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RNA, Chloroplast (0):
Recent article
RNA, Chloroplast
BMC Plant Biology (10) 2010
Abstract
We used Nicotiana tabacum to investigate the effect on sense strand transcripts of overexpressing a natural chloroplast asRNA, AS5, which is complementary to the region which encodes the 5S rRNA and tRNAArg.
AS5-overexpressing (AS5ox) plants obtained by chloroplast transformation exhibited slower gr...
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PMID: 20920268
PDF is available here.
PDF is available here.
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Plant Molecular Biology (69)5 2009
Abstract
We show that Arabidopsis CSP41a and CSP41b interact in vivo, and that a csp41b null mutant becomes depleted of CSP41a in mature leaves, correlating with a pale green phenotype and reduced accumulation of the ATP synthase and cytochrome b ( 6 )/f complexes. RNA gel blot analyses revealed up to four-f...
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PMID: 19067181
PDF is available here.
PDF is available here.
BMC Bioinformatics (10)1 2009
Abstract
In this paper, we extend our algorithm CURE, which can accurately predict the C-to-U RNA editing sites in mitochondria, to predict C-to-U RNA editing sites in the chloroplasts of seed plants. The algorithm achieves over 80% sensitivity and over 99% specificity. We implement the algorithm as an onlin...
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PMID: 19422723
PDF is available here.
PDF is available here.
Nucleic Acids Research (37)Database 2009
Abstract
The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, e...
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PMID: 18953030
PDF is available here.
PDF is available here.
Plant Journal (56)4 2008
Abstract
We have characterized CLB19 (also known as PDE247), a gene that is required for editing of two distinct chloroplast transcripts, rpoA and clpP. Loss-of-function clb19 mutants present a yellow phenotype with impaired chloroplast development and early seedling lethality under greenhouse conditions. Tr...
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PMID: 18657233
PDF is available here.
PDF is available here.
Abstract
We determined the genomic and cDNA sequences of moss Takakia lepidozioides chloroplast genes, then computationally analyzed the sequences within -30 to +10 nucleotides of RNA editing sites (neighbor sequences) likely to be recognized by trans-factors. As the T. lepidozioides chloroplast has many RNA...
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PMID: 18650260
PDF is available here.
PDF is available here.
FEBS Letters (582)21-22 2008
Abstract
We found that cpSRP54 of higher plants lacks the ability to bind SRP-RNA because of two amino acid substitutions within a region corresponding to the RNA binding domain of cytosolic SRP54, whereas the C-terminal extension does not affect RNA binding. Phylogenetic analysis revealed that these mutatio...
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PMID: 18755190
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)12 2008
Abstract
We show that transcripts encompassing two editing sites, ZMrpoB C467 and ZMrps14 C80, can compete editing activity from each other in vitro despite limited sequence similarity. The signal causing competition overlaps a 5'-cis element required for editing efficiency. A single five-nucleotide mutation...
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PMID: 18192271
PDF is available here.
PDF is available here.
Phytopathology (98)3 2008
Abstract
Brittle leaf disease or maladie des feuilles cassantes (MFC) is a lethal disorder of date palms that has assumed epidemic proportions in the oases of southern Tunisia. After a prolonged period during which palms are declining, the disease ends with the death of the palms. Whereas no pathogen could e...
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PMID: 18944085
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
Like its three chlorophycean homologues, the 196,547-bp Oedogonium chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns), and dis...
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PMID: 18558012
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)1 2008
Abstract
We addressed this question with the aid of an in vitro RNA editing system from tobacco chloroplast extracts and with UV-crosslinking experiments. We found that the ndhB-9 and ndhF-1 editing sites of tobacco chloroplast transcripts are both bound by the site-specific trans-acting factors of 95 kDa. C...
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PMID: 18032432
PDF is available here.
PDF is available here.
Abstract
We show here that translation of the tobacco plastid psbC mRNA initiates from the GUG. This mRNA possesses a long Shine-Dalgarno (SD)-like sequence, GAGGAGGU, nine nucleotides upstream of the GUG. Point mutations in this sequence abolished translation, suggesting that a strong interaction between th...
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PMID: 17664183
PDF is available here.
