A study of RNA-editing in Populus trichocarpa nuclei revealed acquisition of RNA-editing on the endosymbiont-derived genes, and a preference for intracellular remodeling genes in adaptation to endosymbiosis

Abstract

RNA-editing is a post-transcriptional modification that can diversify genome-encoded information by modifying individual RNA bases. In contrast to the well-studied RNA-editing in organelles, little is known about nuclear RNA-editing in higher plants. We performed a genome-wide study of RNA-editing in Populus trichocarpa nuclei using the RNA-seq data generated from the sequenced poplar genotype, 'Nisqually-1'. A total of 24,653 nuclear RNA-editing sites present in 8,603 transcripts were identified. Notably, RNA-editing in P. trichocarpa nuclei tended to occur on endosymbiont-derived genes. We then scrutinized RNA-editing in a cyanobacterial strain closely related to chloroplast. No RNA-editing sites were identified therein, implying that RNA-editing of these endosymbiont-derived genes was acquired after endosymbiosis. Gene ontology enrichment analysis of all the edited genes in P. trichocarpa nuclei demonstrated that nuclear RNA-editing was primarily focused on genes involved in intracellular remodeling processes, which suggests that RNA-editing plays contributing roles in organellar establishment during endosymbiosis. We built a coexpression network using all C-to-U edited genes and then decomposed it to obtain 18 clusters, six of which contained a conserved core motif, A/G-C-A/G. Such a short core motif not only attracted the RNA-editing machinery but also enabled large numbers of sites to be targeted though further study is necessary to verify this finding.

Keywords: Endosymbionts; Endosymbiosis; Nuclear RNA-editing; Populus trichocarpa; and Organelles.

Figure 1

Characteristics of RNA-editing sites in Populus trichocarpa nuclear genome. (a) The numbers of the 12 RNA-editing types. (b) The numbers of the four dominant nuclear RNA-editing types in respect to the positions within genetic codons. 1st, 2nd and 3rd represent the first, second and third positions within codons. (c) The numbers of the four dominant nuclear RNA-editing types in respect to synonymous and non-synonymous RNA-editing. Synonymous RNA-editing refers to RNA-editing events that change the RNA sequence but do not change the amino acid sequences, whereas non-synonymous RNA-editing is regarding the events that alter both RNA and amino acid sequences. (d) RNA-editing densities of the 12 RNA-editing types for 5’ untranslated regions (UTR), 3’UTRs and coding regions (CDS). (e) RNA-editing densities of the 12 editing types in respect to 5’UTR, coding regions and 3’ UTRs. CDS represents coding region.

Figure 2

Boxplot of the expression levels of edited transcripts in seven groups. A: Transcripts with RNA-editing only in 5’UTR; B: Transcripts with RNA-editing only in the coding region; C: Transcripts with RNA-editing only in 3’UTR; AB: Transcripts with RNA-editing in 5’UTR and the coding region simultaneously; AC: Transcripts with RNA-editing in 5’UTR and 3’UTR simultaneously; BC: Transcripts with RNA-editing in the coding region and 3’-UTR simultaneously; ABC: Transcripts with RNA-editing in 5’UTR, the coding region and 3’UTR simultaneously. The median and the mean of each group is represented by a horizontal bar and diamond, respectively. The numbers above the boxes represent the numbers of the transcripts in each group.

Figure 3

Distinct discrepancy of nuclear RNA-editing events in relation to different amino acids. The red dots represent the ratios of editing sites to the number of degenerate codons.

Figure 4

Gene ontology (GO) enrichment results of all the edited genes in Populus trichocarpa nuclei. Orange bars and blue bars represent the percentages of edited genes and non-edited genes, respectively, in each GO category.

Figure 5

Phylogenetic tree analysis of putative adenosine deaminases in the Populus trichocarpa and A. thaliana nuclear genome. Protein sequences were aligned with ClustalW, and MEGA was used to construct the phylogenetic tree based on the neighbor-joining method with 1,000 bootstrap replications.

Figure 6

Flanking sequences of the edited C residues, and subcellular location of the edited genes in the six clusters. Using the coexpression based method, we clustered PPR genes and the C-to-U edited genes into six clusters. The pie chart represents the subcellular location of the C-to-U edited genes in each cluster. The line chart represents the ten adjacent bases of the edited C residues in each cluster. For the X axis, C represents the edited C residues; -5 to -1 represent the five upstream bases of the edited C residues; 1 to 5 represent the five downstream bases of the edited C residues. The Y axis represents the number of RNA-editing sites in each cluster.

Figure 7

Identification of RNA-editing sites using expressed sequence tags (EST) of Populus trichocarpa (Nisqually-1). (a), (b), (e) and (f) showed the identified RNA editing sites in P. trichocarpa while (c) and (d) showed the RNA editing sites identified in A. thaliana chloroplasts that have been experimentally verified (Fig. 7c, d).

Figure 8

A model of the establishment of plant organelles and possible roles of RNA-editing during this process. Protein complexes or cellular components with red dots indicated they were subjected to RNA-editing. At the beginning of endosymbiosis (1), the plant ancestral cell engulfed a prokaryotic bacterium. (2) Upon engulfment, plant ancestral cells performed significant intracellular remodeling, which altered the nuclear membrane, the protein degradation system and the chromatin remodeling system, to embrace this bacterium. (3) After successful establishment of organelles, the genome of the organelle was significantly smaller compared to its ancestor. HGT: horizontal gene transfer. CRC: chromatin remodeling complex. UPS: ubiquitin-proteasome system. SPR: signal recognition particle, chloroplast targeting.