1
|
Bolle N, Hinrichsen I, Kempken F. Plastid mRNAs are neither spliced nor edited in maize and cauliflower mitochondrial in organello systems. RNA (NEW YORK, N.Y.) 2007; 13:2061-2065. [PMID: 17951330 PMCID: PMC2080585 DOI: 10.1261/rna.758307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 09/11/2007] [Indexed: 05/25/2023]
Abstract
The process of RNA editing in chloroplasts and higher plant mitochondria displays some similarities, raising the question of common or similar components in editing apparatus of these two organelles. To investigate the ability of plant mitochondria to edit plastid transcripts, we employed a previously established mitochondrial maize and cauliflower in organello system. Two plastid genes, Zea mays ndhB and ycf3 containing group II introns and several editing sites, were introduced into mitochondria. The genes were transcribed in organello. However, these transcripts of the plastid genes are neither spliced nor edited in plant mitochondria. A comparison of maize ndhB editing sites and maize mitochondrial editing sites reveals considerable sequence similarities between three ndhB editing sites and several mitochondrial sites. Nevertheless, these ndhB editing sites were not recognized in the mitochondria. Thus, we present for the first time direct evidence that the factors present in the plant mitochondria are not sufficient to allow editing and splicing of plastid transcripts.
Collapse
|
2
|
Glanz S, Bunse A, Wimbert A, Balczun C, Kück U. A nucleosome assembly protein-like polypeptide binds to chloroplast group II intron RNA in Chlamydomonas reinhardtii. Nucleic Acids Res 2006; 34:5337-51. [PMID: 17012281 PMCID: PMC1636423 DOI: 10.1093/nar/gkl611] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In the unicellular green alga Chlamydomonas reinhardtii, the chloroplast-encoded tscA RNA is part of a tripartite group IIB intron, which is involved in trans-splicing of precursor mRNAs. We have used the yeast three-hybrid system to identify chloroplast group II intron RNA-binding proteins, capable of interacting with the tscA RNA. Of 14 candidate cDNAs, 13 encode identical polypeptides with significant homology to members of the nuclear nucleosome assembly protein (NAP) family. The RNA-binding property of the identified polypeptide was demonstrated by electrophoretic mobility shift assays using different domains of the tripartite group II intron as well as further chloroplast transcripts. Because of its binding to chloroplast RNA it was designated as NAP-like (cNAPL). In silico analysis revealed that the derived polypeptide carries a 46 amino acid chloroplast leader peptide, in contrast to nuclear NAPs. The chloroplast localization of cNAPL was demonstrated by laser scanning confocal fluorescence microscopy using different chimeric cGFP fusion proteins. Phylogenetic analysis shows that no homologues of cNAPL and its related nuclear counterparts are present in prokaryotic genomes. These data indicate that the chloroplast protein described here is a novel member of the NAP family and most probably has not been acquired from a prokaryotic endosymbiont.
Collapse
Affiliation(s)
| | | | | | | | - Ulrich Kück
- To whom correspondence should be addressed. Tel: +49 234 3226212; Fax: +49 234 3214184;
| |
Collapse
|
3
|
Balczun C, Bunse A, Schwarz C, Piotrowski M, Kück U. Chloroplast heat shock protein Cpn60 fromChlamydomonas reinhardtiiexhibits a novel function as a group II intron-specific RNA-binding protein. FEBS Lett 2006; 580:4527-32. [PMID: 16872603 DOI: 10.1016/j.febslet.2006.07.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 07/10/2006] [Accepted: 07/10/2006] [Indexed: 11/22/2022]
Abstract
Intron-binding proteins in eukaryotic organelles are mainly encoded by the nuclear genome and are thought to promote the maturation of precursor RNAs. Here, we present a biochemical approach that enable the isolation of a novel nuclear-encoded protein from Chlamydomonas reinhardtii showing specific binding properties to organelle group II intron RNA. Using FPLC chromatography of chloroplast protein extracts, a 61-kDa RNA-binding protein was isolated and then tentatively identified by mass spectrometry as the chloroplast heat shock protein Cpn60. Heterologous Cpn60 protein was used in RNA protein gel mobility shift assays and revealed that the ATPase domains of Cpn60 mediates the specific binding of two group II intron RNAs, derived from the homologous chloroplast psaA gene and the heterologous mitochondrial LSU rRNA gene. The function of Cpn60 as a general organelle splicing factor is discussed.
