Most if not all genomes contain genes that occur in several copies. The existence of such multigene families poses several special genetic problems that fall into three overlapping categories. The first relates to the specific role in the cell of each individual gene, the second concerns the exchange of information between copies, while the third relates to the promotion of chromosomal rearrangement through the provision of large homologies. All three have major implications for genome evolution. This project addresses these problems through the study of an unusual family of composite genetic elements that collectively comprise nearly 1% of the chromosome of Escherichia coli K-12. This Rhs element family is interesting from several perspectives. They serve as paradigms of complex multigene families which clearly interact through recombination. They are a completely novel class of accessory genetic element whose behavior is still largely not understood. Finally, and possibly most importantly, their novel structure and occurrence in independent E. coli suggest they may have a fundamentally important role in the success of E. coli populations. The most prominent feature of an Rhs element is a large open reading frame that encodes a protein predicted to be in excess of 150 kDa. This large ORF is a mosaic, being composed of a 3.7 kb core and a shorter core-extension. The cores are highly conserved among different Rhs elements, while the core-extensions are highly divergent. The association of core-extensions with particular elements varies in independent E. coli in a fashion that correlates with the clonal structure of natural populations. The degree of this correlation is unprecedented among accessory genetic elements. Properties predicted from the core protein's primary sequence suggest that this protein may function on the cell surface.
The specific aims of the project address the functions of these elements, the control of their expression and their genetic behavior in natural populations of E. coli.
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