Ectothermic organisms may expand their thermal tolerance by producing multiple protein isoforms with differing thermal sensitivities.While such isoforms commonly originate from allelic variation at a single locus(allo...Ectothermic organisms may expand their thermal tolerance by producing multiple protein isoforms with differing thermal sensitivities.While such isoforms commonly originate from allelic variation at a single locus(allozymes)or from gene duplication that gives rise to paralogs with distinct thermal responses,this study investigated mRNA editing as an alternative,post-transcriptional mechanism for generating mRNA variants.Cytosolic malate dehydrogenase(cMDH)was examined in foot tissue of two congeners of the marine mussel genus Mytilus,which occupy different thermal environments.Multiple editing events were detected within the mRNA coding region in both species.Editing sites were species-specific,with no shared positions identified.In M.coruscus,editing occurred at 117,123,135,190,195,204,279,and 444,while in M.galloprovincialis,editing was detected at 216 and 597.Each species exhibited multiple edited mRNA variants,and these isoforms were associated with differential protein expression.These findings suggest that mRNA editing may contribute an additional layer of molecular variation.The generation of diverse mRNA isoforms from a single DNA coding sequence may enhance enzymatic flexibility across temperature ranges,supporting eurythermal physiological performance and mitigating thermal stress.Moreover,the presence of multiple edited transcripts within individual organisms raises important caveats about the limitations of approaches that deduce amino acid sequences or estimate adaptive variation solely from genomic data.展开更多
In plants, RNA editing is a post-transcriptional process that changes specific cytidine to uridine in both mitochondria and plastids. Most pentatricopeptide repeat（PPR） proteins are involved in organelle RNA editing...In plants, RNA editing is a post-transcriptional process that changes specific cytidine to uridine in both mitochondria and plastids. Most pentatricopeptide repeat（PPR） proteins are involved in organelle RNA editing by recognizing specific RNA sequences. We here report the functional characterization of a PPR protein from the DYW subclass, Baili Xi（BLX）, which contains five PPR motifs and a DYW domain. BLX is essential for early seed development, as plants lacking the BLX gene was embryo lethal and the endosperm failed to initiate cellularization. BLX was highly expressed in the embryo and endosperm, and the BLX protein was specifically localized in mitochondria, which is essential for BLX function. We found that BLX was required for the efficient editing of 36 editing sites in mitochondria. Moreover, BLX was involved in the splicing regulation of the fourth intron of nad1 and the first intron of nad2. The loss of BLX function impaired the mitochondrial function and increased the reactive oxygen species（ROS） level. Genetic complementation with truncated variants of BLX revealed that, in addition to the DYW domain, only the fifth PPR motif was essential for BLX function. The upstream sequences of the BLX-targeted editing sites are not conserved, suggesting that BLX serves as a novel and major mitochondrial editing factor（MEF） via a new non-RNA-interacting manner. This finding provides new insights into how a DYW-type PPR protein with fewer PPR motifs regulates RNA editing in plants.展开更多
Osteoarthritis(OA)is one of the most common degenerative joint diseases worldwide,causing pain,disability,and decreased quality of life.The balance between regeneration and inflammation-induced degradation results in ...Osteoarthritis(OA)is one of the most common degenerative joint diseases worldwide,causing pain,disability,and decreased quality of life.The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA.Currently,there is a lack of effective therapeutic strategies for OA treatment.With the development of CRISPR-based genome,epigenome,and RNA editing tools,OA treatment has been improved by targeting genetic risk factors,activating chondrogenic elements,and modulating inflammatory regulators.Supported by cell therapy and in vivo delivery vectors,genome,epigenome,and RNA editing tools may provide a promising approach for personalized OA therapy.This review summarizes CRISPR-based genome,epigenome,and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment.Moreover,in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.展开更多
In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identi...In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identified, the mechanisms underlying such development are not fully understood. In this study, a rice(Oryza sativa) mutant exhibiting pale green color and seedling lethality was isolated from a mutant library. The mutated gene was identified as an ortholog of THA8(thylakoid assembly 8) in Arabidopsis and maize. This gene is designated as OsTHA8 hereafter. OsTHA8 showed a typical pentatricopeptide repeat(PPR) characteristic of only four PPR motifs. Inactivation of OsTHA8 led to a deficiency in chloroplast development in the rice seedling stage. OsTHA8 was expressed mainly in young leaves and leaf sheaths.The OsTHA8 protein was localized to the chloroplast. Loss of function of OsTHA8 weakened the editing efficiency of ndhB-611/737 and rps8-182 transcripts under normal conditions. Y2H and BiFC indicated that OsTHA8 facilitates RNA editing by forming an editosome with multiple organellar RNA editing factor(OsMORF8) and thioredoxin z(OsTRXz), which function in RNA editing in rice chloroplasts. Defective OsTHA8 impaired chloroplast ribosome assembly and resulted in reduced expression of PEP-dependent genes and photosynthesis-related genes. Abnormal splicing of the chloroplast gene ycf3 was detected in ostha8. These findings reveal a synergistic regulatory mechanism of chloroplast biogenesis mediated by RNA, broaden the function of the PPR family, and shed light on the RNA editing complex in rice.展开更多
