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I Introduction
Plant Editosome Database
Plant Editosome Database (PED) is a comprehensive resource focused on the curation, prediction, and systematic reclassification of plant RNA editing factors, which are involved in multiple physiological activities, such as growth, development, and stress tolerance. For each curated editing factor, PED provides diverse annotations, including basic characteristics, molecular & biological functions, regulated RNA editing events, and detailed experimental evidence. Furthermore, based on domain composition and subcellular localization, PED systematically identify candidate PPR, MORF, ORRM, and OZ editing factors, provides related expression matrices under various biological contexts, and establishes a reclassified framework for MORF, ORRM, and OZ proteins. Beyond editing factors, PED integrates numerous editing sites from published organelle genome annotations. Additionally, PED is equipped with two online tools EFDetector and BLASTP.
II Curation
Publications
To curate experimentally validated editing factors and their relevant information, PED has collected publications from 2004 to 2026, utilizing key terms, such as "PPR", "Pentatricopeptide repeat", "MORF", "ORRM", "OZ", "Plant", and "RNA editing".
Curation model
To integrate detailed information on editing factors and their mediated editing events across various experimental conditions, PED establishes a standardized manual curation model.
| Data type | Description | Value |
|---|---|---|
| PMID/DOI | Publications reporting editing factors | Publication identifier |
| Species | Controlled vocabulary | Species name |
| Gene ID | Controlled vocabulary | Gene ID |
| Editing factor | Controlled vocabulary | Protein name |
| Protein family | Controlled vocabulary | e.g., PPR, MORF, ORRM, and OZ |
| Subfamily/Subgroup | Controlled vocabulary | e.g., P, PLS, E (E1 and E2), E+, DYW, and DYW:KP |
| Structure | Composition of editing factor | Domain composition |
| Physical interaction | Proteins interacting with the identified editing factor | Protein name |
| Allele | Experimental group | Conclusion term |
| Treatment | Treatment of editing factor | Conclusion term |
| Treatment details | Treatment details of editing factor | Conclusion term |
| Mutant type | Controlled vocabulary | Homozygous, Heterozygous, Knockout, Knockdown, Recessive |
| Phenotype | Plant phenotypes in different experimental groups | Conclusion term |
| Development stage | Controlled vocabulary | Conclusion term |
| Trait ontology | Controlled vocabulary | Conclusion term |
| Genotype/Ecotype | Controlled vocabulary | e.g., Columbia (Col-0) |
| Development stage | Development stage of samples | Conclusion term |
| Tissue | Controlled vocabulary | Conclusion term |
| Organelle | Controlled vocabulary | Mitochondrion, Chloroplast, and Plastid |
| Edited gene | Controlled vocabulary | Gene name |
| Organelle complex | Protein encoded by the edited gene | e.g. Acetyl-CoA carboxylase beta subunit (encoded by chloroplast gene accD) |
| Nuclear genome | Controlled vocabulary | Conclusion term |
| Organelle genome | Controlled vocabulary | Conclusion term |
| Editing type | Controlled vocabulary | e.g., Cytidine-to-Uridine (C-to-U), Uridine-to-Cytidine (U-to-C), and Adenosine-to-Inosine (A-to-I) |
| Region | Controlled vocabulary | e.g., CDS, 3'UTR, and 5'UTR |
| CDS position | Editing sites in CDS | Conclusion term |
| Other regions | Controlled vocabulary | e.g., cDNA, and genomic position |
| Other positions | Editing site position in other regions | Conclusion term |
| Codon from | Controlled vocabulary | Codon before editing |
| Codon to | Controlled vocabulary | Codon after editing |
| AA from | Controlled vocabulary | Amino acid before editing |
| AA to | Controlled vocabulary | Amino acid after editing |
| Molecular effect | Controlled vocabulary | Recoding, Synonymous |
| Editing frequency | Percentage of edited RNAs | Conclusion term |
| Editing extent | Controlled vocabulary | Unedited: 0%; Poor: (0%-20%); Low: [20%-40%); Medium: [40%-60%); High: [60%-100%); Complete 100% |
| Mutant effect | Controlled vocabulary (The effect is compared to wild type group. WEF: wild-type editing frequency; MEF: mutant editing frequency; CEF: complementary editing frequency) | None: WT/Control; Absent: MEF=0%; Decreased: MEF–WEF<-10%; Increased: MEF–WEF>10%; Restored: |CEF–WEF|≤10%; Similar: |MEF–WEF|≤10% |
| Detection method | Methods to detect editing frequency | Conclusion term |
III Data Integration
Candidate editing factors
To identify candidate RNA editing factors, PED has integrated 364 high-quality genomes across Archaeplastida, including glaucophytes (n=1), rhodophytes (n=7), prasinodermophytes (n=1), chlorophytes (n=33), charophytes (n=7), hornworts (n=12), mosses (n=13), liverworts (n=4), lycophytes (n=6), ferns (n=5), gymnosperms (n=13), and angiosperms (n=262).
