1
|
Hsu YW, Juan CT, Wang CM, Jauh GY. Mitochondrial Heat Shock Protein 60s Interact with What's This Factor 9 to Regulate RNA Splicing of ccmFC and rpl2. PLANT & CELL PHYSIOLOGY 2019; 60:116-125. [PMID: 30289547 DOI: 10.1093/pcp/pcy199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
Mitochondrial intron splicing is a plant-specific feature that was acquired during the co-evolution of eukaryotic host cells and a-proteobacteria. The elimination of these introns is facilitated by mitochondrial-targeted proteins encoded by its host, nucleus. What's this factor 9 (WTF9), a nuclear-encoded plant organelle RNA recognition (PORR) protein, is involved in the splicing of the mitochondrial group II introns rpl2 and ccmFC. Disruption of WTF9 causes developmental defects associated with the loss of Cyt c and Cyt c1 in Arabidopsis. In the present study, using a co-immunoprecipitation assay, we found that HSP60s interacted with WTF9, which was further confirmed by a pull-down assay. HSP60s are molecular chaperones that assist with protein folding in both eukaryotic and prokaryotic cells. However, accumulating evidence suggests that HSP60s also participate in other biological functions such as RNA metabolism and RNA protection. In this study, we found that consistently with their interaction with WTF9, HSP60s interacted with 48 nucleotides of the ccmFC intron. In mutant studies, the double mutant hsp60-3a1hsp60-3b1 exhibited a small stature phenotype and reduced splicing efficiency for rpl2 and ccmFC. These observations were similar to those in wtf9 mutants and suggest that HSP60s are involved in the RNA splicing of rpl2 and ccmFC introns in mitochondria. Our findings suggest that HSP60s participate in mitochondrial RNA splicing through their RNA-binding ability.
Collapse
Affiliation(s)
- Ya-Wen Hsu
- Institute of Plant and Microbial Biology,Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, Taiwan, ROC
| | - Chien-Ta Juan
- Institute of Plant and Microbial Biology,Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, Taiwan, ROC
| | - Chung-Min Wang
- Institute of Plant and Microbial Biology,Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, Taiwan, ROC
| | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology,Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, Taiwan, ROC
- Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan, ROC
| |
Collapse
|
2
|
|
3
|
Zhao Q, Liu C. Chloroplast Chaperonin: An Intricate Protein Folding Machine for Photosynthesis. Front Mol Biosci 2018; 4:98. [PMID: 29404339 PMCID: PMC5780408 DOI: 10.3389/fmolb.2017.00098] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/28/2017] [Indexed: 11/13/2022] Open
Abstract
Group I chaperonins are large cylindrical-shaped nano-machines that function as a central hub in the protein quality control system in the bacterial cytosol, mitochondria and chloroplasts. In chloroplasts, proteins newly synthesized by chloroplast ribosomes, unfolded by diverse stresses, or translocated from the cytosol run the risk of aberrant folding and aggregation. The chloroplast chaperonin system assists these proteins in folding into their native states. A widely known protein folded by chloroplast chaperonin is the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), an enzyme responsible for the fixation of inorganic CO2 into organic carbohydrates during photosynthesis. Chloroplast chaperonin was initially identified as a Rubisco-binding protein. All photosynthetic eucaryotes genomes encode multiple chaperonin genes which can be divided into α and β subtypes. Unlike the homo-oligomeric chaperonins from bacteria and mitochondria, chloroplast chaperonins are more complex and exists as intricate hetero-oligomers containing both subtypes. The Group I chaperonin requires proper interaction with a detachable lid-like co-chaperonin in the presence of ATP and Mg2+ for substrate encapsulation and conformational transition. Besides the typical Cpn10-like co-chaperonin, a unique co-chaperonin consisting of two tandem Cpn10-like domains joined head-to-tail exists in chloroplasts. Since chloroplasts were proposed as sensors to various environmental stresses, this diversified chloroplast chaperonin system has the potential to adapt to complex conditions by accommodating specific substrates or through regulation at both the transcriptional and post-translational levels. In this review, we discuss recent progress on the unique structure and function of the chloroplast chaperonin system based on model organisms Chlamydomonas reinhardtii and Arabidopsis thaliana. Knowledge of the chloroplast chaperonin system may ultimately lead to successful reconstitution of eukaryotic Rubisco in vitro.