PDF is available here.
Abstract
We found that even in the absence of an SRP RNA, the chloroplast SRP and receptor GTPases can interact efficiently with one another; the kinetics of interaction between the chloroplast GTPases is 400-fold faster than their bacterial homologues, and matches the rate at which the bacterial SRP and rec...
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PMID: 17475780
PDF is available here.
PDF is available here.
Plant Cell Online (19)3 2007
Abstract
We studied the chloroplast ribonuclease polynucleotide phosphorylase (PNPase), which consumes and generates phosphate, by comparing wild-type Chlamydomonas reinhardtii cells with strains with reduced PNPase expression. In the wild type, chloroplast RNA (cpRNA) accumulates under P limitation, correla...
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PMID: 17351118
PDF is available here.
PDF is available here.
Methods in Enzymology (424) 2007
Abstract
We provide an overview of cytosine-to-uridine (C-to-U) RNA editing in the plastids of higher plants. Particular emphasis will be placed on the role plastid transformation played in understanding the editing process. We discuss how plastid transformation enabled identification of mRNA cis elements fo...
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PMID: 17662856
PDF is available here.
PDF is available here.
Plant Journal (49)2 2007
Abstract
We previously developed an in vitro translation system derived from tobacco chloroplasts. Here, we report a significantly improved in vitro translation system. By modifying preparation procedures for chloroplast extracts and reaction conditions, we achieved 100-fold higher translation activity than...
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PMID: 17156414
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)17 2007
Abstract
We describe a rapid, high-throughput method to scan for new RNA editing sites. This method is adapted from high-resolution melting (HRM) analysis of amplicons, a technique used in clinical research to detect mutations in genomes. The assay was validated by the discovery of six new editing sites in d...
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PMID: 17726051
PDF is available here.
PDF is available here.
Photosynthesis Research (94)2-3 2007
Abstract
Chloroplast gene expression is primarily controlled during the translation of plastid mRNAs. Translation is regulated in response to a variety of biotic and abiotic factors, and requires a coordinate expression with the nuclear genome. The translational apparatus of chloroplasts is related to that o...
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PMID: 17661159
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (281)49 2006
Abstract
We have previously shown that an Arabidopsis thaliana crr4 mutant is defective with respect to RNA editing for creating the translational initial codon of the plastid ndhD gene (the ndhD-1 site). CRR4 contains 11 pentatricopeptide repeat motifs but does not contain any domains that are likely to be...
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PMID: 17015439
PDF is available here.
PDF is available here.
Abstract
The "Maladie des feuilles cassantes" (MFC) or "Brittle leaf disease" of date palms is associated with the accumulation of two populations of small, chloroplast-encoded RNAs. A plasmid vector containing a cDNA with partial sequences of both of these RNA populations was used to synthesize a DIG-labele...
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PMID: 16829023
PDF is available here.
PDF is available here.
Abstract
We provide a detailed analysis of data on C-to-U editing sites in land plant chloroplasts and propose a model for the evolution of RNA editing in land plants. First, our data suggest that the limited RNA-editing system of seed plants and the much more extensive systems found in hornworts and ferns a...
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PMID: 16835291
PDF is available here.
PDF is available here.
Abstract
We have identified ten ABA-regulated RNA-binding proteins in Arabidopsis seedlings. Among those genes, AtCSP41B and cpRNP29 are highly expressed in seedlings. Using promoter:reporter gene analyses, we showed that both AtCSP41B and cpRNP29 were in particular expressed in photosynthetically active org...
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PMID: 16633814
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)13 2006
Abstract
We conclude that within the -20/-5 region, sequences common to editing sites in the transcripts of rpoB, psbL and rps14 are critical for efficient NTrpoB C473 editing....
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PMID: 16893957
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)14 2006
Abstract
We have thus generated cDNA libraries from size-selected mammalian mitochondrial RNA and plant chloroplast RNA and searched for small ncRNA species in these two types of DNA-containing cell organelles. In total, we have identified 18 novel candidates for organellar ncRNAs in these two cellular compa...
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PMID: 16899451
PDF is available here.
PDF is available here.
