|Regulation by DNA Rearrangements
Expression of certain genes in prokaryotes are also regulated through DNA rearrangements (for DNA rearrangements in eukaryotes, consult-Regulation of Gene Expression 3. A Variety of Mechanisms in Eukaryotes
). These DNA rearrangements can be broadly classified into two groups.
Stochastic (random) gene rearrangements
These rearrangements take place without any need, so that a small fraction of the cell population carrying rearranged genes behave like boy scouts, always ready (if the eventuality for which they are prepared does not occur, no problem). One of the best studied examples of these gene rearrangements involves inversion of the DNA elements carrying the promoter for one of the flagellar protein operons in Salmonella typhimurium.
In one orientation, the element promotes transcription of a gene encoding one 'flagellar protein' and 'repressor' of a distant gene encoding an alternative flagellar protein. Inversion of the elements blocks transcription of both, the 'first flagellar protein gene' and the 'repressor gene', thus permitting expression of the second flagellar protein.
Developmentally regulated gene rearrangements
These gene rearrangements take place during the differentiation of heterocysts (not in vegetative cells) in cyanobacteria or in the mother cell (not in forespore, which forms sores) of Bacillus subtilis during sporulation. Both the heterocyst (in cyanobacteria) and the mother cell (in B. subtilis)are such cells, which do not give rise to cells of next generation, so that the gene rearrangements are not transmitted. These developmentally regulated gene rearrangements involve excision of DNA segments that interrupt coding regions of the genes. Moreover, these gene rearrangements are not random and require a series of signal transductions, gene activations and morphological differentiation.
Many species of filamentous nitrogen fixing cyanobacteria like Nostoc and Anabaena have specialized cells called heterocysts, where nitrogen fixation occurs during conditions of nitrogen limitation. Heterocysts occur at regular intervals making upto 10% of the cells in free living Anabaena and Nostoc, this frequency being much higher in symbiotic associations. The nitrogen fixation is facilitated by the presence of a 'nitrogenase complex' with three polypeptide components, that are encoded by three linked genes, nifHDK. In Anabaena, nifK gene is 11kb downstream from NifHD genes. This 11kb element is excised and the nifHDK operon is reconstructed. A second excision removes a 55kb element, which interrupts the coding region of a gene called fdxN. Both excisions are catalyzed by site-specific recombinases encoded within the interrupting elements themselves. In the absence of these excisions, it is impossible to transcribe the genes downstream of the interrupting elements.
Another example of DNA rearrangement is found in Bacillus subtilis, where some of the mother cell-specific transcriptions (including those for spore coat proteins) require a form of RNA polymerase carrying σK (sigK, a 27kD protein). The sigK is encoded by sigk gene resulting from the DNA rearrangements between two open reading frames (ORFs), spoIVB and spoIIIC (formerly believed to be separate genes). The DNA rearrangement, in this case, involves excision of a 42kb element. It was shown that the strains with this 42kb element are unable to sporulate (they sporulate if a copy of sigk gene is supplied) and the strains with this 42kb element sporulate normally. (For more details on DNA rearrangements in prokaryotes consult Ann. Rev. Genet. 26 : 113-130, 1992).