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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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OZ1 and its family members contain multiple domains.(A) motifs detected by MEME prediction for OZ family members. Motif4 is the RanBP2 type Zinc finger domain. Arrows indicate the cysteines characteristic of zinc finger domains. (B) motif locations in the OZ family.
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pgen.1005028.g013: OZ1 and its family members contain multiple domains.(A) motifs detected by MEME prediction for OZ family members. Motif4 is the RanBP2 type Zinc finger domain. Arrows indicate the cysteines characteristic of zinc finger domains. (B) motif locations in the OZ family.

Mentions: Except for the zinc finger motif, no other annotated domain or motif was found in the OZ1 family. In order to find hidden uncharacterized motifs, motif scanning was performed using MEME against all four members to look for motifs between 15aa to 70aa. Five motifs were returned (Fig. 13). The zinc finger domain has 4 characteristic cysteine residues. As shown in Fig. 13, the zinc finger motif is shared by all four members, but the number of repeats varies. OZ1 and OZ2 (At1g55040) contain two zinc finger motifs, while OZ3 (At1g70650) has three and OZ4 (At1g48570) has four. The regions preceding the zinc finger motifs are relatively highly conserved, briefly spanning 3 distinct domains. The region downstream of the zinc finger domains is quite variable. OZ1 has three repeats of motif 5, which is either missing or poorly conserved in the other members (S2 Fig). Portions of motif 5 were previously identified as three “long repeats” in At5g17790 [28].


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)

OZ1 and its family members contain multiple domains.(A) motifs detected by MEME prediction for OZ family members. Motif4 is the RanBP2 type Zinc finger domain. Arrows indicate the cysteines characteristic of zinc finger domains. (B) motif locations in the OZ family.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005028.g013: OZ1 and its family members contain multiple domains.(A) motifs detected by MEME prediction for OZ family members. Motif4 is the RanBP2 type Zinc finger domain. Arrows indicate the cysteines characteristic of zinc finger domains. (B) motif locations in the OZ family.
Mentions: Except for the zinc finger motif, no other annotated domain or motif was found in the OZ1 family. In order to find hidden uncharacterized motifs, motif scanning was performed using MEME against all four members to look for motifs between 15aa to 70aa. Five motifs were returned (Fig. 13). The zinc finger domain has 4 characteristic cysteine residues. As shown in Fig. 13, the zinc finger motif is shared by all four members, but the number of repeats varies. OZ1 and OZ2 (At1g55040) contain two zinc finger motifs, while OZ3 (At1g70650) has three and OZ4 (At1g48570) has four. The regions preceding the zinc finger motifs are relatively highly conserved, briefly spanning 3 distinct domains. The region downstream of the zinc finger domains is quite variable. OZ1 has three repeats of motif 5, which is either missing or poorly conserved in the other members (S2 Fig). Portions of motif 5 were previously identified as three “long repeats” in At5g17790 [28].

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