The complete nucleotide sequence of the rhsA locus and selected portions of other members of the rhs multigene family of Escherichia coli K-12 have been determined. A definition of the limits of the rhsA and rhsC loci was established by comparing sequences from E. coli K-12 with sequences from an independent E. coli isolate whose DNA contains no homology to the rhs core. This comparison showed that rhsA comprises 8,249 base pairs (bp) in strain K-12 and that the Rhs°strain, instead, contains an unrelated 32-bp sequence.Similarly, the K-12 rhsC locus is 9.6 kilobases in length and a 10-bp sequence resides at its location in the Rhso Families of homologous but nonidentical genes present a number of special genetic questions. These questions include the possible specific roles of individual members, the degree to which members exchange heterologies through intrachromosomal recombination, and the effects of these exchanges on function. The presence of these multigene families also has important implications for chromosome rearrangement and evolution (17). However, except for the rrn operons encoding ribosomal RNA, multigene families are quite rare in Escherichia coli (19). We have recently reported an unusual and complex family, the rhs family, that is comparable to the rrn family in number, length of shared homology, and degree of sequence similarity. The rhs loci were originally detected through their action as rearrangement hot spots, providing homology for recA-dependent intrachromosomal recombination (4, 11). Consequently, the rhs loci were defined to include the homologous sequences shared by two or more of the respective loci. Four rhs loci of E. coli strain K-12 have been characterized extensively, and evidence for a fifth has been noted (4,11,20).A distinctive feature of the rhs loci is that they share a highly conserved 3.7-kilobase (kb) core sequence. The cores are generally flanked by dissimilar sequences, and for two of the loci, rhsA and rhsC, one or more partial core repetitions are present downstream from the intact core. Sequence comparison of the first 300 nucleotides of the rhs cores (20) revealed that the core homology begins precisely with a start codon initiating an open reading frame (ORF) and that the rhsA, rhsB, and rhsC cores are closely related, showing only 1 to 2% sequence divergence. By contrast, rhsD is 18% divergent from the others. A total of nine mismatches distinguish rhsA, rhsB, and rhsC through these 300 nucleotides, but none of the nine causes an amino acid substitution in the core ORFs. However, rhsD differs from the others by eight amino acids. This degree of divergence through predominantly neutral mutation indicates that the cores have been evolving independently for quite some time. Application of the mutation rate estimated for enteric bacteria by Ochman and Wilson (15) suggests that the rhsA and rhsC cores diverged on the order of 10 million years ago, and the extent of sequence divergence of rhsD would indicate that it radiated from the others on the order of 100 mill...
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