Isolation of regulated genes of the cyanobacterium Synechocystis sp strainPCC 6803 by differential display

Global identification of differentially regulated genes in prokaryotes is c onstrained because the mRNA does not have a 3' polyadenylation extension; t his precludes specific separation of mRNA from rRNA and tRNA and synthesis of cDNAs from the entire mRNA population, from ledge of the entire genome s equence of Synechocystis sp. strain PCC 6803 has enabled us to develop a di fferential display procedure that takes advantage of a short palindromic se quence that is dispersed throughout the Synechocystis sp. strain PCC 6803 g enome. This sequence, designated the HIP (highly iterated palindrome) eleme nt, occurs in approximately half of the Synechocystis sp, strain PCC 6803 g enes but is absent in rRNA and tRNA. genes. To determine the feasibility of exploiting the HIP element, alone or in combination with specific primer s ubsets, for analyzing differential gene expression, we used HIP-based prime rs to identify light intensity-regulated genes. Several gene fragments, inc luding those encoding ribosomal proteins and phycobiliprotein subunits, wer e differentially amplified from RNA templates derived from cells grown in l ow light or exposed to high light for 3 h. One novel finding was that expre ssion of certain genes of the pho regulon, which are under the control of e nvironmental phosphate levels, were markedly elevated in high light. High-l ight activation of pho regulon genes correlated with elevated growth rates that occur when the cells are transferred from low to high fight. These res ults suggest that in high light, the rate of growth of Synechocystis sp. st rain PCC 6803 exceeds its capacity to assimilate phosphate, which, in turn, may trigger a phosphate starvation response and activation of the pho regu lon.