Collapse
Affiliation(s)
- Qian Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cuimin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Zedler JA, Mullineaux CW, Robinson C. Efficient targeting of recombinant proteins to the thylakoid lumen in Chlamydomonas reinhardtii using a bacterial Tat signal peptide. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
5
|
Lefebvre-Legendre L, Reifschneider O, Kollipara L, Sickmann A, Wolters D, Kück U, Goldschmidt-Clermont M. A pioneer protein is part of a large complex involved in trans-splicing of a group II intron in the chloroplast of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:57-69. [PMID: 26611495 DOI: 10.1111/tpj.13089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/17/2015] [Indexed: 05/08/2023]
Abstract
Splicing of organellar introns requires the activity of numerous nucleus-encoded factors. In the chloroplast of Chlamydomonas reinhardtii, maturation of psaA mRNA encoding photosystem I subunit A involves two steps of trans-splicing. The exons, located on three separate transcripts, are flanked by sequences that fold to form the conserved structures of two group II introns. A fourth transcript contributes to assembly of the first intron, which is thus tripartite. The raa7 mutant (RNA maturation of psaA 7) is deficient in trans-splicing of the second intron of psaA, and may be rescued by transforming the chloroplast genome with an intron-less version of psaA. Using mapped-based cloning, we identify the RAA7 locus, which encodes a pioneer protein with no previously known protein domain or motif. The Raa7 protein, which is not associated with membranes, localizes to the chloroplast. Raa7 is a component of a large complex and co-sediments in sucrose gradients with the previously described splicing factors Raa1 and Raa2. Based on tandem affinity purification of Raa7 and mass spectrometry, Raa1 and Raa2 were identified as interacting partners of Raa7. Yeast two-hybrid experiments indicate that the interaction of Raa7 with Raa1 and Raa2 may be direct. We conclude that Raa7 is a component of a multimeric complex that is required for trans-splicing of the second intron of psaA. The characterization of this psaA trans-splicing complex is also of interest from an evolutionary perspective because the nuclear spliceosomal introns are thought to derive from group II introns, with which they show mechanistic and structural similarity.
Collapse
Affiliation(s)
- Linnka Lefebvre-Legendre
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| | - Olga Reifschneider
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr University Bochum, Universitätsstraße 150, Bochum, 44801, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften- ISAS - e.V., Otto Hahn Straße 6b, Dortmund, 44227, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften- ISAS - e.V., Otto Hahn Straße 6b, Dortmund, 44227, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK
- Medizinische Fakultät, Medizinisches Proteom-Center, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44801, Germany
| | - Dirk Wolters
- Department of Analytical Chemistry, Ruhr-University Bochum, Universitätsstraße 150, Bochum, 44801, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr University Bochum, Universitätsstraße 150, Bochum, 44801, Germany
| | - Michel Goldschmidt-Clermont
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| |
Collapse
|
6
|
Lefebvre-Legendre L, Choquet Y, Kuras R, Loubéry S, Douchi D, Goldschmidt-Clermont M. A nucleus-encoded chloroplast protein regulated by iron availability governs expression of the photosystem I subunit PsaA in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2015; 167:1527-40. [PMID: 25673777 PMCID: PMC4378161 DOI: 10.1104/pp.114.253906] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The biogenesis of the photosynthetic electron transfer chain in the thylakoid membranes requires the concerted expression of genes in the chloroplast and the nucleus. Chloroplast gene expression is subjected to anterograde control by a battery of nucleus-encoded proteins that are imported in the chloroplast, where they mostly intervene at posttranscriptional steps. Using a new genetic screen, we identify a nuclear mutant that is required for expression of the PsaA subunit of photosystem I (PSI) in the chloroplast of Chlamydomonas reinhardtii. This mutant is affected in the stability and translation of psaA messenger RNA. The corresponding gene, TRANSLATION OF psaA1 (TAA1), encodes a large protein with two domains that are thought to mediate RNA binding: an array of octatricopeptide repeats (OPR) and an RNA-binding domain abundant in apicomplexans (RAP) domain. We show that as expected for its function, TAA1 is localized in the chloroplast. It was previously shown that when mixotrophic cultures of C. reinhardtii (which use both photosynthesis and mitochondrial respiration for growth) are shifted to conditions of iron limitation, there is a strong decrease in the accumulation of PSI and that this is rapidly reversed when iron is resupplied. Under these conditions, TAA1 protein is also down-regulated through a posttranscriptional mechanism and rapidly reaccumulates when iron is restored. These observations reveal a concerted regulation of PSI and of TAA1 in response to iron availability.
