The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry

Thorpe, Peter H.; Ternent, Diane; Murray, Noreen E.

doi:10.1093/nar/25.9.1694

Cited by 23 publications

(19 citation statements)

References 52 publications

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“…This similarity correlates with a similarity of target sequence evident in the complementary strands (Fig. 3b), a finding consistent with the amino-and carboxy- terminal TRDs being inversely oriented when they bind their target sequences (179). (iii) Permutations of the hsdS gene of EcoAI have been made in which HsdS remained active when a sequence from the N-terminal conserved region was transferred to the carboxy terminus ( Fig.…”

Section: Specificity Subunit-hsdssupporting

confidence: 74%

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Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Murray

2000

Microbiol Mol Biol Rev

406

481

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SUMMARY Restriction enzymes are well known as reagents widely used by molecular biologists for genetic manipulation and analysis, but these reagents represent only one class (type II) of a wider range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the provenance of the DNA on the basis of specific modifications to their target sequence. Type I restriction and modification (R-M) systems are complex; a single multifunctional enzyme can respond to the modification state of its target sequence with the alternative activities of modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves like a molecular motor, translocating vast stretches of DNA towards itself before eventually breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which will emphasize those aspects that give insights into more general problems of molecular and microbial biology. Current molecular experiments explore target recognition, intramolecular communication, and enzyme activities, including DNA translocation. Type I R-M systems are notable for their ability to evolve new specificities, even in laboratory cultures. This observation raises the important question of how bacteria protect their chromosomes from destruction by newly acquired restriction specifities. Recent experiments demonstrate proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory.

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Section: Specificity Subunit-hsdssupporting

confidence: 74%

“…The most strongly modified residue lies within the second of the proposed loops (166). Second, the three residues identified by chemical modification of EcoR124I are conserved in the amino-terminal TRD of the type IB system, StySKI (179), which recognizes the same target sequence as the carboxy-terminal TRD of EcoR124I.…”

Section: Specificity Subunit-hsdsmentioning

confidence: 99%

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Murray

2000

Microbiol Mol Biol Rev

406

481

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“…K297 is the most strongly modified residue and it lies within the second of the two proposed loops (Sturrock and Dryden, 1997). The three lysine residues identified by chemical modification are conserved in the amino TRD of Sty SKI (Thorpe et al ., 1997), which recognizes the same target sequence as the carboxy‐TRD of Eco R124I. The circumstantial evidence that is available therefore is consistent with the present data that implicate interaction of the putative loop‐β‐strand‐loop with the target sequence.…”

Section: Discussionmentioning

confidence: 99%

Localization of a protein–DNA interface by random mutagenesis

O’Neill

Dryden

Murray

1998

EMBO J

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The type I restriction and modification enzymes do not possess obvious DNA-binding motifs within their target recognition domains (TRDs) of 150-180 amino acids. To identify residues involved in DNA recognition, changes were made in the amino-TRD of EcoKI by random mutagenesis. Most of the 101 substitutions affecting 79 residues had no effect on the phenotype. Changes at only seven positions caused the loss of restriction and modification activities. The seven residues identified by mutation are not randomly distributed throughout the primary sequence of the TRD: five are within the interval between residues 80 and 110. Sequence analyses have led to the suggestion that the TRDs of type I restriction enzymes include a tertiary structure similar to the TRD of the HhaI methyltransferase, and to a model for a DNA-protein interface in EcoKI. In this model, the residues within the interval identified by the five mutations are close to the protein-DNA interface. Three additional residues close to the DNA in the model were changed; each substitution impaired both activities. Proteins from twelve mutants were purified: six from mutants with partial or wildtype activity and six from mutants lacking activity. There is a strong correlation between phenotype and DNA-binding affinity, as determined by fluorescence anisotropy.

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“…Four Salmonella type 1 restriction enzymes (StySBI, StySPI, StySKI, and StySBLI) have been identified in S. enterica serovar Typhimurium, S. enterica serovar Potsdam, S. enterica serovar Kaduna, and S. enterica serovar Blegdam, respectively (46,75,76). The StySBI and StySBLI sites in the SG-JL2 genome occur only once and three times, respectively, and are distant from gene 0.3, at positions 23718 and 10375, respectively.…”

Section: Vol 74 2008 Characterization Of a T7-like Virus (Sg-jl2) 6973mentioning

confidence: 99%

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

Kwon

Cho²,

Kim

et al. 2008

Appl Environ Microbiol

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SG-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 SG-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 YeO3-12. SG-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 SG-JL2 before intratracheal challenge with wild-type serovar Gallinarum biovar Gallinarum protected most birds from fowl typhoid. Therefore, SG-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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The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry

Cited by 23 publications

References 52 publications

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Localization of a protein–DNA interface by random mutagenesis

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

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