RHS ELEMENTS OF ESCHERICHIA-COLI K-12 - COMPLEX COMPOSITES OF SHARED AND UNIQUE COMPONENTS THAT HAVE DIFFERENT EVOLUTIONARY HISTORIES

The complete sequences of the RhsB and RhsC elements of Escherichia co li K-12 have been determined. These sequence data reveal a new repeate d sequence, called H-rpt (Hinc repeat), which is distinct from the Rhs core repetition that is found in all five Rhs elements. H-rpt is foun d in RhsB, RhsC, and RhsE. Characterization of H-rpt supports the view that the Rhs elements are composite structures assembled from compone nts with very different evolutionary histories and that their incorpor ation into the E. coli genome is relatively recent. In each case, H-rp t is found downstream from the Rhs core and is separated from the core by a segment of DNA that is unique to the individual element. The H-r pt's of RhsB and RhsE are very similar, diverging by only 2.1%. They a re 1,291 bp in length, and each contains an 1,134-bp open reading fram e (ORF). RhsC has three tandem copies of H-rpt, all of which appear de fective in that they have large deletions and/or have the reading fram e interrupted. Features of H-rpt are analogous to features typical of insertion sequences; however, no associated transposition activity has been detected. A 291-bp fragment of H-rpt is found near min 5 of the E. coli K-12 map and is not associated with any Rhs core homology. The complete core sequences of RhsB and RhsC have been compared with that of RhsA. As anticipated, the three core sequences are closely related , all having identical lengths of 3,714 bp each. Like RhsA, the RhsB a nd RhsC cores constitute single ORFs that begin with the first core ba se. In each case, the core ORF extends beyond the core into the unique sequence. Of the three cores, RhsB and RhsA are the most similar, sho wing only 0.9% sequence divergence, while RhsB and RhsC are the least similar, diverging by 2.9%. All three cores conserve the 28 repetition s of a peptide motif noted originally for RhsA. A secondary structure is proposed for this motif, and the possibility of its having an extra cellular binding function is discussed. RhsB contains one additional u nique ORF, and RhsC contains two additional unique ORFs. One of these ORFs includes a signal peptide that is functional when fused to TnphoA .