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A zinc finger motif-containing protein is essential for chloroplast RNA editing.

Sun T, Shi X, Friso G, Van Wijk K, Bentolila S, Hanson MR - PLoS Genet. (2015)

Bottom Line: Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or chloroplasts.The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to chloroplasts and one to mitochondria.With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

ABSTRACT
C-to-U editing of transcripts in plant organelles is carried out by small (<400 kD) protein complexes called editosomes. Recognition of the proper C target for editing is mediated by pentatricopeptide repeat (PPR) containing proteins that recognize cis-elements. Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or chloroplasts. By co-immunoprecipitation of the chloroplast editing factor ORRM1, followed by mass spectrometry, we have now identified a member of the RanBP2 type zinc fingers (pFAM00641) protein family that is required for editing of 14 sites in chloroplasts and affects editing efficiency of another 16 chloroplast C targets. In yeast two-hybrid assays, OZ1 (Organelle Zinc finger 1) interacts with PPR site recognition factors whose cognate sites are affected when OZ1 is mutated. No interaction of OZ1 with the chloroplast editing factors RIP2 and RIP9 was detected; however, OZ1 interacts with ORRM1, which binds to RIP proteins, allowing us to build a model for the chloroplast RNA editosome. The RNA editosomes that act upon most chloroplast C targets are likely to contain a PPR protein recognition factor, either RIP2 or RIP9, ORRM1, and OZ1. The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to chloroplasts and one to mitochondria. With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing.

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Model of the chloroplast editosome that operates on ndhD C878 based on protein-protein interaction data.Data is from yeast two-hybrid assays from this study and prior reports [25,26,31]. The stoichiometry of the components is unknown. The targeted C at position 878 on the ndhD transcript is represented by a yellow star, the cis element upstream of the target C is indicated by a red bar.
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pgen.1005028.g015: Model of the chloroplast editosome that operates on ndhD C878 based on protein-protein interaction data.Data is from yeast two-hybrid assays from this study and prior reports [25,26,31]. The stoichiometry of the components is unknown. The targeted C at position 878 on the ndhD transcript is represented by a yellow star, the cis element upstream of the target C is indicated by a red bar.

Mentions: The action of OZ1 is clearly site-specific, because C targets that reside on the same transcript are differently affected. For example, ndhD C878 has a major loss of editing while ndhD C383 is barely affected. Which editing sites are affected is likely determined by the editing factors with which OZ1 interacts. C targets that share PPR recognition factors are similarly affected in the oz1 mutant. In Y2H assays, OZ1 binds to CRR28 and OTP82, PPR proteins that are required for editing of sites that also require OZ1. Furthermore, OZ1 interacts with ORRM1, and all 14 severely affected chloroplast sites are also affected in the orrm1 mutant. OZ1 interacts with RIP1, though the interaction is not as strong as that with ORRM1. We did not observe direct interaction of OZ1 with RIP2 or RIP9. However, ORRM1 can bind to RIP1 and RIP2. Previously we reported interaction between the RIP-RIP domain of ORRM1 and CRR28 and OTP82 [25]. Another group determined that RIP2 and RIP9 interact with CRR28 [31]. RIP2 and RIP9 have been reported to interact with PPO1, protoporphyrinogen IX oxidase 1, which is required for efficient editing of a number of chloroplast sites [31]. However, PPO1 does not interact with CRR28 or other PPR editing factors, and it is presently unknown whether PPO1 also interacts with either ORRM1 or OZ1 [31]. All of the interaction data, taken together, is consistent with the presence of multi-component editing complexes that contain ORRM1, OZ1, and at least one RIP protein and a PPR protein, at unknown stoichiometry. An example of the model for the editosome acting upon ndhD C878, drawn according to the yeast two-hybrid data, is shown in Fig. 15. Some complexes are also likely to contain PPO1, but we cannot place this protein into our diagram until its interaction with ORRM1 and OZ1 is investigated in the future.


