Organellar rna editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting nonneutral codon mutations. Prominent among these acquired traits are rna splicing and rna editing. Rna editing in chloroplasts proceeds by the conversion of individual cytidine residues to uridine. Therefore, no ppr motifs are invariant within a ppr protein or between different ppr proteins. There could be three main mechanisms that regulate the levels of edited mrnas. U rna editing is the conversion from cytidine to uridine at rna level. Frontiers unveiling chloroplast rna editing events using. In this paper, we investigated 82 proteincoding genes in the chloroplast genome of g. Ppr editing factors contain multiple types of ppr motifs, and ppr motifs of the same type also show sequence variations. Rna editing by cytidinetouridine conversions is an essential step of rna maturation in plant organelles. All of these results indicate that atecb2 is required for chloroplast transcript accd rna editing and early chloroplast biogenesis in arabidopsis thaliana. Rna editing as an important posttranscriptional processing step in organelles is also known to be essential for seed development.
Editing sites are recognized by nucleusencoded rna binding proteins of the pentatricopeptide repeat ppr family, which bind upstream of the editing site in a sequencespecific manner and direct the editing activity to the target position. Editing of rna may play a role in chloroplast tonucleus communication. Establishment of a heterologous rna editing event in. The importance of various components of the editing system was tested, and the nucleotide specificity of the chloroplast editing system is demonstrated to be relatively nonspecific for ntp or dntp. For example, mutations in genes encoding dyw2 and nuwa required for rna editing in both mitochondria and chloroplasts are embryolethal andrescolas et al. Occurrence of plastid rna editing in all major lineages of. Interestingly, all but two editing sites are clustered in a.
Oz1, an rna editing factor that controls the editing of 14 cytidine targets in arabidopsis chloroplasts, contains two ranbp2type zinc finger znf domains. Rna editing in higher plant chloroplasts involves ctou conversion at specific sites in the transcripts. Rna editing is a process of rna maturation involved in the insertion, deletion or modification of nucleotides1. Pdf comparative analysis of asteraceae chloroplast. Structural organization, rna editing and evolution. Rna editing alters the identity of nucleotides in rna molecules such that the information for a protein in the mrna differs from the prediction of the genomic dna.
Establishment of a heterologous rna editing event in chloroplasts. How complex are the editosomes in plant organelles. Frequent chloroplast rna editing in earlybranching. Rna maturation in chloroplasts is complex, and ppr proteins act in cis and transsplicing, translation, rna cleavage, rna stabilization, and rna editing. The ranbp2 znf is a c4type member of the broader zinc. In the mitochondria and chloroplasts of higher plants there is an rna editing activity responsible for specific ctou conversions and for a few utoc conversions leading to rna sequences. The rna editing factor dua1 is crucial to chloroplast.
Sequence analysis of amplified cdnas for 69 potential editing sites revealed real editing sites in transcripts of 11 tobacco chloroplast genes. The recognition of a specific target c site by the editing machinery involves transacting factors that bind to the rna upstream of the c to be edited. Editing sites are recognized by nucleusencoded rna binding proteins of the pentatricopeptide repeat ppr family. China 2these authors contributed equally to this article. Pdf in the mitochondria and chloroplasts of higher plants there is an rna editing activity responsible for specific ctou conversions and for a. Abundant rna editing sites of chloroplast proteincoding. Reverse utoc rna editing in contrast appears to be restricted. Rna editing through the addition and deletion of uracil has been found in kinetoplastsa kinetoplast is a network of circular dna called kdna inside a large mitochondrion from the mitochondria of trypanosoma brucei because this may involve a large fraction of the sites in a gene, it is sometimes called pan editing to distinguish it from topical editing of one or a few sites. Identification of rna editing sites in cotton gossypium.