Collapse
Affiliation(s)
- Linnka Lefebvre-Legendre
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland (L.L.-L., S.L., D.D., M.G.-C.); andUnité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France (Y.C., R.K.)
| | - Yves Choquet
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland (L.L.-L., S.L., D.D., M.G.-C.); andUnité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France (Y.C., R.K.)
| | - Richard Kuras
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland (L.L.-L., S.L., D.D., M.G.-C.); andUnité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France (Y.C., R.K.)
| | - Sylvain Loubéry
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland (L.L.-L., S.L., D.D., M.G.-C.); andUnité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France (Y.C., R.K.)
| | - Damien Douchi
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland (L.L.-L., S.L., D.D., M.G.-C.); andUnité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France (Y.C., R.K.)
| | - Michel Goldschmidt-Clermont
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland (L.L.-L., S.L., D.D., M.G.-C.); andUnité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France (Y.C., R.K.)
| |
Collapse
|
7
|
Trösch R, Mühlhaus T, Schroda M, Willmund F. ATP-dependent molecular chaperones in plastids--More complex than expected. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:872-88. [PMID: 25596449 DOI: 10.1016/j.bbabio.2015.01.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/03/2015] [Accepted: 01/08/2015] [Indexed: 11/27/2022]
Abstract
Plastids are a class of essential plant cell organelles comprising photosynthetic chloroplasts of green tissues, starch-storing amyloplasts of roots and tubers or the colorful pigment-storing chromoplasts of petals and fruits. They express a few genes encoded on their organellar genome, called plastome, but import most of their proteins from the cytosol. The import into plastids, the folding of freshly-translated or imported proteins, the degradation or renaturation of denatured and entangled proteins, and the quality-control of newly folded proteins all require the action of molecular chaperones. Members of all four major families of ATP-dependent molecular chaperones (chaperonin/Cpn60, Hsp70, Hsp90 and Hsp100 families) have been identified in plastids from unicellular algae to higher plants. This review aims not only at giving an overview of the most current insights into the general and conserved functions of these plastid chaperones, but also into their specific plastid functions. Given that chloroplasts harbor an extreme environment that cycles between reduced and oxidized states, that has to deal with reactive oxygen species and is highly reactive to environmental and developmental signals, it can be presumed that plastid chaperones have evolved a plethora of specific functions some of which are just about to be discovered. Here, the most urgent questions that remain unsolved are discussed, and guidance for future research on plastid chaperones is given. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
Collapse
Affiliation(s)
- Raphael Trösch
- TU Kaiserslautern, Molecular Biotechnology & Systems Biology, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany; HU Berlin, Institute of Biology, Chausseestraße 117, 10115 Berlin, Germany; TU Kaiserslautern, Molecular Genetics of Eukaryotes, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany.
| | - Timo Mühlhaus
- TU Kaiserslautern, Molecular Biotechnology & Systems Biology, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany.
