Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria

Abstract

isolates of Escherichia coli for DNA sequences homologous to those encoding each of two unrelated type I restriction and modification systems (EcoK and EcoA). Both K-and A-related hsd genes were identified, but never both in the same strain. S. typhimurium encodes three restriction and modification systems, but its DNA hybridized only to the K-specific probe which we know to identify the StySB system. No homology to either probe was detected in the majority of E. coli strains, but in C. freundii, we identified homology to the A-specific probe. We cloned this region of the C. freundii genome and showed that it encoded a functional, A-related restriction system whose specificity differs from those of known type I enzymes. Sequences immediately flanking the hsd K genes of E. coli K-12 and the hsd A genes of E. coli I1T-were shown to be homologous, indicating similar or even identical positions in their respective chromosomes. E. coli C has no known restriction system, and the organization of its chromosome is consistent with deletion of the three hsd genes and their neighbor, mcrB.The fundamental attribute of a restriction endonuclease is its ability to recognize and selectively attack foreign DNA. This DNA is usually identified by the absence of a sequencespecific modification (methylation). Although modification is always sequence specific, restriction endonucleases do not necessarily cut within the DNA target sequence identified by methylation. Most enzymes classified as type II do, while others, classified as either type I or III, do not (for reviews, see references 6 and 43).This paper is concerned with type I restriction systems. These, in every way, are the most complex; they comprise three subunits, have complex cofactor requirements, and cut DNA nonspecifically some thousands of base pairs from the target sequence for modification. The genes encoding these restriction endonucleases are designated hsd for host specificity of DNA. The specificity polypeptide, encoded by hsdS, associates with that encoded by hsdM to form a modification methylase and with those encoded by hsdM and hsdR to produce a restriction endonuclease.It is generally accepted that restriction endonucleases function to prevent the acquisition and expression of foreign DNA (2). One consequence would be a degree of protection against infection by bacteriophages, an advantageous feature for the initial establishment of populations of bacteria in new habitats (25) Two commonly used laboratory strains, Escherichia coli K-12 and E. coli B, each have a single, chromosomally encoded, type I system, while E. coli 15T-has both a chromosomally encoded type I system, designated A, and a plasmid-encoded type III system, designated P15 (4). Plasmids encoding restriction systems represeptative of all three types have been isolated from E. coli strains, but to date the chromosomally encoded systems are all type I. No E. coli strain has been shown to have more than one chromosomally encoded restriction system, but the chromosomal genes of Salmonella typhim...

Diversity within the Campylobacter jejuni type I restriction–modification loci

“…The hsd loci in most Salmonella and E. coli strains are located in the same relative chromosomal position and are closely linked to the serB locus (Arber & Wauters-Willems, 1970;Bickle, 1993;Daniel et al, 1988;Kannan et al, 1989). The hsd locus in C. jejuni strain NCTC 11168 consists of the genes Cj1549-Cj1553.…”

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

“…Biological evidence currently documents functional type I R-M systems in Bacillus subtilis (194), Citrobacter freundii (34), Klebsiella pneumoniae (101,184), L. lactis (153), Mycoplasma pulmonis (47), Pasteurella haemolytica (66), Salmonella enterica (26), and Staphylococcus aureus (158), in addition to those originally identified in E. coli. All these systems have been shown to provide a barrier to phage infection, either in their original host or after cloning of their genes in E. coli.…”

“…As expected, the nucleotide sequences of the hsd genes for EcoKI and EcoBI would hybridize to each other and antibodies raised against EcoKI reacted with EcoBI, but in contrast, DNA probes comprising the EcoKI genes failed to hybridize with those of E. coli 15T Ϫ , which encoded EcoAI; similarly, antibodies against EcoKI did not cross-react with EcoAI. The hsd genes in these two strains behave as alleles in genetic tests (7) but have very different nucleotide sequences (34,80). EcoAI defines a second family of type I systems, type IB.…”

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

“…Three genes (hsdR, M and S) encode the classical R-M system (EcoKI) first identified by Bertani and Weigle (2). The ICR, however, is hypervariable in E.coli and its close relatives (3)(4)(5). In different strains of E.coli, alternative hsd genes specify type I R-M systems with different specificities.…”