CHARACTERIZATION OF A NUCLEAR‐ENCODED PHOTOGENE FOR A CHLOROPLAST RNA POLYMERASE SIGMA FACTOR IN THE UNICELLULAR ALGA CYANIDIUM CALDARIUM (RHODOPHYTA)

Abstract

Previously we identified the gene (rpoD1) for a σ factor of chloroplast RNA polymerase from the unicellular rhodophyte Cyanidium caldarium Geitler and presented evidence for a multigene family of σ factors in this organism. In the present investigation, a new member of this gene family, rpoD2, was isolated and characterized. This gene was identified in a subgenomic library screened with the “rpoD box” probe, a highly conserved 28‐base sequence found in the −10 promoter recognition motif of σ factors from eubacteria and cyanobacteria. Alignment of the deduced amino acid sequence of RpoD2 (the gene product of rpoD2) with other σ factors from C. caldarium showed that this protein contained all four conserved regions found in eubacterial and cyanobacterial σ factors in addition to a newly identified conserved domain. Northern analyses showed that rpoD2 transcripts were not detectable in dark‐grown cells but were enriched in polyA+ RNA from illuminated cells, which suggests that rpoD2 is a positively regulated, nuclear‐encoded photogene. The patterns of rpoD2 and rpoD1 transcript accumulation after transfer of cells from dark to light were distinct, which suggests that σ‐factor genes are differentially expressed. Collectively, the results obtained support the hypothesis that differentially expressed, nuclear‐encoded σ factors may transcribe subsets of plastid genes for photosynthesis during chloroplast development.