Photosynthesis occurs mainly in chloroplasts,whose development is regulated by proteins encoded by nuclear genes.Among them,pentapeptide repeat(PPR)proteins participate in organelle RNA editing.Although there are more...Photosynthesis occurs mainly in chloroplasts,whose development is regulated by proteins encoded by nuclear genes.Among them,pentapeptide repeat(PPR)proteins participate in organelle RNA editing.Although there are more than 450 members of the PPR protein family in rice,only a few affect RNA editing in rice chloroplasts.Gene editing technology has created new rice germplasm and mutants,which could be used for rice breeding and gene function study.This study evaluated the functions of OsPPR9 in chloroplast RNA editing in rice.The osppr9 mutants were obtained by CRISPR/Cas9,which showed yellowing leaves and a lethal phenotype,with suppressed expression of genes associated with chloroplast development and accumulation of photosynthetic-related proteins.In addition,loss of OsPPR9 protein function reduces the editing efficiency of rps8-C182,rpoC2-C4106,rps14-C80,and ndhB-C611 RNA editing sites,which affects chloroplast growth and development in rice.Our data showed that OsPPR9 is highly expressed in rice leaves and encodes a DYW-PPR protein localized in chloroplasts.Besides,the OsPPR9 protein was shown to interact with OsMORF2 and OsMORF9.Together,our findings provide insights into the role of the PPR protein in regulating chloroplast development in rice.展开更多
Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors. In this study, we identified OsDXR, a gene encoding a reductoisomerase that ...Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors. In this study, we identified OsDXR, a gene encoding a reductoisomerase that positively regulates chlorophyll biosynthesis and chloroplast development in rice. OsDXR knock-out lines displayed the albino phenotype and could not complete the whole life cycle process. OsDXR was highly expressed in rice leaves, and subcellular localization indicated that OsDXR is a chloroplast protein. Many genes involved in chlorophyll biosynthesis and chloroplast development were differentially expressed in the OsDXR knock-out lines compared to the wild type.Moreover, we found that the RNA editing efficiencies of ndhA-1019 and rpl2-1 were significantly reduced in the OsDXR knock-out lines. Furthermore, OsDXR interacted with the RNA editing factor OsMORF1 in a yeast two-hybrid screen and bimolecular fluorescence complementation assay. Finally, disruption of the plastidial 2-C-methyl-derythritol-4-phosphate pathway resulted in defects in chloroplast development and the RNA editing of chloroplast genes.展开更多
Cytidine-to-uridine(C-to-U)RNA editing is common in coding regions of organellar genomes throughout land plants.In most cases RNA editing alters translated amino acids or creates new start codons,potentially confounds...Cytidine-to-uridine(C-to-U)RNA editing is common in coding regions of organellar genomes throughout land plants.In most cases RNA editing alters translated amino acids or creates new start codons,potentially confounds phylogenetic reconstructions.In this study,we used the spike moss genus Selaginella(lycophytes),which has the highest frequency of RNA editing,as a model to test the effects of extreme RNA editing on phylogenetic reconstruction.We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes,and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences,first and second codon positions,and translated amino acid sequences,respectively.We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes.The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions,but not correlated with the GC content of plastomes as a whole.Contrast phylogenetic analyses showed that there were substantial differences(e.g.,the placement of clade B in Selaginella)between the phylogenies generated by the plastome and RNA-edited data sets.This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction,and might even confound phylogenetic reconstruction.Therefore,RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies,particularly in those lineages with abundant organellar RNA editing sites,such as hornworts,quillworts,spike mosses,and some seed plants.展开更多
To study the expression of RNA editing deaminases ADAR2 and ADAR3 in different malignant glioma cell lines and the effect of phenylacetate on the expression of these genes, the primarily glial cells of human brain tis...To study the expression of RNA editing deaminases ADAR2 and ADAR3 in different malignant glioma cell lines and the effect of phenylacetate on the expression of these genes, the primarily glial cells of human brain tissue were isolated and cultured. The human glioma SHG-44, U-251, BT-325 cell lines were maintained in culture. The expressions of ADAP,.2 and ADAR3 mRNA were detected by the semiquantitative reverse transcription-polymerase chain reaction（RT-PCR）. The changes in ADAR2 mRNA expression before and after phenylacetate treatment were detected by RT-PCR and image analysis. The level of ADAR gene expression is expressed as the ratio expression rate（RER） of ADAR gene to β-actin according to computer image analysis. ADAR2 displays moderate expression in glial cells, low expression in low-grade malignant glioma SHG-44 cells, and high level expression in high-grade malignant glioma U-251and BT-325 cells. The expression of ADAR2 can be decreased by phenylacetate treatment in glioma U-251 cells. ADAR3 is not expressed in normal brain glial cells, or glioma SHG-44, U-251 and BT-325 cells before and after phenylacetate treatment. The enhanced expression of ADAR2 may be involved in the tumor progression of malignant glioma. Phenylacetate can decrease the expression of ADAR2 in glioma cells, suggesting that it may act on the RNA editing process in glioma.展开更多
The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize th...The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.展开更多
The CRISPR-Cas13 system,an RNA-guided editing tool,has emerged as a highly efficient and stable RNA editing technique.Although the CRISPR-Cas13 system has been developed in several insect species,its application in le...The CRISPR-Cas13 system,an RNA-guided editing tool,has emerged as a highly efficient and stable RNA editing technique.Although the CRISPR-Cas13 system has been developed in several insect species,its application in lepidopterans has not yet been reported.In the present study,we evaluated the RNA cleavage activity of the CRISPR-Cas13 system in the silkworm(Bombyx mori),a model lepidopteran insect,both ex vivo and in vivo.We established two stable silkworm BmE cell lines expressing PspCas13b and CasRx,respectively.Further analysis demonstrated that both PspCas13b and CasRx effectively down-regulated the transcription of exogenouslyintroduced target and endogenous genes in these cell lines.In addition,we generated two transgenic silkworm strains,one expressing CasRx and the other expressing RNA-guided CRISPR RNA targeting Sex combs reduced(Scr).Further crossing experiments showed that CasRx induced a down-regulation of Scr transcription in silkworms,which impaired systemic growth of larvae.Overall,this study demonstrated that the CRISPR-Cas13RNA editing system works efficiently in the silkworm,providing a potential alternative approach for RNA manipulation in lepidopteran insects.展开更多
Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modif...Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modifications is limited.In this study,we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium,a genus with diverse trophic lifestyles.Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives.This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex,but independent pseudogenization of ndh genes has also occurred in the epiphyte C.mannii,which was reported to use strong crassulacean acid metabolism photosynthesis.RNA editing sites are abundant but variable in number among Cymbidium plastomes.The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial,mycoheterotrophic,and C.mannii plastomes.The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed,leading to nonrandom loss of ancestral edited sites via reduced editing efficiency.This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus.We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.展开更多
Sunflower is one of the most used commercial oilseed crops and suffers due to Powdery mildew. RNA sequence alteration occurs due to RNA editing which is a post transcriptional modification. It causes a deviation from ...Sunflower is one of the most used commercial oilseed crops and suffers due to Powdery mildew. RNA sequence alteration occurs due to RNA editing which is a post transcriptional modification. It causes a deviation from the genomic DNA sequence resulting in RNA-DNA differences. Accurate study of RNA editing events in diverse species is possible by NGS based methods. Here, we performed RNA sequencing of 12 leaf transcriptomes, which include three genotypes of Helianthus annuus (2023B, TX16R and ID25), H. debilis, H. niveus, and H. praecox along with their respective powdery mildew pathogen infected variants and systematically analysed the mitochondrial RNA editing events using computational reference-based mapping approach. We discovered 687 editing sites, 220 editing events in the protein-coding regions, among all species and genotypes considered in this study. These included “C to U” and “U to C” RNA editing events. On further analysis, we observed that these editing events include 14 different types of amino acid changes that involve the creation of two stop codon events. The conserved editing sites identified were 247 accounting for ~36% of all the editing sites identified. This study provides a detailed picture of the Helianthus species’ mitochondrial RNA editing status. We have identified and characterized for the first time, genotype-specific, species-specific, and stress-specific RNA editing events which may be useful as a potential source for stress-responsive studies in the future.展开更多
In the chloroplasts/plastids and mitochondria of flowering plants,RNA editing alters hundreds of cytidines to uridines at specific sites mediated by the editosome.Over the past decade,Multiple Organellar RNA Editing F...In the chloroplasts/plastids and mitochondria of flowering plants,RNA editing alters hundreds of cytidines to uridines at specific sites mediated by the editosome.Over the past decade,Multiple Organellar RNA Editing Factor(MORF)proteins have emerged as essential regulators that affect the editing efficiency of most editing sites in plastids and mitochondria.In Arabidopsis,the MORF family consists of nine members,each possessing a single conserved MORF-box that is distributed among flowering plants.Accumulating studies have demonstrated that MORF proteins interact with many other factors,including the PPR proteins and enzymes in different biosynthetic pathways,indicating that the MORF proteins play a more extensive role in regulating organellar development than RNA editing.Recent studies reveal that MORF2 and MORF9 possess holdase activity and may act as chaperones and that MORF8 undergoes heatdependent phase separation to inhibit RNA editing in chloroplasts.In this review,we provide an overview of our current knowledge of the MORF family proteins and discuss the biological and molecular functions of this family in plants.展开更多
This is a correction to:Hao Cheng,Jun Yu,Chi Chun Wong,Adenosine-to-inosine RNA editing in cancer:molecular mechanisms and downstream targets,Protein&Cell,2024;https://doi.org/10.1093/procel/pwae039 In the origina...This is a correction to:Hao Cheng,Jun Yu,Chi Chun Wong,Adenosine-to-inosine RNA editing in cancer:molecular mechanisms and downstream targets,Protein&Cell,2024;https://doi.org/10.1093/procel/pwae039 In the originally published version of the manuscript there were errors in Figure 2.In panel H,text should read:"Loses capacity"instead of:"oses capacity";a redundant letter"I"that was highlighted should be removed.展开更多
Although the multiple organellar RNA editing factors （MORFs） in the plastids of Arabidopsis thaliana have been extensively studied, molecular details underlying how MORFs affect plant development in other species, p...Although the multiple organellar RNA editing factors （MORFs） in the plastids of Arabidopsis thaliana have been extensively studied, molecular details underlying how MORFs affect plant development in other species, particularly in rice, remain largely unknown. Here we describe the characterization of wspl, a rice mutant with white-stripe leaves and panicles. Notably, wspl exhibited nearly white immature panicles at the heading stage. Transmission electron microscopy analysis and chlorophyll content measurement re- veale i a chloroplast developmental defect and reduced chlorophyll accumulation in wspl. Positional cloning of WSP1 found a point mutation in OsO4g51280, whose putative product shares high sequence similarity with MORF proteins. Complementation experiments demonstrated that WSP1 was responsible for the variegated phenotypes of wspl. WSP1 is localized to chloroplasts and the point mutation in wspl affected the editing of multiple organellar RNA sites. Owing to the defect in plastid RNA editing, chloroplast ribosome biogenesis and ndhA splicing were also impaired in wspl, which may affect normal chloroplast development in the leaves and panicles at the heading stage. Together, our results demonstrate the importance of rice WSP1 protein in chloroplast development and broaden our knowledge about MORF family members in rice.展开更多
