Combinational variation of restriction modification specificities in Lactococcus lactis

Schouler, Catherine; Gautier, Michel; Sd, Ehrlich; Mc, Chopin

doi:10.1046/j.1365-2958.1998.00787.x

Cited by 87 publications

(83 citation statements)

References 77 publications

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“…In Helicobacter, for example, allelic genes specify putative type I R-M systems for which the predicted HsdS subunits seem likely to confer different specificities (11). Similar conclusions can be drawn for Lactococcus lactis (45). However, in this case the genetic experiments add a novel complication to the family status.…”

Section: The Genetic Concept Of Familiesmentioning

confidence: 66%

Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems

Titheradge

King²,

Ryu³

et al. 2001

Nucleic Acids Research

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Current genetic and molecular evidence places all the known type I restriction and modification systems of Escherichia coli and Salmonella enterica into one of four discrete families: type IA, IB, IC or ID. StySBLI is the founder member of the ID family. Similarities of coding sequences have identified restriction systems in E.coli and Klebsiella pneumoniae as probable members of the type ID family. We present complementation tests that confirm the allocation of EcoR9I and KpnAI to the ID family. An alignment of the amino acid sequences of the HsdS subunits of StySBLI and EcoR9I identify two variable regions, each predicted to be a target recognition domain (TRD). Consistent with two TRDs, StySBLI was shown to recognise a bipartite target sequence, but one in which the adenine residues that are the substrates for methylation are separated by only 6 bp. Implications of family relationships are discussed and evidence is presented that extends the family affiliations identified in enteric bacteria to a wide range of other genera.

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Section: The Genetic Concept Of Familiesmentioning

confidence: 66%

Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems

Titheradge

King²,

Ryu³

et al. 2001

Nucleic Acids Research

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“…However, functional type I systems have been described in a wide variety of bacterial taxa, such as Helicobacter pylori (Kong et al, 2000), Neisseria gonorrhoeae (Piekarowicz et al, 2001), Lactococcus lactis (Schouler et al, 1998) and Mycoplasma pulmonis (Dybvig & Yu, 1994). With the genomes of ever more bacteria being sequenced, it is likely that additional type I R-M systems will be identified.…”

Section: Introductionmentioning

confidence: 99%

Diversity within the Campylobacter jejuni type I restriction–modification loci

et al. 2005

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The type I restriction–modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helicobacter pylori has three type I systems; however, no evidence was found that C. jejuni strains contain multiple type I systems, although hsd loci are present in at least two different chromosomal locations. Also, unlike H. pylori, intervening ORFs are present, in some strains, between hsdR and hsdS and between hsdS and hsdM. No definitive function can be ascribed to these ORFs, designated here as rloA–H (R-linked ORF) and mloA–B (M-linked ORF). Based on parsimony analysis of amino acid sequences to assess character relatedness, the C. jejuni type I R–M systems are assigned to one of three families: ‘IAB’, ‘IC’ or ‘IF’. This study confirms that HsdM proteins within a family are highly conserved but share little homology with HsdM proteins from other families. The ‘IC’ hsd loci are >99 % identical at the nucleotide level, as are the ‘IF’ hsd loci. Additionally, whereas the nucleotide sequences of the ‘IAB’ hsdR and hsdM genes show a high degree of similarity, the nucleotide sequences of the ‘IAB’ hsdS and rlo genes vary considerably. This diversity suggests that recombination between ‘IAB’ hsd loci would lead not only to new hsdS alleles but also to the exchange of rlo genes; five C. jejuni hsd loci are presumably the result of such recombination. The importance of these findings with regard to the evolution of C. jejuni type I R–M systems is discussed.

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“…Spot 629 was identified as Type I restriction-modification system, M subunit, which protects a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site-specific modification. The R-M system is a complex containing three polyeptides as M, S and R [34]. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a DNA recognition sequence.…”

Section: Resultsmentioning

confidence: 99%

Comparison of Protein Expression Profiles of Novel Halomonas smyrnensis AAD6T and Halomonas salina DSMZ 5928T

Dilgimen¹,

Arğa²,

Erdmann³

et al. 2014

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In this work, the protein pattern of novel Halomonas smyrnensis AAD6 T was compared to that of Halomonas salina DSMZ5928 T , which is the closest species on the basis of 16S rRNA sequence, to understand how AAD6 T differs from type strains. Using high resolution NEPHEGE technique, the whole cell protein composition patterns of both Halomonas salina DSMZ5928 T and H. smyrnensis AAD6 T were mapped. The expressed proteins of the two microorganisms were mostly located at the acidic side of the gels, at molecular weight values of 60 to 17 kDa, and at isoelectric points 3.8 to 6.0, where they share a significant number of common protein spots. Identification and characterization of protein spots via whole genome sequencing data indicated that these two microorganisms used similar pathways, especially TCA cycle, for their survival; in other words, for their energy requirements. On the other hand, the protein expression differences in AAD6 T and H. salina DSMZ 5928 T showed that they prefer different metabolic pathways for lipid biosynthesis and in adaptation to extreme environments. Thus, we suggested that phylogenetic dissimilarities between these microorganisms could be related to the protein expression differences; in other words, metabolic flux differences in AAD6 T and H. salina DSMZ 5928 T . This is the first study to explain the dissimilarities of phenotypic characters and DNA-DNA hybridization between type strain and novel strain AAD6 T by using protein expression differences.

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Combinational variation of restriction modification specificities in Lactococcus lactis

Cited by 87 publications

References 77 publications

Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems

Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems

Diversity within the Campylobacter jejuni type I restriction–modification loci

Comparison of Protein Expression Profiles of Novel <i>Halomonas smyrnensis</i> AAD6<sup>T</sup> and <i>Halomonas salina</i> DSMZ 5928<sup>T</sup>

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Combinational variation of restriction modification specificities in Lactococcus lactis

Cited by 87 publications

References 77 publications

Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems

Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems

Diversity within the Campylobacter jejuni type I restriction–modification loci

Comparison of Protein Expression Profiles of Novel &lt;i&gt;Halomonas smyrnensis&lt;/i&gt; AAD6&lt;sup&gt;T&lt;/sup&gt; and &lt;i&gt;Halomonas salina&lt;/i&gt; DSMZ 5928&lt;sup&gt;T&lt;/sup&gt;

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Comparison of Protein Expression Profiles of Novel <i>Halomonas smyrnensis</i> AAD6<sup>T</sup> and <i>Halomonas salina</i> DSMZ 5928<sup>T</sup>