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

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).

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

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).

scholarly journals Transcriptional Phase Variation of a Type III Restriction-Modification System in Helicobacter pylori

2002 ◽  
Vol 184 (23) ◽  
pp. 6615-6623 ◽  
Author(s):  
Nicolette de Vries ◽  
Dirk Duinsbergen ◽  
Ernst J. Kuipers ◽  
Raymond G. J. Pot ◽  
Patricia Wiesenekker ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Phase Variation ◽  
Transcriptional Level ◽  
Length Variation ◽  
Phase Variable ◽  
Modification System ◽  
Type Iii ◽  
Restriction Modification System ◽  
H Pylori ◽  
Restriction Modification

ABSTRACT Phase variation is important in bacterial pathogenesis, since it generates antigenic variation for the evasion of immune responses and provides a strategy for quick adaptation to environmental changes. In this study, a Helicobacter pylori clone, designated MOD525, was identified that displayed phase-variable lacZ expression. The clone contained a transcriptional lacZ fusion in a putative type III DNA methyltransferase gene (mod, a homolog of the gene JHP1296 of strain J99), organized in an operon-like structure with a putative type III restriction endonuclease gene (res, a homolog of the gene JHP1297), located directly upstream of it. This putative type III restriction-modification system was common in H. pylori, as it was present in 15 out of 16 clinical isolates. Phase variation of the mod gene occurred at the transcriptional level both in clone MOD525 and in the parental H. pylori strain 1061. Further analysis showed that the res gene also displayed transcriptional phase variation and that it was cotranscribed with the mod gene. A homopolymeric cytosine tract (C tract) was present in the 5′ coding region of the res gene. Length variation of this C tract caused the res open reading frame (ORF) to shift in and out of frame, switching the res gene on and off at the translational level. Surprisingly, the presence of an intact res ORF was positively correlated with active transcription of the downstream mod gene. Moreover, the C tract was required for the occurrence of transcriptional phase variation. Our finding that translation and transcription are linked during phase variation through slipped-strand mispairing is new for H. pylori.

Phase variation in a type III restriction-modification system of Helicobacter pylori

2000 ◽  
Vol 118 (4) ◽  
pp. A736 ◽  
Author(s):  
Nicolette Vries de ◽  
Dirk Duinsbergen ◽  
Ernst J. Kuipers ◽  
Patricia Wiesenekker ◽  
Christina M. Vandenbroucke-Grauls ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Phase Variation ◽  
Modification System ◽  
Type Iii ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals Sequencing and Analysis of the Genome of Propionibacterium freudenreichii T82 Strain: Importance for Industry

Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 348 ◽  
Author(s):  
Kamil Piwowarek ◽  
Edyta Lipińska ◽  
Elżbieta Hać-Szymańczuk ◽  
Marek Kieliszek ◽  
Anna Maria Kot
Keyword(s):  
Gc Content ◽  
Propionibacterium Freudenreichii ◽  
Protein Coding ◽  
Modification System ◽  
Coding Sequences ◽  
Protein Coding Genes ◽  
Restriction Modification System ◽  
Number Of Genes ◽  
Rna Genes ◽  
Restriction Modification

The genome of Propionibacterium freudenreichii ssp. freudenreichii T82, which has a chromosome containing 2,585,340 nucleotides with 67.3% GC content (guanine-cytosine content), is described in this paper. The total number of genes is 2308, of which 2260 are protein-coding genes and 48 are RNA genes. According to the genome analysis and the obtained results, the T82 strain can produce various compounds such as propionic acid, trehalose, glycogen, and B group vitamins (e.g., B6, B9, and B12). From protein-coding sequences (CDSs), genes related to stress adaptation, biosynthesis, metabolism, transport, secretion, and defense machinery were detected. In the genome of the T82 strain, sequences corresponding to the CRISPR loci (Clustered Regularly Interspaced Short Palindromic Repeats), antibiotic resistance, and restriction–modification system were found.

Cloning the KpnI restriction-modification system in Escherichia coli

Gene ◽  
1991 ◽  
Vol 97 (1) ◽  
pp. 97-102 ◽  
Author(s):  
Alan W. Hammond ◽  
Gary F. Gerard ◽  
Deb K. Chatterjee
Keyword(s):  
Escherichia Coli ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI)

2010 ◽  
Vol 38 (9) ◽  
pp. 3019-3030 ◽  
Author(s):  
Feroz Khan ◽  
Yoshikazu Furuta ◽  
Mikihiko Kawai ◽  
Katarzyna H. Kaminska ◽  
Ken Ishikawa ◽  
...  
Keyword(s):  
Mobile Genetic Element ◽  
Genetic Element ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals Complete Genome Sequence of Brevibacterium linens SMQ-1335

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Alessandra G. de Melo ◽  
Simon J. Labrie ◽  
Jeannot Dumaresq ◽  
Richard J. Roberts ◽  
Denise M. Tremblay ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Open Reading Frames ◽  
Type I ◽  
Industrial Strain ◽  
Modification System ◽  
Brevibacterium Linens ◽  
Restriction Modification System ◽  
New Type ◽  
Restriction Modification ◽  
Reading Frames

Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.

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