RNA editing sites in plant mitochondria and plastids are addressed by pentatricopeptide repeat （PPR） proteins with E or E and DYW domains, which recognize a specific nucleotide motif upstream of the edited nucleotid...RNA editing sites in plant mitochondria and plastids are addressed by pentatricopeptide repeat （PPR） proteins with E or E and DYW domains, which recognize a specific nucleotide motif upstream of the edited nucleotide. In addition, some sites require MORF proteins for efficient RNA editing. Here, we assign the novel E domain-containing PPR protein, MEF13, as being required for editing at eight sites in Arabidopsis thaliana. A SNP in ecotype C24 altering the editing level at only one of the eight target sites was located by genomic mapping. An EMS mutant allele of the gene for MEF13 was identified in a SNaPshot screen of a mutated plant population. At all eight target sites of MEF13, editing levels are reduced in both morf3 and morf8 mutants, but at only one site in morfl mutants, suggesting that specific MEF13-MORF interactions are required. Yeast two-hybrid analyses detect solid connections of MEF13 with MORF1 and weak contact with MORF3 proteins. Yeast three-hybrid （Y3H） analysis shows that the presence of MORF8 enhances the connection between MEF13 and MORF3, suggesting that a MORF3-MORF8 heteromer may form stably or transiently to establish interaction with MEF13.展开更多
HBV is considered as a“stealth”virus that does not invoke interferon(IFN)responses;however,the mechanisms by which HBV bypasses innate immune recognition are poorly understood.In this study,we identified adenosine d...HBV is considered as a“stealth”virus that does not invoke interferon(IFN)responses;however,the mechanisms by which HBV bypasses innate immune recognition are poorly understood.In this study,we identified adenosine deaminases acting on RNA 1(ADAR1),which is a key factor in HBV evasion from IFN responses in hepatocytes.Mechanically,ADAR1 interacted with HBV RNAs and deaminated adenosine(A)to generate inosine(I),which disrupted host immune recognition and thus promoted HBV replication.Loss of ADAR1 or its deficient deaminase activity promoted IFN responses and inhibited HBV replication in hepatocytes,and blocking the IFN signaling pathways released the inhibition of HBV replication caused by ADAR1 deficiency.Notably,the HBV X protein(HBx)transcriptionally promoted ADAR1 expression to increase the threshold required to trigger intrinsic immune activation,which in turn enhanced HBV escape from immune recognition,leading to persistent infection.Supplementation with 8-azaadenosine,an ADAR1 inhibitor,efficiently enhanced liver immune activation to promote HBV clearance in vivo and in vitro.Taken together,our results delineate a molecular mechanism by which HBx promotes ADAR1-derived HBV immune escape and suggest a targeted therapeutic intervention for HBV infection.展开更多
RNA editing for the mitochondrlal ATP9 gene of encoding regions has been observed in both cytoplasmic malesterile and maintainer lines of stem mustard, where its editing capacity varied spatially and temporally in the...RNA editing for the mitochondrlal ATP9 gene of encoding regions has been observed in both cytoplasmic malesterile and maintainer lines of stem mustard, where its editing capacity varied spatially and temporally in the cytoplasmic male sterility （CMS） line. There were four RNA editing sites for the mitochondrial ATP9 gene according to Its normal editing sites in mustard, of which three sites occurred as C-to-U changes and one as a U-to-C change. As a result, the hydrophobicity of deduced ATP9 protein was reduced due to the conversions at its 17th, 45th and 64th positions. Meanwhile, the conservation of deduced ATP9 protein was enhanced by changes at the 56th position. Loss of a specific editing site for ATP9 was observed in juvenile roots, senile roots, senile leaves and floret buds of the CMS line. Comparatively, complete RNA editing for ATP9 gene was retained in juvenile roots, juvenile leaves and floret buds of its maintainer line; however, the loss of a specific editing site for ATP9 gene occurred at senile roots and senile leaves in its maintainer line. These observations allow us to produce a hypothesis that the dysfunction of a specific mitochondrial gene arising from RNA editing could probably be a factor triggering CMS and organ senescence through unknown cross-talk pathways during development.展开更多
RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C...RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position, ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.展开更多
基金supported by the National Key Research and Development Program of China(2022-24)National Natural Science Foundation of China(42025604,42376102)Fundamental Research Funds for the Central Universities。
文摘Ectothermic organisms may expand their thermal tolerance by producing multiple protein isoforms with differing thermal sensitivities.While such isoforms commonly originate from allelic variation at a single locus(allozymes)or from gene duplication that gives rise to paralogs with distinct thermal responses,this study investigated mRNA editing as an alternative,post-transcriptional mechanism for generating mRNA variants.Cytosolic malate dehydrogenase(cMDH)was examined in foot tissue of two congeners of the marine mussel genus Mytilus,which occupy different thermal environments.Multiple editing events were detected within the mRNA coding region in both species.Editing sites were species-specific,with no shared positions identified.In M.coruscus,editing occurred at 117,123,135,190,195,204,279,and 444,while in M.galloprovincialis,editing was detected at 216 and 597.Each species exhibited multiple edited mRNA variants,and these isoforms were associated with differential protein expression.These findings suggest that mRNA editing may contribute an additional layer of molecular variation.The generation of diverse mRNA isoforms from a single DNA coding sequence may enhance enzymatic flexibility across temperature ranges,supporting eurythermal physiological performance and mitigating thermal stress.Moreover,the presence of multiple edited transcripts within individual organisms raises important caveats about the limitations of approaches that deduce amino acid sequences or estimate adaptive variation solely from genomic data.
