfJ reveals that the glucose ring moiety of the substrate might similarly bind to the enzyme as to human GlcCerase, suggesting that SrfJ might function as a glycoside hydrolase. Although some structural differences are observed between SrfJ and human GlcCerase in the substrate entrance of the active site, we speculate that, based on the high structural similarities to human GlcCerase in the overall fold and the active-site environment, SrfJ might have a GlcCerase activity and use the activity to enhance Salmonella virulence by modifying SCV membrane lipids.

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