Collapse
Affiliation(s)
- Carsten Balczun
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | | | | | | | | |
Collapse
|
4
|
Balczun C, Bunse A, Hahn D, Bennoun P, Nickelsen J, Kück U. Two adjacent nuclear genes are required for functional complementation of a chloroplast trans-splicing mutant from Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 43:636-48. [PMID: 16115062 DOI: 10.1111/j.1365-313x.2005.02478.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The chloroplast tscA gene from Chlamydomonas reinhardtii encodes a co-factor RNA that is involved in trans-splicing of exons 1 and 2 of the psaA mRNA encoding a core polypeptide of photosystem I. Here we provide molecular and genetic characterization of the trans-splicing mutant TR72, which is defective in the 3'-end processing of the tscA RNA and consequently defective in splicing exons 1 and 2 of the psaA mRNA. Using genomic complementation, two adjacent nuclear genes were identified, Rat1 and Rat2, that are able to restore the photosynthetic growth of mutant TR72. Restoration of the photosynthesis phenotype, however, was successful only with a DNA fragment containing both genes, while separate use of the two genes did not rescue the wild-type phenotype. This was further confirmed by using a set of 10 gene derivatives in complementation tests. The deduced amino acid sequence of Rat1 shows significant sequence homology to the conserved NAD+-binding domain of poly(ADP-ribose) polymerases of eukaryotic organisms. However, mutagenesis of conserved residues in this putative NAD+-binding domain did not reveal any effect on restoration efficiency. Immunodetection analyses with enriched fractions of chloroplast proteins indicated that Rat1 is associated with chloroplast membranes. Using the yeast three-hybrid system, we were able to demonstrate the specific binding of tscA RNA by the Rat1 polypeptide. We propose that the two nuclear factors Rat1 and Rat2 are involved in processing of chloroplast tscA RNA and in subsequent splicing of psaA exons 1 and 2.
Collapse
Affiliation(s)
- Carsten Balczun
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | | | | | | | | | | |
Collapse
|
5
|
Staudinger M, Kempken F. Electroporation of isolated higher-plant mitochondria: transcripts of an introduced cox2 gene, but not an atp6 gene, are edited in organello. Mol Genet Genomics 2003; 269:553-61. [PMID: 12811542 DOI: 10.1007/s00438-003-0863-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2003] [Accepted: 05/07/2003] [Indexed: 10/26/2022]
Abstract
To facilitate the analysis of RNA processing in plant mitochondria, a method was established for introducing foreign DNA into mitochondria isolated from maize and sorghum. This method permits the uptake of DNA of up to 11 kb into the mitochondrial matrix. In vitro incubation of maize mitochondria in a specific buffer system was found to permit splicing and editing of newly synthesized RNAs for a period of at least 7 h. This was shown both for transcripts of endogenous mitochondrial genes (atp6, cox2) and for transcripts derived from an introduced Arabidopsis thaliana cox2 gene. In contrast, when a Sorghum bicolor atp6 gene was introduced into isolated maize mitochondria, the gene was transcribed, but the RNA was not edited, although all the editing sites in maize and sorghum atp6 RNA are identical. This may indicate the presence of transcript-specific cis -acting regions in the up- or downstream untranslated sequences of the mRNA. The system described here should allow further dissection of the mechanism of RNA editing in plant mitochondria.
Collapse
Affiliation(s)
- M Staudinger
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
| | | |
Collapse
|
6
|
Bunse AA, Nickelsen J, Kück U. Intron-specific RNA binding proteins in the chloroplast of the green alga Chlamydomonas reinhardtii. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1519:46-54. [PMID: 11406270 DOI: 10.1016/s0167-4781(01)00211-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mitochondria and chloroplasts both contain group II introns which are believed to be the ancestors of nuclear spliceosomal introns. We used the mitochondrial group II intron rI1 from the green alga Scenedesmus obliquus for biochemical characterization of intron-specific RNA binding proteins. rI1 is correctly spliced from a chloroplast precursor RNA when integrated into the chloroplast genome of Chlamydomonas reinhardtii. Glycerol gradients revealed the sedimentation profile of transcripts containing intron rI1 in native C. reinhardtii extracts and in deproteinized RNA preparations, thus indicating the association of rI1 containing transcripts with high molecular weight ribonucleoprotein complexes in vivo. Furthermore, the specific binding of a 61 kDa protein and a 31 kDa protein with the conserved domain IV was demonstrated using a set of intron derivatives for in vitro RNA binding experiments. We propose that we have biochemically characterized 'general splicing factors', which enable the successful splicing even of mitochondrial introns in chloroplasts.
