A nuclear‐encoded sigma factor, Arabidopsis SIG6, recognizes sigma‐70 type chloroplast promoters and regulates early chloroplast development in cotyledons

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Abstract
Summary: Eubacterial‐type multi‐subunit plastid RNA polymerase (PEP) is responsible for the principal transcription activity in chloroplasts. PEP is composed of plastid‐encoded core subunits and one of multiple nuclear‐encoded sigma factors that confer promoter specificity on PEP. Thus, the replacement of sigma factors associated with PEP has been assumed to be a major mechanism for the switching of transcription patterns during chloroplast development. The null mutant (sig6‐1) of plastid sigma factor geneAtSIG6exhibited a cotyledon‐specific pale green phenotype. Light‐dependent chloroplast development was significantly delayed in thesig6‐1mutant. Genetic complementation of the mutant phenotype by theAtSIG6cDNA demonstrated that AtSIG6 plays a key role in light‐dependent chloroplast development. Northern and array‐based global analyses for plastid transcripts revealed that the transcript levels of most PEP‐dependent genes were greatly reduced in thesig6‐1mutant, but that the accumulation of nuclear‐encoded RNA polymerase (NEP)‐dependent transcripts generally increased. As the PEPαsubunit and PEP‐dependenttrnVaccumulated at normal levels in thesig6‐1mutant, theAtSIG6knockout mutant probably retained functional PEP, and the transcriptional defects are likely to have been directly caused byAtSIG6deficiency. Most of the AtSIG6‐dependent genes are preceded byσ70‐type promoters comprised of conserved −35/−10 elements. Thus, AtSIG6 may act as a major general sigma factor in chloroplasts during early plant development. On the other hand, the mutant phenotype was restored in older seedlings. Arabidopsis probably contains another late general sigma factor, the promoter specificity of which widely overlaps with that of AtSIG6.