Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

Abstract

These authors contributed equally to the manuscript. SUMMARYThe pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterised by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence-specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria, where they play important roles in post-transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide-binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA-editing factors. We show that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes. We report a high error rate in PPR gene models in many public plant proteomes, due to gene fusions and insertions of spurious introns. These consistently annotated datasets across a wide range of species are valuable resources for future comparative genomics studies, and an essential pre-requisite for accurate large-scale computational predictions of PPR targets. We have created a web portal (http://www.-plantppr.com) that provides open access to these resources for the community.

Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species

“…PLS sub-class was further sub categorized into PLS, E1, E2 and DYW and majority of the proteins were found to posess DYW editing motif (Figure 2b) except in Cicer. None of the PPR was categorized into E + sub-group that is known to constitute proteins with a degenerate or truncated DYW domain [15]. A small proportion of sequences were identified with E1 motif present as a C terminal domain in all legumes (Figure 2b).…”

“…Though recently, a documentation of PPR proteins in 109 genomes has been done [15] and includes few legume species, the goal of the current study is to expand the knowledge base on these proteins in legumes. The members of Phaseoleae, Cicereae and Trifolieae tribe i.e., Cajanus cajan, Glycine max, Vigna radiata, Phaseolus vulgaris, Cicer arietinum and Medicago truncatula were selected to provide an understanding of the PPR gene family in legumes.…”

“…Due to certain limitations of demarking PPR motifs by classical system of categorization, PPR motifs has been redefined by Cheng et al [15] whereby 10 PPR motif variants have been described and used to annotate PPR sequences in 109 genomes. Newly identified motif variants in PLS sub-class includes P1 and P2 motifs that differ from classical P motif in first helix; S2 (32 amino acid), SS (31 amino acid), E1 (34 amino acid) and E2 (34 amino acid) motif.…”

“…Non plant organisms have very few PPRs whereas great expansion of this gene family via retrotransposition has been observed in plants [13]. Their number in a particular species could range from less than 30 in eukaryotes (Chlamydomonas reinhardtii) [14] to 1882 members in T. aestivum [15]. PPR proteins are categorized into different sub-classes and subgroups on the basis of the sequence content and arrangement of peptide repeat motifs that constitutes their structural and functional divergence [16].…”

“…Legumes are divided in three sub-families and the important species fall under two papilionoid clades i.e., phaseoloid clade and galegoid clade [32]. Considering the importance of legumes, in depth analysis of their genome structure is important to improve their yield and quality using various genetics and genomics approaches.Though recently, a documentation of PPR proteins in 109 genomes has been done [15] and includes few legume species, the goal of the current study is to expand the knowledge base on these proteins in legumes. The members of Phaseoleae, Cicereae and Trifolieae tribe i.e., Cajanus cajan, Glycine max, Vigna radiata, Phaseolus vulgaris, Cicer arietinum and Medicago truncatula were selected to provide an understanding of the PPR gene family in legumes.…”