Collapse
Affiliation(s)
- A A Bunse
- Lehrstuhl für Allgemeine und Molekulare Botanik, Fakultät für Biologie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | | | | |
Collapse
|
7
|
Schock I, Gregan J, Steinhauser S, Schweyen R, Brennicke A, Knoop V. A member of a novel Arabidopsis thaliana gene family of candidate Mg2+ ion transporters complements a yeast mitochondrial group II intron-splicing mutant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000. [PMID: 11115130 DOI: 10.1111/j.1365-313x.2000.00895.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Autocatalytic activity of some group II introns has been demonstrated in vitro, but helper functions such as the yeast MRS2 protein are essential for splicing in vivo. In our search for such helper factors in plants, we pursued the cloning of two Arabidopsis thaliana homologues, atmrs2-1 and atmrs2-2. Atmrs2-1, but not atmrs2-2, complements the yeast deletion mutant of mrs2, and this is congruent with the prediction of two adjacent transmembrane stretches in AtMRS2-1 and yeast MRS2 but not in AtMRS2-2. This complementation depends on fusion of the native yeast mitochondrial import sequence to atmrs2-1. A differing, non-mitochondrial, cellular targeting in Arabidopsis is supported by the analysis of green fluorescent protein fusion constructs after transient transformation into plant protoplasts. Further members of what now appears to be a family of 10 mrs2 homologues are identified in the Arabidopsis genome. Similarity searches with the PSI-BLAST algorithm in the protein database fail to identify homologues of this novel gene family in any eukaryotes other than yeasts, but do identify its distant relatedness to the corA group of bacterial magnesium transporters. In line with this observation, intramitochondrial magnesium concentrations are indeed restored to wild-type levels in the yeast mutant on complementation with atmrs2-1.
Collapse
MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Biological Transport
- Carrier Proteins/genetics
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Exons
- Genes, Plant/genetics
- Genetic Complementation Test
- Green Fluorescent Proteins
- Introns
- Ion Channels
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Magnesium/metabolism
- Microscopy, Fluorescence
- Mitochondrial Proteins
- Molecular Sequence Data
- Multigene Family
- Mutation
- Nuclear Proteins/genetics
- Phylogeny
- Plants, Toxic
- Protoplasts/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tobacco
- Transcription, Genetic
Collapse
Affiliation(s)
- I Schock
- Department of Molecular Botany, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | | | | | | | | | | |
Collapse
|
8
|
Bock R, Hagemann R. Extranuclear Inheritance: Plastid Genetics: Manipulation of Plastid Genomes and Biotechnological Applications. PROGRESS IN BOTANY 2000. [DOI: 10.1007/978-3-642-57203-6_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
9
|
Holländer V, Kück U. Group II intron splicing in chloroplasts: identificationof mutations determining intron stability and fate of exon RNA. Nucleic Acids Res 1999; 27:2345-53. [PMID: 10325424 PMCID: PMC148801 DOI: 10.1093/nar/27.11.2345] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In order to investigate in vivo splicing of group II introns in chloroplasts, we previously have integrated the mitochondrial intron rI1 from the green alga Scenedesmus obliquus into the Chlamydomonas chloroplast tscA gene. This construct allows a functional analysis of conserved intron sequences in vivo, since intron rI1 is correctly spliced in chloroplasts. Using site-directed mutagenesis, deletions of the conserved intron domains V and VI were performed. In another set of experiments, each possible substitution of the strictly conserved first intron nucleotide G1 was generated, as well as each possible single and double mutation of the tertiary base pairing gamma-gamma ' involved in the formation of the intron's tertiary RNA structure. In most cases, the intron mutations showed the same effect on in vivo intron splicing efficiency as they did on the in vitro self-splicing reaction, since catalytic activity is provided by the intron RNA itself. In vivo, all mutations have additional effects on the chimeric tscA -rI1 RNA, most probably due to the role played by trans -acting factors in intron processing. Substitutions of the gamma-gamma ' base pair lead to an accumulation of excised intron RNA, since intron stability is increased. In sharp contrast to autocatalytic splicing, all point mutations result in a complete loss of exon RNA, although the spliced intron accumulates to high levels. Intron degradation and exon ligation only occur in double mutants with restored base pairing between the gamma and gamma' sites. Therefore, we conclude that intron degradation, as well as the ligation of exon-exon molecules, depends on the tertiary intron structure. Furthermore, our data suggest that intron excision proceeds in vivo independent of ligation of exon-exon molecules.
