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The E domain of CRR2 participates in sequence‐specific recognition of RNA in plastids
Author(s) -
Ruwe Hannes,
Gutmann Bernard,
SchmitzLinneweber Christian,
Small Ian,
Kindgren Peter
Publication year - 2019
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.15578
Subject(s) - pentatricopeptide repeat , rna , biology , arabidopsis , computational biology , rna binding protein , rna editing , microbiology and biotechnology , plastid , genetics , biochemistry , gene , chloroplast , mutant
Summary 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 CRR 2 in plastids. We identified a surprisingly large number of small RNA s that represent in vivo footprints of the Arabidopsis PLS ‐class PPR protein CRR 2. 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 CRR 2. The E domain of CRR 2 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 CRR 2 is involved in sequence‐specific interaction with its RNA ligand and have implications for our ability to predict RNA targets for PLS ‐ PPR s and their use as biotechnological tools to manipulate specific RNA s in vivo .