基金supported by the National Natural Science Foundation of China(Nos.31620103903 and 31621001)partially by the 111 projectsupported by the Peking-Tsinghua Joint Center for Life Sciences
文摘In plants, RNA editing is a post-transcriptional process that changes specific cytidine to uridine in both mitochondria and plastids. Most pentatricopeptide repeat（PPR） proteins are involved in organelle RNA editing by recognizing specific RNA sequences. We here report the functional characterization of a PPR protein from the DYW subclass, Baili Xi（BLX）, which contains five PPR motifs and a DYW domain. BLX is essential for early seed development, as plants lacking the BLX gene was embryo lethal and the endosperm failed to initiate cellularization. BLX was highly expressed in the embryo and endosperm, and the BLX protein was specifically localized in mitochondria, which is essential for BLX function. We found that BLX was required for the efficient editing of 36 editing sites in mitochondria. Moreover, BLX was involved in the splicing regulation of the fourth intron of nad1 and the first intron of nad2. The loss of BLX function impaired the mitochondrial function and increased the reactive oxygen species（ROS） level. Genetic complementation with truncated variants of BLX revealed that, in addition to the DYW domain, only the fifth PPR motif was essential for BLX function. The upstream sequences of the BLX-targeted editing sites are not conserved, suggesting that BLX serves as a novel and major mitochondrial editing factor（MEF） via a new non-RNA-interacting manner. This finding provides new insights into how a DYW-type PPR protein with fewer PPR motifs regulates RNA editing in plants.
基金supported by the National Natural Science Foundation(32001063 and 82201769)the Guangdong Special Support Program(2019BT02Y276)+2 种基金the Guangdong Basic and Applied Basic Research Foundation(2021A1515010759 and 2023A1515010176)the grant from MOE Key Laboratory of Gene Function and Regulation,the Guangzhou Science and Technology Planning Project(202201020411 and 2023A04J1952)the Fundamental Research Funds for the Central Universities,Sun Yat-sen University(23ptpy59).
文摘Osteoarthritis(OA)is one of the most common degenerative joint diseases worldwide,causing pain,disability,and decreased quality of life.The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA.Currently,there is a lack of effective therapeutic strategies for OA treatment.With the development of CRISPR-based genome,epigenome,and RNA editing tools,OA treatment has been improved by targeting genetic risk factors,activating chondrogenic elements,and modulating inflammatory regulators.Supported by cell therapy and in vivo delivery vectors,genome,epigenome,and RNA editing tools may provide a promising approach for personalized OA therapy.This review summarizes CRISPR-based genome,epigenome,and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment.Moreover,in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.
基金supported by the Natural Science Foundation of Hebei Province (C2021208014)the Key R&D Program of Hebei Province (22326312D, 21326332D)。
文摘In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identified, the mechanisms underlying such development are not fully understood. In this study, a rice(Oryza sativa) mutant exhibiting pale green color and seedling lethality was isolated from a mutant library. The mutated gene was identified as an ortholog of THA8(thylakoid assembly 8) in Arabidopsis and maize. This gene is designated as OsTHA8 hereafter. OsTHA8 showed a typical pentatricopeptide repeat(PPR) characteristic of only four PPR motifs. Inactivation of OsTHA8 led to a deficiency in chloroplast development in the rice seedling stage. OsTHA8 was expressed mainly in young leaves and leaf sheaths.The OsTHA8 protein was localized to the chloroplast. Loss of function of OsTHA8 weakened the editing efficiency of ndhB-611/737 and rps8-182 transcripts under normal conditions. Y2H and BiFC indicated that OsTHA8 facilitates RNA editing by forming an editosome with multiple organellar RNA editing factor(OsMORF8) and thioredoxin z(OsTRXz), which function in RNA editing in rice chloroplasts. Defective OsTHA8 impaired chloroplast ribosome assembly and resulted in reduced expression of PEP-dependent genes and photosynthesis-related genes. Abnormal splicing of the chloroplast gene ycf3 was detected in ostha8. These findings reveal a synergistic regulatory mechanism of chloroplast biogenesis mediated by RNA, broaden the function of the PPR family, and shed light on the RNA editing complex in rice.