A zinc finger motif-containing protein is essential for chloroplast RNA editing.

Sun T, Shi X, Friso G, Van Wijk K, Bentolila S, Hanson MR - PLoS Genet. (2015)

Model of the chloroplast editosome that operates on ndhD C878 based on protein-protein interaction data.Data is from yeast two-hybrid assays from this study and prior reports [25,26,31]. The stoichiometry of the components is unknown. The targeted C at position 878 on the ndhD transcript is represented by a yellow star, the cis element upstream of the target C is indicated by a red bar.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4359148&req=5

pgen.1005028.g015: Model of the chloroplast editosome that operates on ndhD C878 based on protein-protein interaction data.Data is from yeast two-hybrid assays from this study and prior reports [25,26,31]. The stoichiometry of the components is unknown. The targeted C at position 878 on the ndhD transcript is represented by a yellow star, the cis element upstream of the target C is indicated by a red bar.
Mentions: The action of OZ1 is clearly site-specific, because C targets that reside on the same transcript are differently affected. For example, ndhD C878 has a major loss of editing while ndhD C383 is barely affected. Which editing sites are affected is likely determined by the editing factors with which OZ1 interacts. C targets that share PPR recognition factors are similarly affected in the oz1 mutant. In Y2H assays, OZ1 binds to CRR28 and OTP82, PPR proteins that are required for editing of sites that also require OZ1. Furthermore, OZ1 interacts with ORRM1, and all 14 severely affected chloroplast sites are also affected in the orrm1 mutant. OZ1 interacts with RIP1, though the interaction is not as strong as that with ORRM1. We did not observe direct interaction of OZ1 with RIP2 or RIP9. However, ORRM1 can bind to RIP1 and RIP2. Previously we reported interaction between the RIP-RIP domain of ORRM1 and CRR28 and OTP82 [25]. Another group determined that RIP2 and RIP9 interact with CRR28 [31]. RIP2 and RIP9 have been reported to interact with PPO1, protoporphyrinogen IX oxidase 1, which is required for efficient editing of a number of chloroplast sites [31]. However, PPO1 does not interact with CRR28 or other PPR editing factors, and it is presently unknown whether PPO1 also interacts with either ORRM1 or OZ1 [31]. All of the interaction data, taken together, is consistent with the presence of multi-component editing complexes that contain ORRM1, OZ1, and at least one RIP protein and a PPR protein, at unknown stoichiometry. An example of the model for the editosome acting upon ndhD C878, drawn according to the yeast two-hybrid data, is shown in Fig. 15. Some complexes are also likely to contain PPO1, but we cannot place this protein into our diagram until its interaction with ORRM1 and OZ1 is investigated in the future.

Bottom Line: Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or chloroplasts.The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to chloroplasts and one to mitochondria.With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

ABSTRACT
C-to-U editing of transcripts in plant organelles is carried out by small (<400 kD) protein complexes called editosomes. Recognition of the proper C target for editing is mediated by pentatricopeptide repeat (PPR) containing proteins that recognize cis-elements. Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or chloroplasts. By co-immunoprecipitation of the chloroplast editing factor ORRM1, followed by mass spectrometry, we have now identified a member of the RanBP2 type zinc fingers (pFAM00641) protein family that is required for editing of 14 sites in chloroplasts and affects editing efficiency of another 16 chloroplast C targets. In yeast two-hybrid assays, OZ1 (Organelle Zinc finger 1) interacts with PPR site recognition factors whose cognate sites are affected when OZ1 is mutated. No interaction of OZ1 with the chloroplast editing factors RIP2 and RIP9 was detected; however, OZ1 interacts with ORRM1, which binds to RIP proteins, allowing us to build a model for the chloroplast RNA editosome. The RNA editosomes that act upon most chloroplast C targets are likely to contain a PPR protein recognition factor, either RIP2 or RIP9, ORRM1, and OZ1. The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to chloroplasts and one to mitochondria. With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing.

Show MeSH