Specifically, the hallmark domains and motifs of PPR (P, P1, P2, S1, S2, SS, L1, L2, E1, E2, E+, DYW, and DYW:KP), MORF (MORF), ORRM (RRM), and OZ (RanBP2 Znf) proteins were identified using hmmsearch in HMMER (version 3.2.1) with corresponding domain and motif profiles. PPR hallmark domain and motif profiles were obtained from a previous study (Gutmann et al. 2020) and searched using hmmsearch with parameters "-domtblout -noali -E 0.1." All hmmsearch scores for P, P1, P2, S1, S2, L1, L2, E1, E2, and E+ domains or motifs were greater than 0, with SS motif greater than 10, and DYW/DYW:KP domain greater than 30. As most PPR hallmark domain-containing proteins localize to mitochondria and/or plastids, they are defined as PPR proteins. In addition, PPR proteins were required to contain at least three of P, P1, P2, L1, L2, or SS motifs, unless they contained a DYW or DYW:KP domain.
The MORF domain profile, constructed using hmmbuild in HMMER (version 3.2.1) with nine MORF domains from A. thaliana, was searched using hmmsearch with parameters "-domtblout -noali -E 1e-10." As MORF domain was homologous to PA domain, only hits with hmmsearch score greater than 36 were kept. The RRM domain profile was obtained from Pfam (PF00076.26) and searched using hmmsearch with parameters "-domtblout -noali -E 1e-10." The hmmsearch score was greater than 0. GR domains, present in some MORF and ORRM proteins, were defined as regions containing at least eight glycines within a 20-amino-acid sliding window. The RanBP2 Znf profile was obtained from Pfam (PF00641.22) and searched using hmmsearch with the same parameters as for the RRM domain. As MORF, ORRM, and OZ proteins are localized to mitochondrion and/or plastids, the subcellular localization of the identified hallmark domain-containing proteins was predicted using DeepLoc (version 2.1) with "Accurate" mode, TargetP (version 2), Plant-mSub (https://bioinfo.usu.edu/Plant-mSubP), and LOCALIZER (https://localizer.csiro.au). Only localization results supported by at least two tools were retained. The domain composition was identified using InterPro (https://www.ebi.ac.uk/interpro).
Expression matrices
To calculate expression for RNA editing factor hallmark domain-containing genes, reference genome indexes were built using hisat2-build in HISAT2 (version 2.0.5) and rsem-prepare-reference in RSEM (version 1.3.1). Raw RNA sequencing data were quality-filtered using fastp (version 0.20.1) with parameters "-q 20 -u 40 -l 15 -g -x -r -W 4 -M 20 -w 12". Strand specificity was inferred using infer_experiment.py in RSeQC (version 2.6.4). Reads mapping was conducted using STAR (version 2.7.1a). Gene expression matrix was generated using rsem-calculate-expression in RSEM (version 1.3.1) with parameters "-keep-intermediate-files -time -star -append-names -output-genome-bam -sort-bam-by-coordinate".
Editing sites
RNA editing sites were extracted from plant organelle (including mitochondrion and plastid/chloroplast) genome annotations in the NCBI Reference Sequence Database (RefSeq, https://www.ncbi.nlm.nih.gov/nuccore). Totally, 2,651 organelle genome annotation files (".gff " and ".gff3") were obtained. For each editing site, detailed information was collected, including species, organelle, gene name, locus, editing type, strand, and codon/amino acid conversion.
