C-to-U conversion in the intercistronic ndhI/ndhG RNA of plastids from monocot plants: conventional editing in an unconventional small reading frame?

Abstract

Editing of plastid RNAs proceeds by C-to-U, in hornwort species also by extensive U-to-C, transitions, which predominantly lead to the restoration of codons for structurally and/or functionally important, conserved amino acid residues. So far, only one instance of editing outside coding regions has been reported - in the psbL/ psbF intergenic region of Ginkgo biloba. This site was proposed to have no functional importance. Here we present an evaluation of an editing site in the ndhI/ ndhG intergenic region in a related group of monocot plants. Efficient editing of this site, as well as the phylogenetic conservation of the resulting uridine residue, point at an important role for the sequence restored by editing. Two potential functions can be envisaged. (1) RNA secondary structure predictions suggest that the C-to-U conversion at this site can lead to a modified stem/loop structure of the ndhG 5' UTR, which could influence ndhG expression. (2) Alternatively, editing of the ndhI/ ndhG intergenic region may tag a so far unidentified small (12-codon) ORF, and lead to the restoration of a conserved phenylalanine codon. A screen with specific antibodies elicited against the putative peptide failed to detect such a peptide in chloroplast fractions. However, this failure may be attributable to its low and/or development-specific expression.

Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosana

“…Previously, a C-to-U conversion at the −10 position of the ndhG 5′UTR in monocot plants was predicted to modify the RNA secondary (stem/loop) structure (Drescher et al 2002 ), but was not observed in moth orchid. Instead, a C-to-U substitution at the −30 position of the psbH 5′UTR that can form an energetically less stable secondary structure was reported in moth orchid (Zeng et al 2007 ).…”

“…Some RNA editing events could result in the creation of translation initiation or termination codons or repair internal stop codons (Bock 2000 ; Fiebig et al 2004 ; Wolf et al 2004 ). Several events occurring in non-coding regions such as tRNA, 5′/3′ untranslated regulatory regions (UTR) or introns might affect RNA stability or splicing by modifying the secondary structure (Drescher et al 2002 ; Farre et al 2012 ; Zeng et al 2007 ). The significance of RNA editing in regulating plant organellar gene expression has been demonstrated, with the alteration of some editing sites having deleteriously effects on plant growth, development, and fertility (Hammani and Giege 2014 ).…”

Variable Frequency of Plastid RNA Editing among Ferns and Repeated Loss of Uridine-to-Cytidine Editing from Vascular Plants

“…3B ) and other species [ 5 , 19 , 25 , 59 – 62 ] appears in some cases to improve intron secondary structure, which is important to increase intron splicing efficiency. Intergenic edit sites in plant organellar transcripts may also have functional importance in some cases, such as regulating translational efficiency [ 7 , 19 , 63 , 64 ].…”

Post-Transcriptional Control of Chloroplast Gene Expression

“…Editing sites have also been detected in the anticodon of tRNA (Leu) and within untranslated regions, including introns. 122,[137][138][139] However, it seems that the frequency of editing within noncoding regions is very low in comparison with the extent of editing within coding regions. The discovery that editing often leads to the conservation of certain amino acid residues in some proteins in both mitochondria and chloroplasts suggests that editing may act as a mechanism to prevent the deleterious effects of point mutations that have been maintained through evolution.…”