Generation of new DNA binding specificity by truncation of the type IC EcoDXXI hsdS gene.

MacWilliams, Maria P.; Bickle, Thomas A.

doi:10.1002/j.1460-2075.1996.tb00855.x

Cited by 29 publications

(42 citation statements)

References 28 publications

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“…Analyses of truncated polypeptides implicate the three conserved regions of HsdS (Fig. 2a) in binding HsdM (109). As predicted, a deletion within the central conserved region of an HsdS subunit prevents binding to HsdM (189 (189) suggested that the mutations identify regions of importance for the assembly of the R-M complex, though not necessarily sites of interaction between HsdS and HsdR.…”

Section: Specificity Subunit-hsdsmentioning

confidence: 68%

“…Two truncated polypeptides can substitute for one normal HsdS subunit if the subunits retain their ability to interact with HsdM. Active complexes, i.e., those in which HsdS retains the ability to bind HsdM, are recognized by their new specificities (1,109,113). Analyses of truncated polypeptides implicate the three conserved regions of HsdS (Fig.…”

Section: Specificity Subunit-hsdsmentioning

confidence: 99%

“…In contrast, all the sequence data for HsdS subunits, whether plasmid or chromosomal in origin, indicate a single family of enzymes with differences in HsdS sequences found principally within the TRDs. The conserved regions of HsdS subunits include those sequences that interact with HsdM, subunits that are well conserved within a family (62,86,109,189). Schouler et al (153) note that, irrespective of the family designation, the C-terminal parts of the HsdM subunits of the lactococcal systems have a common sequence that could identify a region involved in the association of HsdM with HsdS.…”

Section: Detection Distribution and Diversitymentioning

confidence: 99%

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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-hsdsmentioning

confidence: 68%

Section: Specificity Subunit-hsdsmentioning

confidence: 99%

Section: Detection Distribution and Diversitymentioning

confidence: 99%

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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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“…This hypothesis is supported by the fact that artificially truncated HsdS forms, composed only of the N-or C-terminal half of the native polypeptide, can function as a recognition subunit and recognize a quasipalindromic target sequence (1,19,31). For example, the methyltransferase EcoDXXI recognizes the sequence 5Ј-TCA(N 7 )RTTC-3Ј (29). The expression of a truncated hsdS EcoDXXI gene, encoding only the N-terminal TRD and the central CD, generated an enzyme that recognized the interrupted palindrome 5Ј-TCA (N 8 )TGA-3Ј.…”

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confidence: 99%

Deletion of One Nucleotide within the Homonucleotide Tract Present in the hsdS Gene Alters the DNA Sequence Specificity of Type I Restriction-Modification System NgoAV

2011

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As a result of a frameshift mutation, the hsdS locus of the NgoAV type IC restriction and modification (RM) system comprises two genes, hsdS NgoAV1 and hsdS NgoAV2 . The specificity subunit, HsdS NgoAV , the product of the hsdS NgoAV1 gene, is a naturally truncated form of an archetypal specificity subunit (208 N-terminal amino acids instead of 410). The presence of a homonucleotide tract of seven guanines (poly[G]) at the 3 end of the hsdS NgoAV1 gene makes the NgoAV system a strong candidate for phase variation, i.e., stochastic addition or reduction in the guanine number. We have constructed mutants with 6 guanines instead of 7 and demonstrated that the deletion of a single nucleotide within the 3 end of the hsdS NgoAV1 gene restored the fusion between the hsdS NgoAV1 and hsdS NgoAV2 genes. We have demonstrated that such a contraction of the homonucleotide tract may occur in vivo: in a Neisseria gonorrhoeae population, a minor subpopulation of cells appeared to have only 6 guanines at the 3 end of the hsdS NgoAV1 gene. Escherichia coli cells carrying the fused gene and expressing the NgoAV⌬ RM system were able to restrict phage at a level comparable to that for the wild-type NgoAV system. NgoAV recognizes the quasipalindromic interrupted sequence 5-GCA(N 8 )TGC-3 and methylates both strands. NgoAV⌬ recognizes DNA sequences 5-GCA(N 7 )GTCA-3 and 5-GCA(N 7 )CTCA-3, although the latter sequence is methylated only on the complementary strand within the 5-CTCA-3 region of the second recognition target sequence.Restriction and modification (RM) systems are composed of two enzymatic activities that recognize the same specific DNA sequence. The restriction endonuclease cleaves the DNA, unless the recognized sequence is methylated by the modification methylase. RM systems are found in a wide variety of bacteria and archaea, and their main role is to protect cells from bacteriophage infections or the uptake of undesirable foreign DNA (7, 33). The importance of RM systems in host protection is difficult to estimate in the case of bacteria for which no phages or no phage detection methods are known and that encode several RM systems, such as Neisseria gonorrhoeae (43,34). Recently, a new role for RM systems as factors regulating other gene expression was proposed for type III RM systems (16,42).Type I DNA RM systems are multimeric enzyme complexes that recognize and methylate an adenine residue within a specific DNA sequence. The cleavage of double-stranded DNA takes place at an undefined region, several hundreds to thousands of base pairs away from the recognized sequence. The archetypal type I methyltransferases are encoded by two genes, hsdS and hsdM, and are composed of one HsdS subunit and two HsdM subunits. The HsdS subunit is responsible for recognition and binding of DNA by the enzymatic complex and for the interaction of the other subunits of the enzyme. The

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“…In hindsight, perhaps one interesting comment from Argos was the idea of a "pseudodimer," based on the idea of repeating domains. Described later in this review is the existence of such a pseudodimer consisting of a repeating half-HsdS subunit (1,54). At the same time as Argos published his paper on repeating domains within the HsdS subunit of type I R-M enzymes, Fuller-Pace et al (23) described a rearrangement of DNA specificity based on recombination between conserved regions within hsdS that "swapped" DNA specificities by swapping domains within the HsdS subunit.…”

Section: The Central Conserved Region Of Hsdsmentioning

confidence: 99%

EcoR124I: from Plasmid-Encoded Restriction-Modification System to Nanodevice

Youell

Firman

2008

Microbiol Mol Biol Rev

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SUMMARY Plasmid R124 was first described in 1972 as being a new member of incompatibility group IncFIV, yet early physical investigations of plasmid DNA showed that this type of classification was more complex than first imagined. Throughout the history of the study of this plasmid, there have been many unexpected observations. Therefore, in this review, we describe the history of our understanding of this plasmid and the type I restriction-modification (R-M) system that it encodes, which will allow an opportunity to correct errors, or misunderstandings, that have arisen in the literature. We also describe the characterization of the R-M enzyme EcoR124I and describe the unusual properties of both type I R-M enzymes and EcoR124I in particular. As we approached the 21st century, we began to see the potential of the EcoR124I R-M enzyme as a useful molecular motor, and this leads to a description of recent work that has shown that the R-M enzyme can be used as a nanoactuator. Therefore, this is a history that takes us from a plasmid isolated from (presumably) an infected source to the potential use of the plasmid-encoded R-M enzyme in bionanotechnology.

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Generation of new DNA binding specificity by truncation of the type IC EcoDXXI hsdS gene.

Cited by 29 publications

References 28 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)

Deletion of One Nucleotide within the Homonucleotide Tract Present in the hsdS Gene Alters the DNA Sequence Specificity of Type I Restriction-Modification System NgoAV

EcoR124I: from Plasmid-Encoded Restriction-Modification System to Nanodevice

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