| | - Michael Schroda
- TU Kaiserslautern, Molecular Biotechnology & Systems Biology, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany.
| | - Felix Willmund
- TU Kaiserslautern, Molecular Genetics of Eukaryotes, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany.
| |
Collapse
|
8
|
Jacobs J, Marx C, Kock V, Reifschneider O, Fränzel B, Krisp C, Wolters D, Kück U. Identification of a chloroplast ribonucleoprotein complex containing trans-splicing factors, intron RNA, and novel components. Mol Cell Proteomics 2013; 12:1912-25. [PMID: 23559604 PMCID: PMC3708175 DOI: 10.1074/mcp.m112.026583] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/27/2013] [Indexed: 11/06/2022] Open
Abstract
Maturation of chloroplast psaA pre-mRNA from the green alga Chlamydomonas reinhardtii requires the trans-splicing of two split group II introns. Several nuclear-encoded trans-splicing factors are required for the correct processing of psaA mRNA. Among these is the recently identified Raa4 protein, which is involved in splicing of the tripartite intron 1 of the psaA precursor mRNA. Part of this tripartite group II intron is the chloroplast encoded tscA RNA, which is specifically bound by Raa4. Using Raa4 as bait in a combined tandem affinity purification and mass spectrometry approach, we identified core components of a multisubunit ribonucleoprotein complex, including three previously identified trans-splicing factors (Raa1, Raa3, and Rat2). We further detected tscA RNA in the purified protein complex, which seems to be specific for splicing of the tripartite group II intron. A yeast-two hybrid screen and co-immunoprecipitation identified chloroplast-localized Raa4-binding protein 1 (Rab1), which specifically binds tscA RNA from the tripartite psaA group II intron. The yeast-two hybrid system provides evidence in support of direct interactions between Rab1 and four trans-splicing factors. Our findings contribute to our knowledge of chloroplast multisubunit ribonucleoprotein complexes and are discussed in support of the generally accepted view that group II introns are the ancestors of the eukaryotic spliceosomal introns.
Collapse
Affiliation(s)
- Jessica Jacobs
- From the ‡Department for General and Molecular Botany, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Christina Marx
- From the ‡Department for General and Molecular Botany, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Vera Kock
- From the ‡Department for General and Molecular Botany, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Olga Reifschneider
- From the ‡Department for General and Molecular Botany, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Benjamin Fränzel
- ¶Department of Analytical Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Christoph Krisp
- ¶Department of Analytical Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Dirk Wolters
- ¶Department of Analytical Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Ulrich Kück
- From the ‡Department for General and Molecular Botany, Ruhr-University Bochum, D-44780 Bochum, Germany
| |
Collapse
|
9
|
Henderson B, Fares MA, Lund PA. Chaperonin 60: a paradoxical, evolutionarily conserved protein family with multiple moonlighting functions. Biol Rev Camb Philos Soc 2013; 88:955-87. [DOI: 10.1111/brv.12037] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 02/20/2013] [Accepted: 03/04/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Brian Henderson
- Department of Microbial Diseases, UCL-Eastman Dental Institute; University College London; London WC1X 8LD U.K
| | - Mario A. Fares
- Department of Genetics; University of Dublin, Trinity College Dublin; Dublin 2 Ireland
- Department of Abiotic Stress; Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas (CSIC-UPV); Valencia 46022 Spain
| | - Peter A. Lund
- School of Biosciences; University of Birmingham; Birmingham B15 2TT U.K
| |
Collapse
|
10
|
Glanz S, Jacobs J, Kock V, Mishra A, Kück U. Raa4 is a trans-splicing factor that specifically binds chloroplast tscA intron RNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:421-431. [PMID: 21954961 DOI: 10.1111/j.1365-313x.2011.04801.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
During trans-splicing of discontinuous organellar introns, independently transcribed coding sequences are joined together to generate a continuous mRNA. The chloroplast psaA gene from Chlamydomonas reinhardtii encoding the P(700) core protein of photosystem I (PSI) is split into three exons and two group IIB introns, which are both spliced in trans. Using forward genetics, we isolated a novel PSI mutant, raa4, with a defect in trans-splicing of the first intron. Complementation analysis identified the affected gene encoding the 112.4 kDa Raa4 protein, which shares no strong sequence identity with other known proteins. The chloroplast localization of the protein was confirmed by confocal fluorescence microscopy, using a GFP-tagged Raa4 fusion protein. RNA-binding studies showed that Raa4 binds specifically to domains D2 and D3, but not to other conserved domains of the tripartite group II intron. Raa4 may play a role in stabilizing folding intermediates or functionally active structures of the split intron RNA.
