The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids

Hannes Ruwe, Bernard Gutmann, Christian Schmitz-Linneweber, Ian Small, Peter Kindgren

Research output: Contribution to journalArticle

Abstract

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 languageEnglish
Pages (from-to)218-229
Number of pages12
JournalNew Phytologist
Volume222
Issue number1
DOIs
Publication statusPublished - Apr 2019

Cite this

Ruwe, Hannes ; Gutmann, Bernard ; Schmitz-Linneweber, Christian ; Small, Ian ; Kindgren, Peter. / The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids. In: New Phytologist. 2019 ; Vol. 222, No. 1. pp. 218-229.
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abstract = "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.",
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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, 04.2019, p. 218-229.

Research output: Contribution to journalArticle

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 - 2019/4

Y1 - 2019/4

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

KW - PENTATRICOPEPTIDE REPEAT PROTEINS

KW - MESSENGER-RNA

KW - CONSERVED DOMAIN

KW - EDITING FACTORS

KW - PPR PROTEIN

KW - DYW DOMAIN

KW - CHLOROPLAST

KW - SITE

KW - BINDING

KW - STABILIZES

U2 - 10.1111/nph.15578

DO - 10.1111/nph.15578

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SP - 218

EP - 229

JO - The New Phytologist

JF - The New Phytologist

SN - 0028-646X

IS - 1

ER -