基金funded by the Central Public-Interest Scientific Institution Basal Research Fund,China(CPSIBRF-CNRRI-202111 and CPSIBRF-CNRRI-202110)the Agricultural Science and Technology Innovation Program,Chinese Academy of Agricultural Sciences(ASTIP)+1 种基金the Project of State Key Laboratory of Rice Biology,China(2020ZZKT10205)the Key Research and Development Project of China Rice Research Institute(CNRRI-2020-01)。
文摘Photosynthesis occurs mainly in chloroplasts,whose development is regulated by proteins encoded by nuclear genes.Among them,pentapeptide repeat(PPR)proteins participate in organelle RNA editing.Although there are more than 450 members of the PPR protein family in rice,only a few affect RNA editing in rice chloroplasts.Gene editing technology has created new rice germplasm and mutants,which could be used for rice breeding and gene function study.This study evaluated the functions of OsPPR9 in chloroplast RNA editing in rice.The osppr9 mutants were obtained by CRISPR/Cas9,which showed yellowing leaves and a lethal phenotype,with suppressed expression of genes associated with chloroplast development and accumulation of photosynthetic-related proteins.In addition,loss of OsPPR9 protein function reduces the editing efficiency of rps8-C182,rpoC2-C4106,rps14-C80,and ndhB-C611 RNA editing sites,which affects chloroplast growth and development in rice.Our data showed that OsPPR9 is highly expressed in rice leaves and encodes a DYW-PPR protein localized in chloroplasts.Besides,the OsPPR9 protein was shown to interact with OsMORF2 and OsMORF9.Together,our findings provide insights into the role of the PPR protein in regulating chloroplast development in rice.
基金supported by the Program for Subsidized Project of Suzhou Academy of Agricultural Sciences,China(20028)the Science and Technology Foundation of Suzhou(SNG2020048)+3 种基金the Huaishang Talents,China,the National Natural Science Foundation of China(32070345)the Huai’an Academy of Agricultural Sciences Initiation and Development of Scientific Research Fund for High-level Introduced Talents,China(0062019016B)the Six Talents Summit Project of Jiangsu Province,China(NY-129)the Natural Science Foundation of Jiangsu Province,China(BK20190239 and BK20180107)。
文摘Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors. In this study, we identified OsDXR, a gene encoding a reductoisomerase that positively regulates chlorophyll biosynthesis and chloroplast development in rice. OsDXR knock-out lines displayed the albino phenotype and could not complete the whole life cycle process. OsDXR was highly expressed in rice leaves, and subcellular localization indicated that OsDXR is a chloroplast protein. Many genes involved in chlorophyll biosynthesis and chloroplast development were differentially expressed in the OsDXR knock-out lines compared to the wild type.Moreover, we found that the RNA editing efficiencies of ndhA-1019 and rpl2-1 were significantly reduced in the OsDXR knock-out lines. Furthermore, OsDXR interacted with the RNA editing factor OsMORF1 in a yeast two-hybrid screen and bimolecular fluorescence complementation assay. Finally, disruption of the plastidial 2-C-methyl-derythritol-4-phosphate pathway resulted in defects in chloroplast development and the RNA editing of chloroplast genes.
基金We thank Dr.Peng-Fei Ma for improving the manuscript.We also thank the two anonymous reviewers for their constructive comments and suggestions.The study was supported by the Strategic Priority Research Program,Chinese Academy of Sciences,China(XDB 31000000)the National Natural Science Foundation of China(31970232)+1 种基金the Large-scale Scientific Facilities of the Chinese Academy of Sciences,China(2017-LSF-GBOWS-02)the technological leading talent project of Yunnan,China(2017HA014).
文摘Cytidine-to-uridine(C-to-U)RNA editing is common in coding regions of organellar genomes throughout land plants.In most cases RNA editing alters translated amino acids or creates new start codons,potentially confounds phylogenetic reconstructions.In this study,we used the spike moss genus Selaginella(lycophytes),which has the highest frequency of RNA editing,as a model to test the effects of extreme RNA editing on phylogenetic reconstruction.We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes,and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences,first and second codon positions,and translated amino acid sequences,respectively.We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes.The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions,but not correlated with the GC content of plastomes as a whole.Contrast phylogenetic analyses showed that there were substantial differences(e.g.,the placement of clade B in Selaginella)between the phylogenies generated by the plastome and RNA-edited data sets.This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction,and might even confound phylogenetic reconstruction.Therefore,RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies,particularly in those lineages with abundant organellar RNA editing sites,such as hornworts,quillworts,spike mosses,and some seed plants.
文摘To study the expression of RNA editing deaminases ADAR2 and ADAR3 in different malignant glioma cell lines and the effect of phenylacetate on the expression of these genes, the primarily glial cells of human brain tissue were isolated and cultured. The human glioma SHG-44, U-251, BT-325 cell lines were maintained in culture. The expressions of ADAP,.2 and ADAR3 mRNA were detected by the semiquantitative reverse transcription-polymerase chain reaction（RT-PCR）. The changes in ADAR2 mRNA expression before and after phenylacetate treatment were detected by RT-PCR and image analysis. The level of ADAR gene expression is expressed as the ratio expression rate（RER） of ADAR gene to β-actin according to computer image analysis. ADAR2 displays moderate expression in glial cells, low expression in low-grade malignant glioma SHG-44 cells, and high level expression in high-grade malignant glioma U-251and BT-325 cells. The expression of ADAR2 can be decreased by phenylacetate treatment in glioma U-251 cells. ADAR3 is not expressed in normal brain glial cells, or glioma SHG-44, U-251 and BT-325 cells before and after phenylacetate treatment. The enhanced expression of ADAR2 may be involved in the tumor progression of malignant glioma. Phenylacetate can decrease the expression of ADAR2 in glioma cells, suggesting that it may act on the RNA editing process in glioma.
