Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psb N gene in plastids

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Abstract
We have investigated the function of one of the six plastid sigma-like transcription factors, sigma 3 (SIG3), by analysing two different Arabidopsis T-DNA insertion lines having disrupted SIG3 genes. Hybridization of wild-type and sig3 plant RNA to a plastid specific microarray revealed a strong reduction of the plastid psb N mRNA. The microarray result has been confirmed by northern blot analysis. The SIG3-specific promoter region has been localized on the DNA by primer extension and mRNA capping experiments. Results suggest tight regulation of psb N gene expression by a SIG3-PEP holoenzyme. The psb N gene is localized on the opposite strand of the psb B operon, between the psb T and psb H genes, and the SIG3-dependent psb N transcription produces antisense RNA to the psb T– psb H intergenic region. We show that this antisense RNA is not limited to the intergenic region, i.e. it does not terminate at the end of the psb N gene but extends as antisense transcript to cover the whole psb T coding region. Thus, by specific transcription initiation at the psb N gene promoter, SIG3-PEP holoenzyme could also influence the expression of the psb B operon by producing psb T antisense RNA.