The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids
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The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids. / Ruwe, Hannes; Gutmann, Bernard; Schmitz-Linneweber, Christian; Small, Ian; Kindgren, Peter.
In: New Phytologist, Vol. 222, No. 1, 2019, p. 218-229.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids
AU - Ruwe, Hannes
AU - Gutmann, Bernard
AU - Schmitz-Linneweber, Christian
AU - Small, Ian
AU - Kindgren, Peter
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
KW - Arabidopsis
KW - E domain
KW - pentatricopeptide repeat (PPR) proteins
KW - RNA footprints
KW - RNA processing
U2 - 10.1111/nph.15578
DO - 10.1111/nph.15578
M3 - Journal article
C2 - 30393849
AN - SCOPUS:85057989157
VL - 222
SP - 218
EP - 229
JO - New Phytologist
JF - New Phytologist
SN - 0028-646X
IS - 1
ER -
ID: 213856346