基金supported by the National Natural Science Foundation of China(32100342,U1902204,31771415,31801054)Bureau of Science and Technology of Yunnan Province(2015FA026)+1 种基金Youth Innovation Promotion AssociationWest Light Foundation of CAS(Y902401081)。
文摘The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.
基金supported by the National Natural Science Foundation of China(32070496,32370555)Fundamental Research Funds for the Central Universities(SWU120033)Technology Innovation and Application Development Program of Chongqing(CSTB2024TIADKPX0023)。
文摘The CRISPR-Cas13 system,an RNA-guided editing tool,has emerged as a highly efficient and stable RNA editing technique.Although the CRISPR-Cas13 system has been developed in several insect species,its application in lepidopterans has not yet been reported.In the present study,we evaluated the RNA cleavage activity of the CRISPR-Cas13 system in the silkworm(Bombyx mori),a model lepidopteran insect,both ex vivo and in vivo.We established two stable silkworm BmE cell lines expressing PspCas13b and CasRx,respectively.Further analysis demonstrated that both PspCas13b and CasRx effectively down-regulated the transcription of exogenouslyintroduced target and endogenous genes in these cell lines.In addition,we generated two transgenic silkworm strains,one expressing CasRx and the other expressing RNA-guided CRISPR RNA targeting Sex combs reduced(Scr).Further crossing experiments showed that CasRx induced a down-regulation of Scr transcription in silkworms,which impaired systemic growth of larvae.Overall,this study demonstrated that the CRISPR-Cas13RNA editing system works efficiently in the silkworm,providing a potential alternative approach for RNA manipulation in lepidopteran insects.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(grant no.XDB31010000)by the Large-scale Scientific Facilities of the Chinese Academy of Sciences(grant no.2017-LSF-GBOWS-02)+1 种基金by an open research project for“Cross-Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciencesby the CAS Pioneer Hundred Talents Program(to A.Z.).
文摘Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modifications is limited.In this study,we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium,a genus with diverse trophic lifestyles.Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives.This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex,but independent pseudogenization of ndh genes has also occurred in the epiphyte C.mannii,which was reported to use strong crassulacean acid metabolism photosynthesis.RNA editing sites are abundant but variable in number among Cymbidium plastomes.The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial,mycoheterotrophic,and C.mannii plastomes.The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed,leading to nonrandom loss of ancestral edited sites via reduced editing efficiency.This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus.We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.
文摘Sunflower is one of the most used commercial oilseed crops and suffers due to Powdery mildew. RNA sequence alteration occurs due to RNA editing which is a post transcriptional modification. It causes a deviation from the genomic DNA sequence resulting in RNA-DNA differences. Accurate study of RNA editing events in diverse species is possible by NGS based methods. Here, we performed RNA sequencing of 12 leaf transcriptomes, which include three genotypes of Helianthus annuus (2023B, TX16R and ID25), H. debilis, H. niveus, and H. praecox along with their respective powdery mildew pathogen infected variants and systematically analysed the mitochondrial RNA editing events using computational reference-based mapping approach. We discovered 687 editing sites, 220 editing events in the protein-coding regions, among all species and genotypes considered in this study. These included “C to U” and “U to C” RNA editing events. On further analysis, we observed that these editing events include 14 different types of amino acid changes that involve the creation of two stop codon events. The conserved editing sites identified were 247 accounting for ~36% of all the editing sites identified. This study provides a detailed picture of the Helianthus species’ mitochondrial RNA editing status. We have identified and characterized for the first time, genotype-specific, species-specific, and stress-specific RNA editing events which may be useful as a potential source for stress-responsive studies in the future.
基金supported by grants from the Key Research and Development Program of Zhejiang Province(2024SSYS0100)the National Natural Science Foundation of China(32030009)。
文摘In the chloroplasts/plastids and mitochondria of flowering plants,RNA editing alters hundreds of cytidines to uridines at specific sites mediated by the editosome.Over the past decade,Multiple Organellar RNA Editing Factor(MORF)proteins have emerged as essential regulators that affect the editing efficiency of most editing sites in plastids and mitochondria.In Arabidopsis,the MORF family consists of nine members,each possessing a single conserved MORF-box that is distributed among flowering plants.Accumulating studies have demonstrated that MORF proteins interact with many other factors,including the PPR proteins and enzymes in different biosynthetic pathways,indicating that the MORF proteins play a more extensive role in regulating organellar development than RNA editing.Recent studies reveal that MORF2 and MORF9 possess holdase activity and may act as chaperones and that MORF8 undergoes heatdependent phase separation to inhibit RNA editing in chloroplasts.In this review,we provide an overview of our current knowledge of the MORF family proteins and discuss the biological and molecular functions of this family in plants.
文摘This is a correction to:Hao Cheng,Jun Yu,Chi Chun Wong,Adenosine-to-inosine RNA editing in cancer:molecular mechanisms and downstream targets,Protein&Cell,2024;https://doi.org/10.1093/procel/pwae039 In the originally published version of the manuscript there were errors in Figure 2.In panel H,text should read:"Loses capacity"instead of:"oses capacity";a redundant letter"I"that was highlighted should be removed.