Abstract
Abstract
Plant Physiology (137)2 2005
Abstract
We used two known Chlamydomonas reinhardtii nonphotosynthetic mutants carrying mutations in the Mcd1 nuclear gene (mcd1-1 and mcd1-2). We previously reported that these mutants fail to accumulate the chloroplast petD mRNA and its product, subunit IV of the cytochrome b6/f complex, which is essential...
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PMID: 15665248
PDF is available here.
PDF is available here.
Abstract
To test the general applicability of the PREP-Mt methodology, RNA editing sites were predicted for 370 full-length or nearly full-length DNA sequences and then compared to the known sites of RNA editing for these sequences. Of 60,263 cytidines in this test set, PREP-Mt correctly classified 58,994 as...
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PMID: 15826309
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)8 2005
Abstract
We show that this role can be largely ascribed to RNR1, for which homozygous mutants germinate only on sucrose-containing media, and have white cotyledons and pale green rosette leaves. Accumulation of chloroplast-encoded mRNAs and tRNAs is unaffected in such mutants, suggesting that RNR1 activity i...
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PMID: 15891117
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)15 2005
Abstract
We show for an essential RNA-stabilizing stem-loop at the 5' end of rbcL gene transcripts in Chlamydomonas that it neither prevents ribonucleases from binding to the RNA nor impedes their movement along the RNA strand. The stem-loop has a formative function in that it mediates folding of a short seq...
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PMID: 16116040
PDF is available here.
PDF is available here.
Plant and Cell Physiology (45)11 2004
Abstract
We have analysed chloroplast genomes from 27 organisms. In higher plant chloroplasts, no SRP RNA genes were identified. However, eight plastids from red algae and Chlorophyta were found to contain an SRP RNA gene. These results suggest that SRP RNA forms a complex in these plastids with cpSRP54, rem...
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PMID: 15574839
PDF is available here.
PDF is available here.
Plant Biology (6)5 2004
Abstract
Structure, variability, and molecular evolution of the trnT-F region in the Bryophyta (mosses and liverworts) is analyzed based on about 200 sequences of the trnT-L spacer and trnL 5' exon, 1000 sequences of the trnL intron, and 800 sequences of the trnL 3' exon and trnL-F spacer, including comparis...
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PMID: 15375725
PDF is available here.
PDF is available here.
BMC Bioinformatics (5)1 2004
Abstract
The average prediction accuracy for a 16S or 23S rRNA sequence with Mfold 3.1 is 41%, while the prediction accuracies for the majority of 16S and 23S rRNA structures tested are between 20% and 60%, with some having less than 20% prediction accuracy. The average prediction accuracy was 71% for 5S rRN...
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PMID: 15296519
PDF is available here.
PDF is available here.
Plant Molecular Biology (55)4 2004
Abstract
We examined the RNA profile in chloroplasts. In rnr1 the intercistronic cleavage between 23S and 4.5S rRNA was impaired, and a significant reduction in rRNA in chloroplasts was found, suggesting that RNR1 functions in the maturation of chloroplast rRNA. The present results suggest that defects in th...
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PMID: 15604703
PDF is available here.
PDF is available here.
Abstract
Chloroplasts were acquired by eukaryotic cells through endosymbiosis and have retained their own gene expression machinery. One hallmark of chloroplast gene regulation is the predominance of posttranscriptional control, which is exerted both at the gene-specific and global levels. This review focuse...
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PMID: 15210334
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)12 2004
Abstract
We provide a phylogenetic analysis of RNA editing in a small plastid gene, petL, encoding subunit VI of the cytochrome b6f complex. Analyzing representatives from most major groups of seed plants, we find an unexpectedly high frequency and dynamics of RNA editing. High-frequency editing has previous...
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PMID: 15240834
PDF is available here.
PDF is available here.
Abstract
We conclude that the catalytic deficiency is most likely due to the perturbation of the global structure of the plastid P RNAs compared to the bacterial counterpart. As a consequence, the plastid P RNAs are unable to bind to the precursor tRNA substrates. We discuss these results in the context of p...
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PMID: 14636991
PDF is available here.
PDF is available here.