Rna editing refers to processes that change the identities of nucleotides and processes that add or delete nucleotides from rnas. We have therefore chosen this transcript to study the distribution of chloroplast editing within the plant kingdom. Critical to this question is the quantification of chloroplast rna editing efficiency in different tissue types. The rna editing factor dua1 is crucial to chloroplast development at low temperature in rice xuean cui, yanwei wang, jinxia wu, xiao han, xiaofeng gu, tiegang lu and zhiguo zhang biotechnology research institutenational key facility for genetic resources and gene improvement, the chinese academy of agricultural sciences, beijing 81, china. However, in some early diverging plant lineages, a relatively high level of. Six editing sites have been reported in maize 16, eight in rice, and nine in barley and tobacco 20. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves c. Rna editing in higher plant organelles results in the conversion of specific cytidine residues to uridine residues in rna. The loss of plastid editing events, resulting from mutations in rna editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. In chloroplasts and plant mitochondria, specific cytidines in mrnas are posttranscriptionally converted to uridines by rna editing. In organellar transcripts of higher plants, specific cytidine residues are. Cytosine c to uracil u rna editing in plant mitochondria and chloroplasts is facilitated by sitespecific pentatricopeptide repeat ppr editing factors. Chloroplast rna editing by pentatricopeptide repeat. Noncanonical features of pentatricopeptide repeat protein.
The discovery of rna editing in chloroplasts has provided researchers with a wealth of molecular puzzles and with extraordinarily high precision 36 bock r. Genetic information in chloroplast dna is sometimes altered at the transcript level by a process known as rna editing. The highly oxidative environment inside chloroplasts increases the rate of mutation so posttranscription repairs are needed to conserve functional sequences. A study of new arabidopsis chloroplast rna editing. Frequent chloroplast rna editing in earlybranching flowering plants. A study of new arabidopsis chloroplast rna editing mutants reveals general features of editing factors and their target sites w oa kamel hammani,a,b,1 kenji okuda,c,1 sandra k. These increases can be a response to keep the homeostasis of chloroplast protein functions in response to salt stress. During the evolution of chloroplasts from their bacterial ancestor traits emerged that are absent or rare in bacteria. Identification of rna editing sites in cotton gossypium hirsutum chloroplasts and editing events that affect secondary and threedimensional protein structures y. Rna editing is the insertion, deletion, and substitution of nucleotides in a mrna transcript prior to translation to protein. U rna editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornworttracheophyte clade. Effects of rna editing and gene processing on phylogenetic reconstruction l. To examine whether pea shares editing sites with other angiosperms, a systematic search for editing sites in pea chloroplast transcripts was performed.
Rna editing is the posttranscriptional conversion from c to u before translation, providing a unique feature in the regulation of gene expression. Rna editing in chloroplasts alters the rna sequence by converting c. In a few cases, a strong argument can be made that specific ctou editing events are essential for the production of functional plant mitochondrial proteins. Nucleotide specificity of the rna editing reaction in pea. Chloroplast rna editing was hypothesized to have evolved simultaneously with the origin of the first land plants 31 because it was poorly observed in plastidencoded rnas of algae groups 8. Rna editing has been reported in viruses and diverse eukaryotes. In chloroplasts and mitochondria of flowering plants, rna editing changes c nucleotides to u nucleotides. Mapping of plastid rna editing sites of helianthus and. Yu2 1college of life sciences, shaanxi normal university, xian, shaanxi, p.
Rna editing is a post transcriptional modification which occurs at specific sites of rna molecules in the chloroplasts of higher plants. During the study of the complete nucleotide sequence of the chloroplast genome from the hornwort anthoceros formosae, rna editing events have been systematically investigated. The net effect of ctou rna editing in plants is to make proteins encoded by plant organelles more similar in sequence to their nonplant homologs. Pdf a study of new arabidopsis chloroplast rna editing. Salk scientists uncover a link between rna editing and chloroplast tonucleus communication that could help plants adapt to a changing world. Pdf rna editing in plant mitochondria and chloroplasts. Unveiling chloroplast rna editing events using next. Rna editing in chloroplasts of spirodela polyrhiza, an. Some 5 years later, after the discovery of small rna templates that seem to guide the editing process and the identification of editing intermediates, kinetoplastid rna editing has been elevated.
