The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids
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Pentatricopeptide repeat (PPR) proteins are modular RNA-binding proteins involved in different aspects of RNA metabolism in organelles. PPR proteins of the PLS subclass often contain C-terminal domains that are important for their function, but the role of one of these domains, the E domain, is far from resolved. Here, we elucidate the role of the E domain in CRR2 in plastids. We identified a surprisingly large number of small RNAs that represent in vivo footprints of the Arabidopsis PLS-class PPR protein CRR2. An unexpectedly strong base conservation was found in the nucleotides aligned to the E domain. We used both in vitro and in vivo experiments to reveal the role of the E domain of CRR2. The E domain of CRR2 can be predictably altered to prefer different nucleotides in its RNA ligand, and position 5 of the E1-motif is biologically important for the PPR–RNA interaction. The ‘code’ of the E domain PPR motifs is different from that of P- and S-motifs. The findings presented here show that the E domain of CRR2 is involved in sequence-specific interaction with its RNA ligand and have implications for our ability to predict RNA targets for PLS-PPRs and their use as biotechnological tools to manipulate specific RNAs in vivo.
Original language | English |
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Journal | New Phytologist |
Volume | 222 |
Issue number | 1 |
Pages (from-to) | 218-229 |
ISSN | 0028-646X |
DOIs | |
Publication status | Published - 2019 |
Externally published | Yes |
- Arabidopsis, E domain, pentatricopeptide repeat (PPR) proteins, RNA footprints, RNA processing
Research areas
ID: 213856346