Collapse
Affiliation(s)
- V Holländer
- Lehrstuhl für Allgemeine Botanik, Fakultät für Biologie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | | |
Collapse
|
10
|
Holländer V, Kück U. Group II intron splicing in Escherichia coli: phenotypes of cis-acting mutations resemble splicing defects observed in organelle RNA processing. Nucleic Acids Res 1999; 27:2339-44. [PMID: 10325423 PMCID: PMC148800 DOI: 10.1093/nar/27.11.2339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mitochondrial group IIB intron rI1, from the green algae Scenedesmus obliquus ' LSUrRNA gene, has been introduced into the lacZ gene encoding beta-galacto-sidase. After DNA-mediated transformation of the recombinant lacZ gene into Escherichia coli, we observed correct splicing of the chimeric precursor RNA in vivo. In contrast to autocatalytic in vitro self-splicing, intron processing in vivo is independent of the growth temperature, suggesting that in E.coli, trans -acting factors are involved in group II intron splicing. Such a system would seem suitable as a model for analyzing intron processing in a prokaryotic host. In order to study further the effect of cis -mutations on intron splicing, different rI1 mutants were analyzed (with respect to their splicing activity) in E.coli. Although the phenotypes of these E. coli intron splicing mutants were identical to those which can be observed during organellar splicing of rI1, they are different to those observed in in vitro self-splicing experiments. Therefore, in both organelles and prokaryotes, it is likely that either similar splicing factors or trans -acting factors exhibiting similar functions are involved in splicing. We speculate that ubiquitous trans -acting factors, via recent horizontal transfer, have contributed to the spread of group II introns.
Collapse
Affiliation(s)
- V Holländer
- Lehrstuhl für Allgemeine Botanik, Fakultät für Biologie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | | |
Collapse
|
11
|
Rochaix JD. Post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii. PLANT MOLECULAR BIOLOGY 1996; 32:327-341. [PMID: 8980486 DOI: 10.1007/bf00039389] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The biosynthesis of the photosynthetic apparatus depends on the concerted action of the nuclear and chloroplast genetic systems. Numerous nuclear and chloroplast mutants of Chlamydomonas deficient in photosynthetic activity have been isolated and characterized. While several of these mutations alter the genes of components of the photosynthetic complexes, a large number of the mutations affect the expression of chloroplast genes involved in photosynthesis. Most of these mutations are nuclear and only affect the expression of a single chloroplast gene. The mutations examined appear to act principally at post-transcriptional steps such as RNA stability, RNA processing, cis- and trans-splicing and translation. Directed chloroplast DNA surgery through biolistic transformation has provided a powerful tool for identifying important cis elements involved in chloroplast gene expression. Insertion of chimeric genes consisting of chloroplast regulatory regions fused to reporter genes into the chloroplast genome has led to the identification of target sites of the nuclear-encoded functions affected in some of the mutants. Biochemical studies have identified a set of RNA-binding proteins that interact with the 5'-untranslated regions of plastid mRNAs. The binding activity of some of these factors appears to be modulated by light and by the growth conditions.
Collapse
Affiliation(s)
- J D Rochaix
- Department of Molecular Biology, University of Geneva, Switzerland
| |
Collapse
|
12
|
Deshpande NN, Hollingsworth M, Herrin DL. The atpF group-II intron-containing gene from spinach chloroplasts is not spliced in transgenic Chlamydomonas chloroplasts. Curr Genet 1995; 28:122-7. [PMID: 8590462 DOI: 10.1007/bf00315777] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In order to determine whether the group-II trans-splicing machinery of the chloroplast of Chlamydomonas reinhardtii can splice a heterologous group-II cis intron, the atpF gene of spinach was transferred into the chloroplast genome of C. reinhardtii using the atpX expression vector. The atpF gene contains a group-II intron which, like other higher plant chloroplast introns, does not self-splice in vitro. The chimeric transgene was expressed at high levels, based on the accumulation of the precursor; however, spliced products could not be detected by Northern blotting, or by RT-PCR coupled with Southern-blot hybridization of the amplified products with an exon-junction probe. These results indicate that the spinach atpF intron is not spliced in transgenic C. reinhardtii chloroplasts. Thus, splicing of chloroplast introns mediated by cellular factors may be species-specific; alternately, the group-II splicing machinery of C. reinhardtii is specific for trans spliced introns.
Collapse
Affiliation(s)
- N N Deshpande
- Department of Botany, University of Texas at Austin 78713, USA
| | | | | |
Collapse
|