Plant Molecular Biology (53)4 2003
Abstract
These results suggest that DCL is required for chloroplast rRNA processing, and emphasize the importance of plastid function during embryogenesis....
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PMID: 15010617
PDF is available here.
PDF is available here.
Plant Physiology (133)1 2003
Abstract
In Arabidopsis, the nuclear genes PetC and AtpD code for the Rieske protein of the cytochrome b(6)/f (cyt b(6)/f) complex and the delta-subunit of the chloroplast ATP synthase (cpATPase), respectively. Knock-out alleles for each of these loci have been identified. Greenhouse-grown petc-2 and atpd-1...
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PMID: 12970486
PDF is available here.
PDF is available here.
Planta Medica (69)7 2003
Abstract
Chloroplast trnK gene and nuclear 18S rRNA gene sequences of 13 Panax taxa, collected mainly from Sino-Japanese floristic region, were investigated in order to construct phylogenetic relationship and to assist taxonomic delimitation within this genus. The length of trnK gene sequence varied from 253...
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PMID: 12898422
PDF is available here.
PDF is available here.
Plant Cell Online (15)6 2003
Abstract
We performed mutational analysis using Arabidopsis. The allelic nuclear mutants hcf152-1 and hcf152-2 were identified that are affected specifically in the accumulation of the plastidial cytochrome b(6)f complex. In both mutants, reduced amounts of spliced petB RNAs (encoding the cytochrome b(6) sub...
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PMID: 12782738
PDF is available here.
PDF is available here.
Abstract
RNA motifs are directed and ordered stacked arrays of non-Watson-Crick base pairs forming distinctive foldings of the phosphodiester backbones of the interacting RNA strands. They correspond to the 'loops' - hairpin, internal and junction - that intersperse the Watson-Crick two-dimensional helices a...
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PMID: 12831880
PDF is available here.
PDF is available here.
Nucleic Acids Research (31)10 2003
Abstract
We quantified the editing extent at 34 sites in wild-type tobacco and at three sites in spinach and Arabidopsis. We observed that transcripts of most NADH dehydrogenase subunits are edited inefficiently in roots. With few exceptions, members of the same editing site cluster co-varied in editing exte...
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PMID: 12736308
PDF is available here.
PDF is available here.
Plant Journal (34)3 2003
Abstract
We discuss a possible mechanism for the negative regulation of rps2 mRNA translation....
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PMID: 12713543
PDF is available here.
PDF is available here.
Nucleic Acids Research (31)9 2003
Abstract
RNA editing in chloroplasts alters the RNA sequence by converting C-to-U or U-to-C at a specific site. During the study of the complete nucleotide sequence of the chloroplast genome from the hornwort Anthoceros formosae, RNA editing events have been systematically investigated. A total of 509 C-to-U...
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PMID: 12711687
PDF is available here.
PDF is available here.
Plant Molecular Biology (51)5 2003
Abstract
We analyzed in detail a yellow colored transposon-tagged mutant (dal1-2) that is allelic to the dal mutant previously identified (Babiychuk et al., 1997). Mesophyll cells of mutant plants possess abnormal nucleoids and more but smaller plastids than wild type cells. Plastid development in dal1-2 is...
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PMID: 12678554
PDF is available here.
PDF is available here.
Plant Cell Online (15)1 2003
Abstract
We propose that sigma interaction with the -10 element in PrrnP1 is replaced in part by direct PEP-RUA (protein-DNA) interaction or by protein-protein interaction between the PEP and an RUA binding transcription factor....
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PMID: 12509531
PDF is available here.
PDF is available here.
Nucleic Acids Research (31)1 2003
Abstract
We have designed and implemented GOpop, a Java system for population and verification of the database. We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html....
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PMID: 12519975
PDF is available here.
PDF is available here.
Plant Cell Online (14)12 2002
Abstract
Our data suggest that transcripts with UGA stop codons are terminated exclusively by AtprfB in chloroplasts and that AtprfB is involved in the regulation of both mRNA stability and protein synthesis. Furthermore, sequence data reveal a +1 frameshift at an internal in-frame TGA stop codon in the prog...
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PMID: 12468741
PDF is available here.
PDF is available here.
