Recombination sequence similarity

In fact, the cross-talk between histone methylation and DNA methylation has been experimentally demonstrated for the first time in Neurospora [145] (see commentary by Bird [146]) and proved the second scenario. Using the power of Neurospora genetics, Tamaru and Selker [145] have identified a gene which, when mutated, abolishes methylation of all tested DNA sequences. This gene, dim-5, is different from dim-2, the previously identified gene that encodes the only DNA methyltransferase in Neurospora responsible for all known cytosine methylation in this fungus. The dim-5 gene encodes a histone H3 methyltransferase the deduced polypeptide sequence contains a SET domain with sequence similarity to some known histone methyltransferases moreover, the recombinant DIM-5 protein exhibits histone methyltransferase activity in vitro. Additional in vivo experiments... 

The parameters to be optimized for experimental recombination include the crossover frequency, the number of parents, and the sequence similarity between parents. Additionally, it is important to understand the conditions under which recombination is useful. For all these questions, the optimal parameters represent a balance between the exploration and exploitation capabilities of the search algorithm. Any process that creates more diversity, such as using many parents, very disparate parents, or small fragment sizes, will improve exploration at the cost of exploitation. The balance between these effects will shift according to the landscape ruggedness and the sampling ability of the mutant library. 

The intermediates that form in recombination reactions, with their tyrosine adducts possessing 3 -phosphoryl groups, are reminiscent of the intermediates that form in the reactions catalyzed by topoisomerases. This mechanistic similarity reflects deeper evolutionary relationships. Examination of the three-dimensional structures of recombinases and type I topoisomerases reveals that these proteins are related by divergent evolution despite little amino acid sequence similarity (Figure 27,40). From this perspective, the action of a recombinase can be viewed as an intermolecular topoisomerase reaction. In each case, a tyrosine-DNA adduct is formed. In a topoisomerase reaction, this... 

Based on the functional similarities between the pertussis toxin and the selectins (including their ability to bind to similar sialic acid-containing oligosaccharides structures), Rozdzinski et al. [166] and Heerze et al. [169] synthesized peptides from the regions of sequence similarity in an effort to find molecules that adhere to sialic acid-containing glycoconjugates. The recombinant subunits S2 and S3 of pertussis toxin and the synthetic peptides competitively inhibited adherence of neutrophils to selectin-coated surfaces and to endothelial cells in vitro. 

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