A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA

Abstract

Sty SBLI using the PILEUP program), the sequence for Sty SBLI is anticipated to initiate at codon 27 if translation begins at the first methionine.In the legend to Fig. 5, the lengths of the open reading frames are in error. The legend is corrected below. Fig. 5.Map of the hsd region of S. enterica serovar blegdam. The numbers below the map identify the ORFs; orf3 (540 codons) is hsdM, orf4 (435 codons) is hsdS, and orf5 (1089 codons) is hsdR. The first methionine codon of orf4 overlaps the penultimate codon of orf3. The orientation of the sequence with respect to serB is indicated by the arrow below the map. The order differs from that in E. coli K-12 and S. enterica serovar typhimurium where hsdR is the closest hsd gene to serB.

Immigration control of DNA in bacteria: self versus non-self

“…Additional conserved sequences in the N-terminal part of the R subunits of type I R-M systems (Titheradge et al, 1996) show similarities with those motifs associated with DNA nicking in other nucleases (Davies et al, 1999b). Site-directed mutagenesis proved the relevance of this motif to the endonuclease activity of EcoAI (Janscak et al, 1999b) and EcoKI (Davies et al, 1999a, b).…”

“…A type I R subunit includes motifs characteristic of ATP-binding proteins (Loenen et al, 1987), consistent with the ATP-dependence of restriction. In addition, they include conserved sequences indicating the presence of motifs characteristic of ATPdependent helicases (Gorbalenya & Koonin, 1991 ;Murray et al, 1993 ;Titheradge et al, 1996). It has been suggested that these motifs, the DEAD-box motifs, define an ' engine ' that powers DNA translocation (Hall & Matson, 1999).…”

Diversity within the Campylobacter jejuni type I restriction–modification loci

“…Titheradge et al (2001) used an HsdM identity value of 45 % to place novel HsdM polypeptides into the four existing families of type I enzymes; HsdM proteins with >45 % identity were placed into the same family. Based on this sole criterion, many of the newly characterized type I R-M systems can be assigned to one of four families identified in the Enterobacteriaceae (Fuller-Pace et al, 1985;Price et al, 1987;Suri & Bickle, 1985;Titheradge et al, 1996Titheradge et al, , 2001. However, only 17 % of the pairwise combinations between the 32 HsdM proteins in Fig.…”

“…The type IC family, represented by EcoR124I, includes both plasmid-encoded (Firman et al, 1983;Skrzypek & Piekarowicz, 1989) and chromosomally encoded (Kong et al, 2000;Piekarowicz et al, 2001;Tyndall et al, 1994) members. A fourth family, type ID, was first identified in Salmonella enterica serovar Blegdam (Titheradge et al, 1996). HsdM and HsdR proteins within the same family are highly conserved, with any pairwise amino acid sequences having >90 % identity; however, sequence identity between HsdM proteins from different families is usually very low (<35 %) (Sharp et al, 1992;Titheradge et al, 2001).…”

Structural and functional analysis of pCI65st, a 6·5 kb plasmid from Streptococcus thermophilus NDI-6

“…extremely highly conserved across the animal and plant kingdoms. ORF5 could encode a 412 aa protein with significant similarity to the HsdS or specificity proteins from type 1 restriction-modification (R/M) systems, including those of EcoRI24II from E. coli (Price et al, 1989;27.5 % identity, 52 % similarity), StySBL1 from Salmonella enterica (Titheradge et al, 1996;32-5 YO identity, 52% similarity) and to the S proteins of R/M systems of Methanococcus jannaschii (Cfrl ; accession no. L77158 ; 33 % identity, 53 YO similarity), Mycoplasma pulmonis (Dybvig &Yu, 1994; 35 % identity, 52 '/o similarity) and Spiroplasma citri (Laigret et al, 1996; 36 Yo identity, 56 YO similarity) (Fig.…”