Abstract
mRNA localization efficiently targets gene products to specific subcellular compartments, thereby controlling cell fate and polar cell growth. Plants also localize RNAs to target proteins in the endomembrane system, and to different tissues by long-distance transport. Recent developments support the...
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PMID: 12393019
PDF is available here.
PDF is available here.
Plant Cell Online (14)11 2002
Abstract
The Chlamydomonas reinhardtii plastid and mitochondrial transcriptomes were surveyed for changes in RNA profiles resulting from growth in 12 culture conditions representing 8 abiotic stimuli. Organellar RNA abundance exhibited marked changes during nutrient stress and exposure to UV light, as reveal...
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PMID: 12417695
PDF is available here.
PDF is available here.
Plant Journal (32)4 2002
Abstract
I rRNA intron of Chlamydomonas reinhardtii, Cr.LSU. In vitro assays showed that these substitutions had surprisingly strong effects on Cr.LSU self-splicing; however, splicing of all but the P6 mutations could be at least partially recovered by increasing the Mg2+ concentration. The mutant constructs...
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PMID: 12445119
PDF is available here.
PDF is available here.
Nucleic Acids Research (30)20 2002
Abstract
We have investigated the biochemical mechanism responsible for the dark-induced decrease of relative half-lives for mRNAs encoding photosynthetic proteins. Protein fractions isolated from plastids of light-grown and dark-adapted plants correctly reproduced an RNA degradation pathway in the dark that...
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PMID: 12384600
PDF is available here.
PDF is available here.
Plant and Cell Physiology (43)10 2002
Abstract
RB60, a chloroplast protein disulfide isomerase, modulates the binding of RB47, chloroplast poly(A)-binding protein, to the 5'-UTR of the psbA mRNA using redox potential, allowing for a reversible switch capable of regulating psbA mRNA translation in a light/dark dependent manner. RB60 contains two...
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PMID: 12407204
PDF is available here.
PDF is available here.
Plant Molecular Biology (50)3 2002
Abstract
Several membrane proteins were previously shown to bind to the 5' leader of the chloroplast psbC mRNA in the unicellular eukaryotic alga Chlamydomonas reinhardtii. This study showed that these proteins have affinity for AU-rich RNAs, as determined by competition experiments. In addition, their bindi...
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PMID: 12369632
PDF is available here.
PDF is available here.
Plant Journal (31)6 2002
Abstract
We have characterized a nuclear mutation, mda1-ncc1, that affects mRNA stability for the atpA gene cluster in the chloroplast of Chlamydomonas. Unlike all nuclear mutations altering chloroplast gene expression described to date, mda1-ncc1 is a dominant mutation that still allows accumulation of dete...
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PMID: 12220261
PDF is available here.
PDF is available here.
Abstract
We used Chlamydomonas chloroplast transformation to test the effects of mRNA homopolymer tails in vivo, with either the endogenous atpB gene or a version of green fluorescent protein developed for chloroplast expression as reporters. Strains were created in which, after transcription of atpB or gfp,...
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PMID: 11891297
PDF is available here.
PDF is available here.
Nucleic Acids Research (30)5 2002
Abstract
When the sequence of the Euglena gracilis chloroplast genome was reported in 1993 the alpha-subunit gene (rpoA) of RNA polymerase appeared to be missing, based on a comparison of all putative reading frames to the then known rpoA loci. Since there has been a large increase in known rpoA sequences, t...
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PMID: 11861918
PDF is available here.
PDF is available here.
Nucleic Acids Research (30)1 2002
Abstract
FUGOID is a web-based, taxonomically broad organelle intron database that collects and integrates various functional and structural data on organellar (mitochondrial and chloroplast) introns. The main information provided by FUGOID includes intron sequence, subclass, resident ORF, self-splicing capa...
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PMID: 11752344
PDF is available here.
PDF is available here.
Nucleic Acids Research (29)23 2001
Abstract
Translational stop codon readthrough provides a regulatory mechanism of gene expression that is extensively utilised by positive-sense ssRNA viruses. The misreading of termination codons is achieved by a variety of naturally occurring suppressor tRNAs whose structure and function is the subject of t...
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PMID: 11726686
PDF is available here.
PDF is available here.