IV Database Usage
Editing factor search
PED provides numerous RNA editing factors, alongside their basic descriptions, molecular & biological functions, experimental details, and mediated editing events in the "Editing Factors" module. Furthermore, PED accommodates candidate editing factors and their sequences in the "Candidate Factors" module, together with expression matrices of editing factor hallmark domain-containing genes in the "Expression Matrices" module.
Candidate editing factor identification
EFDetector (https://ngdc.cncb.ac.cn/bit/efdetector) enables large-scale identification of PPR, MORF, ORRM, and OZ candidate editing factors. Protein sequences are required as input for EFDetector. Additionally, online BLASTP can be used to align sequences of editing factors.
Editing site search
The "Edited Genes" module provides comprehensive information on edited sites, including their positions, types, counts, and molecular consequences, as well as their associated genes, organelles, species, and editing factors. In addition, to inspect all editing sites for a specific organism, please visit the "Species" module.
V Terminology
RNA Editing
RNA editing, a post-transcriptional modification primarily involving cytidine-to-uridine (C-to-U) and uridine-to-cytidine (U-to-C) alterations in mitochondria and plastids, serves as a pivotal layer of genetic regulation in plants. This modification is essential for various physiological processes, such as development, growth, and stress tolerance.
Editing factor & Editosome
Editing factors, a group of nuclear-encoded proteins, are assembled into an editosome to mediate RNA editing. To date, RNA editing factors have been primarily found in Pentatricopeptide Repeat (PPR) protein, Multiple Organelle RNA Editing Factor (MORF) (also known as RNA Editing Factor Interacting Protein (RIP)), Organelle RNA Recognition Motif-containing (ORRM) protein and Organelle Zinc (OZ) finger protein families, as well as other proteins. Among them, PPR proteins constitute the largest family of RNA editing factors, specifically recognizing RNA sequences through P/PLS motif tracts and catalyzing C-to-U and U-to-C editing via carboxyl-terminal (C-terminal) DYW and DW:KP domains, respectively. Furthermore, PPR proteins are classified into two subfamilies, P and PLS. Specifically, those in the P subfamily play multiple roles in diverse molecular processes, including RNA editing, as well as transcription, RNA stabilization, RNA cleavage, RNA splicing, and translation, while those in the PLS subfamily are predominantly dedicated to RNA editing. Moreover, the PLS subfamily can be further divided into PLS, E (E1 and E2), E+, and DYW subgroups. The four subgroups contain P, L, and S motifs in common, and the latter three contain specific motifs, namely, E, E+, and DYW motifs, respectively. MORF, ORRM, and OZ are PPRs' accessory proteins, named after their hallmark domains: MORF, RRM, and Ran Binding Protein 2 (RanBP2) type Zinc finger (Znf). Beyond hallmark domains, these proteins also incorporate diverse additional domains, such as Glycine-Rich (GR) domain in MORF proteins and PPR/MORF domains in ORRM proteins.
Hallmark domain-containing proteins
RNA editing factor hallmark domain-containing proteins may play important roles in RNA editing, as well as other molecular processes. Specifically, PPR proteins include P (P, P1, and P2), L (L1, and L2), S (S1, S2, and SS), E (E1 and E2), E+, DYW, and DYW:KP hallmark domains/motifs, while MORF, ORRM, and OZ proteins harbour MORF, RRM, and RanBP2 Znf hallmark domains, respectively.
Reclassification of non-PPR proteins
In terms of domain composition, MORF proteins are classified into four groups: (1) Single-Pure MORF (SP-MORF), containing a single MORF domain; (2) Single-Mixed MORF (SM-MORF), containing a single MORF domain plus one or more non-MORF domains; (3) Multiple-Pure MORF (MP-MORF), containing multiple MORF domains; and (4) Multiple-Mixed MORF (MM-MORF), containing multiple MORF domains plus one or more non-MORF domains. ORRM and OZ proteins are classified using the same approach applied to MORF proteins.
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VI Support
Comments & Collaborations
We look forward to worldwide comments, suggestions, and guidance from colleagues and peers with common research interests. We also invite the scientific community to submit their analysis results on RNA editing factors and events, and to collaborate with us to enhance the functionality and applicability of PED.