Collapse
Affiliation(s)
- Stephanie Glanz
- Department for General and Molecular Botany, Ruhr-University Bochum, D-44780 Bochum, Germany
| | | | | | | | | |
Collapse
|
11
|
Jacobs J, Kück U. Function of chloroplast RNA-binding proteins. Cell Mol Life Sci 2011; 68:735-48. [PMID: 20848156 PMCID: PMC11115000 DOI: 10.1007/s00018-010-0523-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 08/25/2010] [Accepted: 08/30/2010] [Indexed: 12/18/2022]
Abstract
Chloroplasts are eukaryotic organelles which represent evolutionary chimera with proteins that have been derived from either a prokaryotic endosymbiont or a eukaryotic host. Chloroplast gene expression starts with transcription of RNA and is followed by multiple post-transcriptional processes which are mediated mainly by an as yet unknown number of RNA-binding proteins. Here, we review the literature to date on the structure and function of these chloroplast RNA-binding proteins. For example, the functional protein domains involved in RNA binding, such as the RNA-recognition motifs, the chloroplast RNA-splicing and ribosome maturation domains, and the pentatricopeptide-repeat motifs, are summarized. We also describe biochemical and forward genetic approaches that led to the identification of proteins modifying RNA stability or carrying out RNA splicing or editing. Such data will greatly contribute to a better understanding of the biogenesis of a unique organelle found in all photosynthetic organisms.
Collapse
Affiliation(s)
- Jessica Jacobs
- Department for General and Molecular Biology, Ruhr-University Bochum, Universitätsstraße 150, Bochum, Germany.
| | | |
Collapse
|
12
|
Jacobs J, Glanz S, Bunse-Grassmann A, Kruse O, Kück U. RNA trans-splicing: identification of components of a putative chloroplast spliceosome. Eur J Cell Biol 2010; 89:932-9. [PMID: 20705358 DOI: 10.1016/j.ejcb.2010.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Group II introns with highly complex RNA structures have been discovered in both prokaryotes and eukaryotic organelles. Usually, excision of non-coding group II intron sequences occurs by cis-splicing, the intramolecular ligation of exons in the same precursor RNA, but some group II introns are excised by intermolecular ligation. This process is called trans-splicing, and genome sequencing predicted that this type of RNA processing occurs in more than 180 organelle genomes from eukaryotes. A well characterised trans-spliced intron RNA is represented by the chloroplast psaA gene of the model alga Chlamydomonas reinhardtii. The psaA gene is split into three exons, which are widely distributed over the plastome and transcribed independently. PsaA exons are flanked by sequences typical for group II introns and joined by trans-splicing via two transesterification reactions. Although it is known that some group II introns are able to splice autocatalytically, trans-splicing of the psaA RNA depends on several nucleus and chloroplast encoded factors. The phylogenetic relationship between group II introns and nuclear spliceosomal RNA led to the hypothesis that these factors are part of large multiprotein and ribonucleoprotein complexes akin to the nuclear spliceosome. Here, we give a concise overview of experimental strategies to identify novel factors involved in trans-splicing of psaA RNA and review recent results that have elucidated the composition and function of a putative chloroplast spliceosome involved in processing of chloroplast precursor RNAs.
