Analysis of theEscherichia coligenome VI: DNA sequence of the region from 92.8 through 100 minutes

Abstract

The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had been previously located here by mapping or partial sequencing have been confirmed. Several ORFs have functions suggested by similarities to other characterised genes but cannot be assigned with certainty. Fifteen of the ORFs of unknown function had been previously sequenced. Eight transfer RNAs are encoded in the region and there are two grey holes in which no features were found. The attachment site for phage P4 and three insertion sequences were located. The region was also analysed for chi sites, bend sites, REP elements and other repeats. A computer search identified potential promoters and tentative transcription units were assigned. The occurrence of the rare tetramer CTAG was analysed in 1.6 Mb of contiguous E.coli sequence. Hypotheses addressing the rarity and distribution of CTAG are discussed.

FhuF, an iron‐regulated protein of Escherichia coli with a new type of [2Fe‐2S] center

“…Sequencing revealed that Mud1 was inserted at residue 164 in the open reading frame orf f262b at 99.2 min (Fig. 1) on the E. coli DNA genome sequence from min 92.8 to 100 [10]; this identified orf f262b as the fhuF gene. The insertion site of λplacMu in strain H1717 was similarly identified to be at residue 94, and the insertion site of Mud1 in strain Zi352 was identified at residue 233 ( Fig.…”

“…All E. coli chromosomal DNA positions and section numbers are those of the E. coli genome sequence [10,11].…”

“…DNA was sequenced by the dideoxy chain-termination method using the AutoRead sequencing kit and the A. L. F. sequencer (Pharmacia Biotech). A DNA Thermal Cycler (Perkin Elmer Cetus) was used for PCR.All E. coli chromosomal DNA positions and section numbers are those of the E. coli genome sequence [10,11].The fhuF gene region was cloned on a 3-kb EcoRV DNA fragment from λ phage 8D1 (672) of the Kohara collection [12] in the high-copy-number vector pSU18 and recloned into vector pT7-5, resulting in plasmid pKF7572. To obtain an insert coding…”

Clonal descent and microevolution of Neisseria meningitidis during 30 years of epidemic spread

“…Arrows indicate the direction of transcription from consensus ¹35/ -10 promoter sequences, whereas U represents inverted DNA uptake sequences (Goodman and Scocca, 1988). The predicted protein Orf185 was 44% identical to YDJA (Sawers et al, 1991) from E. coli ; Orf544 was 45% identical to YJDB (Burland et al, 1995) from E. coli and SerC was 44-48% identical to SerC proteins from Haemophilus influenzae, Yersinia enterocolitica and Salmonella gallinarum. Sequenced regions: the designations of individual opaB and ingA alleles are indicated above each bar.…”

The positive activator of cephamycin C and clavulanic acid production in Streptomyces clavuligerus is mistranslated in a bldA mutant The GenBank accession number for the sequence reported in this paper is AF436078.

“…ndez-Moreno et al, 1991), actII-orf4 (Ferna! ndez-Moreno et al, 1991, strR (Distler et al, 1987), redZ (White & Bibb, 1997), celA2 (Garda et al, 1997), lipR (Servin-Gonzalez et al, 1997), lacZ, ampC and aad (Burland et al, 1995 ;Hollingshead & Vapnek, 1985 ;Kalnins et al, 1983 ;Leskiw et al, 1991b)] must not be mistranslated efficiently, at least under the conditions tested. In an effort to elucidate what this context effect might be, the sequence within one ribosomal binding unit [12 codons (Chen & Inouye, 1990)] of the TTA codon in the bldA independent ccaR gene was compared to the TTA-surrounding sequences in the 12 target genes (see above for list) known to be bldA dependent (available as supplementary data at http :\\mic.sgmjournals.org).…”