A Major Role for the Plastid-Encoded RNA Polymerase Complex in the Expression of Plastid Transfer RNAs

Rosalind Williams-Carrier,Alice Barkan,Susan Belcher,Jeannette Pfalz,Reimo Zoschke

doi:10.1104/pp.113.228726

Rosalind Williams-Carrier, Alice Barkan + Show 3 more

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https://doi.org/10.1104/pp.113.228726

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Abstract

Chloroplast transcription in land plants relies on collaboration between a plastid-encoded RNA polymerase (PEP) of cyanobacterial ancestry and a nucleus-encoded RNA polymerase of phage ancestry. PEP associates with additional proteins that are unrelated to bacterial transcription factors, many of which have been shown to be important for PEP activity in Arabidopsis (Arabidopsis thaliana). However, the biochemical roles of these PEP-associated proteins are not known. We describe phenotypes conditioned by transposon insertions in genes encoding the maize (Zea mays) orthologs of five such proteins: ZmPTAC2, ZmMurE, ZmPTAC10, ZmPTAC12, and ZmPRIN2. These mutants have similar ivory/virescent pigmentation and similar reductions in plastid ribosomes and photosynthetic complexes. RNA gel-blot and microarray hybridizations revealed numerous changes in plastid transcript populations, many of which resemble those reported for the orthologous mutants in Arabidopsis. However, unanticipated reductions in the abundance of numerous transfer RNAs (tRNAs) dominated the microarray data and were validated on RNA gel blots. The magnitude of the deficiencies for several tRNAs was similar to that of the most severely affected messenger RNAs, with the loss of trnL-UAA being particularly severe. These findings suggest that PEP and its associated proteins are critical for the robust transcription of numerous plastid tRNAs and that this function is essential for the prodigious translation of plastid-encoded proteins that is required during the installation of the photosynthetic apparatus.

Highlights

Chloroplast transcription in land plants relies on collaboration between a plastid-encoded RNA polymerase (PEP) of cyanobacterial ancestry and a nucleus-encoded RNA polymerase of phage ancestry
We discovered a deficiency for numerous plastid transfer RNAs (tRNAs), several of which were as severely affected as the “classic” PEP-dependent mRNAs
The fifth gene encodes the maize ortholog of Arabidopsis PRIN2 (Kindgren et al, 2012), which has not been detected as a PEP-associated protein but which localizes to the plastid nucleoid and influences plastid transcript profiles in a manner that is similar to PEP-associated proteins (Kindgren et al, 2012)

Summary

Introduction

Chloroplast transcription in land plants relies on collaboration between a plastid-encoded RNA polymerase (PEP) of cyanobacterial ancestry and a nucleus-encoded RNA polymerase of phage ancestry. Pioneering studies that explored the contributions of PEP and NEP with a tobacco (Nicotiana tabacum) plastome mutant lacking RpoB concluded that plastid photosystem genes are transcribed primarily by PEP, whereas most other genes can be transcribed by either NEP or PEP (Allison et al, 1996; Hajdukiewicz et al, 1997) This question was subsequently addressed more comprehensively by analysis of the plastid transcriptome in a tobacco rpoA knockout (Legen et al, 2002), by comparison of transcription start sites in normal and ribosome-deficient barley (Hordeum vulgare) plastids (Zhelyazkova et al, 2012), and by profiling plastid transcriptomes in the presence of an inhibitor of PEP (Demarsy et al, 2006, 2012). A recent model posits that the PEP-associated proteins are required to establish a subdomain in the plastid nucleoid that is required for PEP-mediated transcription (Pfalz and Pfannschmidt, 2013)

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