Collapse
Affiliation(s)
- Jessica Jacobs
- Department for General and Molecular Biology, Ruhr-University Bochum, 44780 Bochum, Germany
| | | | | | | | | |
Collapse
|
13
|
Samaha H, Delorme V, Pontvianne F, Cooke R, Delalande F, Van Dorsselaer A, Echeverria M, Sáez-Vásquez J. Identification of protein factors and U3 snoRNAs from a Brassica oleracea RNP complex involved in the processing of pre-rRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:383-398. [PMID: 19891704 DOI: 10.1111/j.1365-313x.2009.04061.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report on the structural characterization of a functional U3 snoRNA ribonucleoprotein complex isolated from Brassica oleracea. The BoU3 snoRNP complex (formerly NF D) binds ribosomal DNA (rDNA), specifically cleaves pre-rRNA at the primary cleavage site in vitro and probably links transcription to early pre-rRNA processing in vivo. Using a proteomic approach we have identified 62 proteins in the purified BoU3 snoRNP fraction, including small RNA associated proteins (Fibrillarin, NOP5/Nop58p, Diskerin/Cbf5p, SUS2/PRP8 and CLO/GFA1/sn114p) and 40S ribosomal associated proteins (22 RPS and four ARCA-like proteins). Another major protein group is composed of chaperones/chaperonins (HSP81/TCP-1) and at least one proteasome subunit (RPN1a). Remarkably, RNA-dependent RNA polymerase (RdRP) and Tudor staphylococcal nuclease (TSN) proteins, which have RNA- and/or DNA-associated activities, were also revealed in the complex. Furthermore, three U3 snoRNA variants were identified in the BoU3 snoRNP fraction, notably an evolutionarily conserved and variable stem loop structure located just downstream from the C-box domain of the U3 sequence structures. We conclude that the BoU3 snoRNP complex is mainly required for 40S pre-ribosome synthesis. It is also expected that U3 snoRNA variants and interacting proteins might play a major role in BoU3 snoRNP complex assembly and/or function. This study provides a basis for further investigation of these novel ribonucleoprotein factors and their role in plant ribosome biogenesis.
Collapse
Affiliation(s)
- Hala Samaha
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-UPVD, Perpignan France
| | | | | | | | | | | | | | | |
Collapse
|
14
|
New Insights into the Roles of Molecular Chaperones in Chlamydomonas and Volvox. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 285:75-113. [DOI: 10.1016/b978-0-12-381047-2.00002-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
15
|
Abstract
In eukaryotes, RNA trans-splicing is an important RNA-processing form for the end-to-end ligation of primary transcripts that are derived from separately transcribed exons. So far, three different categories of RNA trans-splicing have been found in organisms as diverse as algae to man. Here, we review one of these categories: the trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. Trans-spliced exons can be predicted from DNA sequences derived from a large number of sequenced organelle genomes. Further molecular genetic analysis of mutants has unravelled proteins, some of which being part of high-molecular-weight complexes that promote the splicing process. Based on data derived from the alga Chlamydomonas reinhardtii, a model is provided which defines the composition of an organelle spliceosome. This will have a general relevance for understanding the function of RNA-processing machineries in eukaryotic organelles.
Collapse
Affiliation(s)
- Stephanie Glanz
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | | |
Collapse
|
16
|
|
17
|
|
18
|
Abstract
Group II introns are large autocatalytic RNAs found in organellar genomes of plants and lower eukaryotes, as well as in some bacterial genomes. Interestingly, these ribozymes share characteristic traits with both spliceosomal introns and non-LTR retrotransposons and may have a common evolutionary ancestor. Furthermore, group II intron features such as structure, folding and catalytic mechanism differ considerably from those of other large ribozymes, making group II introns an attractive model system to gain novel insights into RNA biology and biochemistry. This review explores recent advances in the structural and mechanistic characterization of group II intron architecture and self-splicing.
Collapse
Affiliation(s)
- Olga Fedorova
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
| | | |
Collapse
|
19
|
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
|