文摘Although the multiple organellar RNA editing factors （MORFs） in the plastids of Arabidopsis thaliana have been extensively studied, molecular details underlying how MORFs affect plant development in other species, particularly in rice, remain largely unknown. Here we describe the characterization of wspl, a rice mutant with white-stripe leaves and panicles. Notably, wspl exhibited nearly white immature panicles at the heading stage. Transmission electron microscopy analysis and chlorophyll content measurement re- veale i a chloroplast developmental defect and reduced chlorophyll accumulation in wspl. Positional cloning of WSP1 found a point mutation in OsO4g51280, whose putative product shares high sequence similarity with MORF proteins. Complementation experiments demonstrated that WSP1 was responsible for the variegated phenotypes of wspl. WSP1 is localized to chloroplasts and the point mutation in wspl affected the editing of multiple organellar RNA sites. Owing to the defect in plastid RNA editing, chloroplast ribosome biogenesis and ndhA splicing were also impaired in wspl, which may affect normal chloroplast development in the leaves and panicles at the heading stage. Together, our results demonstrate the importance of rice WSP1 protein in chloroplast development and broaden our knowledge about MORF family members in rice.
文摘RNA editing sites in plant mitochondria and plastids are addressed by pentatricopeptide repeat （PPR） proteins with E or E and DYW domains, which recognize a specific nucleotide motif upstream of the edited nucleotide. In addition, some sites require MORF proteins for efficient RNA editing. Here, we assign the novel E domain-containing PPR protein, MEF13, as being required for editing at eight sites in Arabidopsis thaliana. A SNP in ecotype C24 altering the editing level at only one of the eight target sites was located by genomic mapping. An EMS mutant allele of the gene for MEF13 was identified in a SNaPshot screen of a mutated plant population. At all eight target sites of MEF13, editing levels are reduced in both morf3 and morf8 mutants, but at only one site in morfl mutants, suggesting that specific MEF13-MORF interactions are required. Yeast two-hybrid analyses detect solid connections of MEF13 with MORF1 and weak contact with MORF3 proteins. Yeast three-hybrid （Y3H） analysis shows that the presence of MORF8 enhances the connection between MEF13 and MORF3, suggesting that a MORF3-MORF8 heteromer may form stably or transiently to establish interaction with MEF13.
基金This work was supported by grants from the National Science Foundation of China(Key program 81830017,Nos.81672425 and 81902051)the National Natural Science Fund for Outstanding Youth Fund(81425012)+3 种基金Taishan Scholarship(No.tspd20181201)Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong,Key Research and Development Program of Shandong(2019GSF108238)the National Key Research and Development Program(2018YFE0126500 and 2016YFE0127000)China Mobility Grant jointly funded by the National Science Foundation of China and the Swedish Foundation for International Cooperation in Research and Higher Education(STINT),and China Postdoctoral Science Foundation(No.2018 M30782).
文摘HBV is considered as a“stealth”virus that does not invoke interferon(IFN)responses;however,the mechanisms by which HBV bypasses innate immune recognition are poorly understood.In this study,we identified adenosine deaminases acting on RNA 1(ADAR1),which is a key factor in HBV evasion from IFN responses in hepatocytes.Mechanically,ADAR1 interacted with HBV RNAs and deaminated adenosine(A)to generate inosine(I),which disrupted host immune recognition and thus promoted HBV replication.Loss of ADAR1 or its deficient deaminase activity promoted IFN responses and inhibited HBV replication in hepatocytes,and blocking the IFN signaling pathways released the inhibition of HBV replication caused by ADAR1 deficiency.Notably,the HBV X protein(HBx)transcriptionally promoted ADAR1 expression to increase the threshold required to trigger intrinsic immune activation,which in turn enhanced HBV escape from immune recognition,leading to persistent infection.Supplementation with 8-azaadenosine,an ADAR1 inhibitor,efficiently enhanced liver immune activation to promote HBV clearance in vivo and in vitro.Taken together,our results delineate a molecular mechanism by which HBx promotes ADAR1-derived HBV immune escape and suggest a targeted therapeutic intervention for HBV infection.
基金Supported by the National Natural Science Foundation of China （30571270）.
文摘RNA editing for the mitochondrlal ATP9 gene of encoding regions has been observed in both cytoplasmic malesterile and maintainer lines of stem mustard, where its editing capacity varied spatially and temporally in the cytoplasmic male sterility （CMS） line. There were four RNA editing sites for the mitochondrial ATP9 gene according to Its normal editing sites in mustard, of which three sites occurred as C-to-U changes and one as a U-to-C change. As a result, the hydrophobicity of deduced ATP9 protein was reduced due to the conversions at its 17th, 45th and 64th positions. Meanwhile, the conservation of deduced ATP9 protein was enhanced by changes at the 56th position. Loss of a specific editing site for ATP9 was observed in juvenile roots, senile roots, senile leaves and floret buds of the CMS line. Comparatively, complete RNA editing for ATP9 gene was retained in juvenile roots, juvenile leaves and floret buds of its maintainer line; however, the loss of a specific editing site for ATP9 gene occurred at senile roots and senile leaves in its maintainer line. These observations allow us to produce a hypothesis that the dysfunction of a specific mitochondrial gene arising from RNA editing could probably be a factor triggering CMS and organ senescence through unknown cross-talk pathways during development.
基金supported by the Fundamental Research Fund for the Central Universities (Grant No. GK200902028)
文摘RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position, ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.
