Identification of RNA Editing Sites in Chloroplast Transcripts from the Maternal and Paternal Progenitors of Tobacco (Nicotiana tabacum): Comparative Analysis Shows the Involvement of Distinct Trans-Factors for ndhB Editing

Abstract

RNA editing alters genomic nucleotide sequences at the transcript level. In higher plant chloroplasts, C-to-U conversion is known to occur at around 30 specific sites. The tobacco cultivar Nicotiana tabacum is an amphidiploid derived from ancestors of N. sylvestris (maternal) and N. tomentosiformis (paternal). The chloroplast genome of N. tabacum is believed to originate from an ancestor of N. sylvestris. To study the evolution of RNA editing in higher plant chloroplasts, editing sites in the two likely progenitors have first been identified based on those found in N. tabacum. Altogether 34, 33, and 32 editing sites have been found in the chloroplast transcripts from N. tabacum, N. sylvestris, and N. tomentosiformis, respectively. Thirty-one sites are conserved among the three species, whereas remarkable differences are observed in the editing of ndhB and ndhD transcripts. Sites 7 and 8 in ndhB mRNAs are separated only by five nt, and both are edited in N. tabacum and N. sylvestris. However, site 8 is not edited in N. tomentosiformis, indicating that distinct trans-factors are involved in the two editing events. The first site in ndhD mRNAs is edited to produce an AUG start codon in N. sylvestris as well as in N. tabacum but not in N. tomentosiformis, suggesting that a distinct mechanism operates for the translational initiation of N. tomentosiformis ndhD mRNAs. Four to six sites are edited partially in green leaves. Some of these sites may represent evolutionary intermediates in the process of losing editing events.

Plastid Transcriptomics and Translatomics of Tomato Fruit Development and Chloroplast-to-Chromoplast Differentiation: Chromoplast Gene Expression Largely Serves the Production of a Single Protein

“…One of the two RNA editing sites resides in the translation initiation codon and creates a canonical AUG start codon from a genomically encoded ACG codon. A lack of editing is unlikely to render the ndhD mRNA untranslatable, as previous work has established that ACG-to-AUG editing is not essential for ndhD translation in tobacco (Sasaki et al, 2003;ZanduetaCriado and Bock, 2004). However, in the absence of clearly defined functions of the NAD(P)H dehydrogenase in green and nongreen plastids, it remains difficult to assess the physiological consequences of the developmentally regulated RNA editing patterns in ndh transcripts.…”

Pigment Deficiency in Nightshade/Tobacco Cybrids Is Caused by the Failure to Edit the Plastid ATPase α-Subunit mRNA

“…Several studies suggest that these interactions may be evolutionarily labile. Editing sites evolve with extreme rapidity (Shields and Wolfe, 1997;Sasaki et al, 2003). In addition, the responsible nucleus-encoded RNA editing factors are evolutionarily labile as well (Bock et al, 1994;Bock and Koop, 1997;Reed and Hanson, 1997).…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…The genes psbT, rpl2, and ndhD had the alternative start codon ACG, and rps19 started with GTG. Use of ACG and GTG as start codons is common for a variety of genes in the chloroplast genomes of land plants [17][18][19][20]. Finally, the cemA gene was identified as a pseudogene with a premature stop codon in the F. cirrhosa cp genome.…”