PPR_71 - Plant Editosome Database

Summary

Editing Factor:	PPR_71
Synonym:	Phypa_181369
Description:	RNA editing of the ccmF-2 downstream site was specifically impaired by disruption of the PpPPR_71 gene that encodes a polypeptide with 17 pentatricopeptide repeat motifs and a C-terminal DYW domain; The recombinant PpPPR_71 protein expressed in Escherichia coli specifically bound to the 46-nucleotide sequence containing the ccmF-2 editing site; The binding affinity of the recombinant PpPPR_71 was strongest when using the edited RNA at ccmF-1; PpPPR_71 is an RNA-binding protein that acts as a site recognition factor in mitochondrial RNA editing; PpPPR_71 was identified as a ccmFc-C122-specific editing factor; This assay showed that both E and DYW domains are required for RNA editing at the target sites, and that the conserved zinc-binding signature and the terminal triplet of the DYW domain are essential for editing; In addition, DYW domain-swapping experiments demonstrated that DYW domains are functionally different between PpPPR_56 and other mitochondrial PPR editing factors, and that residues 37-42 of the DYW domain are involved in site-specific editing
Protein Family:	Pentatricopeptide repeat (PPR)
Subclass:	DYW
Physical Interaction:	NA
Construct Structure:	PLS-DYW
Gene ID & Species:	PP1S48_253V6 (Physcomitrium patens)
Edited Gene(s):	ccmFc
Editing Type(s):	C-to-U (17)
Publication(s):	[1] The DYW Domains of Pentatricopeptide Repeat RNA Editing Factors Contribute to Discriminate Target and Non-Target Editing Sites, Plant Cell Physiol, 2018. [PMID=29718364] [2] Two DYW Subclass PPR Proteins are Involved in RNA Editing of ccmFc and atp9 Transcripts in the Moss Physcomitrella patens: First Complete Set of PPR Editing Factors in Plant Mitochondria, Plant Cell Physiology, 2013. [PMID=24058147] [3] The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript, The Plant Journal, 2010. [PMID=20163555]

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Nuclear Genome

Organelle Genome

Other Position Region

Other Position

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Physcomitrium patens

PP1S48_253V6

Mitochondrion

ccmFc

122

CDS

C-to-U

UCU=>UUU
NA=>NA

S=>F
NA=>NA

Recoding
NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
NA	6-11	Polyethylene Glycolmediated Transformation	NA	Knockout	Significantly poor growth of the protonemata	Protonema	4 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	20163555
NA	7-9	Biolistic Transformation	NA	Knockout	Significantly poor growth of the protonemata	Protonema	4 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	20163555
NA	WT	Control	Control	No mutant	Normal	Protonema	4 days	Direct Sequencing of PCR Products	82.40%	High	None	20163555
NA	WT	Control	Control	No mutant	Normal	Protonema	4 days	Direct Sequencing of PCR Products	80.00%	High	None	24058147
NA	△71-6-11	Polyethylene Glycolmediated Transformation	NA	Knockout	Severe growth retardation of the moss protonemata	Protonema	4 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	24058147
NA	WT	Wild Type	Wild Type	No mutant	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	79.17%	High	None	29718364
NA	△71 6-11	Knockout line	Procedures to obtain moss lines PpPPR_56 KO (Δ56-22) and PpPPR_71 KO (Δ71 6-11) have been previously described (Ohtani et al. 2010, Tasaki et al. 2010).	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71FL	Complementation	Full-length (FL) version of PpPPR_71 was transformed into the respective KO moss background.	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	84.09%	High	Restored	29718364
NA	71△DYW	Complementation	Truncated version (ΔDYW) of PpPPR_71 was transformed into the respective KO moss background.	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71△E	Complementation	Truncated version (ΔE) of PpPPR_71 was transformed into the respective KO moss background.	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71PPR+71E/71DYW	Complementation	Two editing mutants were transformed by various constructs obtained by swapping from the E and/or DYW domains of PpPPR_56 or PpPPR_71 to the cognate region of another P. patens editing factor.	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	80.00%	High	Restored	29718364
NA	71PPR+71E/45DYW	Complementation	Two editing mutants were transformed by various constructs obtained by swapping from the E and/or DYW domains of PpPPR_56 or PpPPR_71 to the cognate region of another P. patens editing factor.	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71PPR+71E/56DYW	Complementation	Two editing mutants were transformed by various constructs obtained by swapping from the E and/or DYW domains of PpPPR_56 or PpPPR_71 to the cognate region of another P. patens editing factor.	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71PPR+71E/77DYW	Complementation	Two editing mutants were transformed by various constructs obtained by swapping from the E and/or DYW domains of PpPPR_56 or PpPPR_71 to the cognate region of another P. patens editing factor.	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71M1	Complementation	To investigate their roles in RNA editing, we generated transgenic lines with mutated DYW domains in which the HxExnCxxC signature was changed to AxAxnCxxC (56M1 and 71M1) and HxExnAxxA (56M2 and 71M2	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71M2	Complementation	To investigate their roles in RNA editing, we generated transgenic lines with mutated DYW domains in which the HxExnCxxC signature was changed to AxAxnCxxC (56M1 and 71M1) and HxExnAxxA (56M2 and 71M2	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364
NA	71M3	Complementation	To investigate their roles in RNA editing, we generated transgenic lines with mutated DYW domains in which the HxExnCxxC signature was changed to AxAxnCxxC (56M1 and 71M1) and HxExnAxxA (56M2 and 71M2	Knockout	NA	Protonemata	4-day-old	Direct sequencing was performed on the cDNA	0.00%	Unedited	Absent	29718364