Ctou rna editing in plants was first discovered in mitochondria covello and gray, 1989. Salt stress affects mrna editing in soybean chloroplasts. Although, systematic studies have been carried out in several plants, very scant information is available with regard to the oilseed crop, sunflower. The individual nucleotides are identified in the complex rna molecule population of either organelle by their sequence context. Arabidopsis ranbp2type zinc finger proteins related to. A study of new arabidopsis chloroplast rna editing mutants. The ranbp2 znf is a c4type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. Frontiers editing of chloroplast rps14 by ppr editing.
In the last few years, analysis of mutants affected in chloroplast biogenesis has identified several pentatricopeptide. Reverse utoc editing exceeds ctou rna editing in some. Comparative analysis of asteraceae chloroplast genomes. In flowering plants, rna editing converts cytidines to uridines in the rnas transcribed from the chloroplast and mitochondrial genomes 3. Rna splicing and rna editing in chloroplasts springerlink. Here, we present a method to screen chloroplast rna editing using public srna libraries from arabidopsis, soybean and rice. Rna editing has been observed in chloroplast transcripts from most land plants, but not from algae. In higher plant chloroplasts, ctou conversion occurs at around 30 specific sites in mrnas, many of which result in amino acid alteration. Tanz,a annelaure chateignerboutin,a toshiharu shikanai,c and ian smalla,2 a australian research council centre of excellence in plant energy biology, university of western australia, crawley 6009 wa.
The rna editing factor wsp1 is essential for chloroplast development in rice zhiguo zhang 1,2, xuean cui, yanwei wang, jinxia wu, xiaofeng gu1, and tiegang lu1, 1biotechnology research institutenational key facility for genetic resources and gene improvement, the chinese academy of agricultural sciences, beijing 81, p. The chloroplast genome encodes proteins required for photosynthesis, gene expression, and other essential organellar functions. Here, we used a robust and efficient method based on rna seq from nonribosomal total rna to simultaneously measure chloroplast gene expression and rna editing efficiency in the greater duckweed, spirodela polyrhiza, a species that provides a new. Oz1, an rna editing factor that controls the editing of 14 cytidine targets in arabidopsis chloroplasts, contains two ranbp2type zinc.
A complex target for a simple reaction in chloroplasts and mitochondria of most land plants, rna editing modifies specific nucleotides. Rna editing implicated in chloroplasttonucleus communication. We found that the expression levels of chloroplast genes were relatively constant, but 11 rna editing sites show significant changes in editing. The plant journal atecb2, a pentatricopeptide repeat. Rna editing in chloroplasts of spirodela polyrhiza, an aquatic. Rna editing by ctou conversions is nearly omnipresent in land plant chloroplasts and mitochondria, where it mainly serves to reconstitute conserved codon identities in the organelle mrnas. A pentatricopeptide repeat protein is essential for rna. Therefore, the atecb2 protein must regulate the rna editing of this site, and the dysfunctional accd protein from the unedited rna molecules could lead to the mutated phenotype.
This result suggests that a rna helicase may also be involved in the chloroplast editing reaction. The rna editing factor wsp1 is essential for chloroplast. Pdf rna editing alters the nucleotide sequence of an rna molecule so that it deviates from the sequence of its dna template. Rna editing in plant mitochondria and chloroplasts. Hornworts are crucial to understand the phylogeny of early land plants. In chloroplasts and plant mitochondria, specific cytidines in mrnas are posttranscriptionally. In this context, the question arises to which degree rna editing evolved in lemnoideae as a distinct clade of basal monocots. Derived from a cyanobacterial ancestor, the chloroplast combines prokaryotic and eukaryotic features of gene expression and is regulated by many nucleusencoded proteins. Editing of rna may play a role in chloroplasttonucleus. In higher plant chloroplasts, ctou conversion occurs at. Rna splicing and rna editing in chloroplasts request pdf.
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