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Carmel Ezra S, Tuller T. Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts. Comput Struct Biotechnol J 2022; 20:2521-2538. [PMID: 35685358 PMCID: PMC9157439 DOI: 10.1016/j.csbj.2022.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/15/2022] [Accepted: 05/15/2022] [Indexed: 11/15/2022] Open
Abstract
The process of translation initiation in prokaryotes is mediated by the hybridization of the 16S rRNA of the small ribosomal subunit with the mRNA in a short region called the ribosomal binding site. However, translation initiation in chloroplasts, which have evolved from an ancestral bacterium, is not well understood. Some studies suggest that in many cases it differs from translation initiation in bacteria and involves various novel interactions of the mRNA structures with intracellular factors; however currently, there is no generic quantitative model related to these aspects in chloroplasts. We developed a novel computational pipeline and models that can be used for understanding and modeling translation regulation in chloroplasts. We demonstrate that local folding and co-folding energy of the rRNA and the mRNA correlates with codon usage estimators of expression levels (r = -0.63) and infer predictive models that connect these energies and codon usage to protein levels (with correlation up to 0.71). In addition, we demonstrate that the ends of the transcripts in chloroplasts are populated with various structural elements that may be functional. Furthermore, we report a database of 166 novel structures in the chloroplast transcripts that are predicted to be functional. We believe that the models reported here improve existing understandings of genomic evolution and the biophysics of translation in chloroplasts; as such, they can aid gene expression engineering in chloroplasts for various biotechnological objectives.
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Affiliation(s)
- Stav Carmel Ezra
- Department of Biomedical Engineering, Tel Aviv University, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Israel
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2
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Tarelkina TV, Galibina NA, Moshchenskaya YL, Novitskaya LL. In Silico Analysis of Regulatory cis-Elements in the Promoters of Genes Encoding Apoplastic Invertase and Sucrose Synthase in Silver Birch. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420050082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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3
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Wei Y, Xia X. Unique Shine-Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation. Genome Biol Evol 2020; 11:3194-3206. [PMID: 31621842 PMCID: PMC6847405 DOI: 10.1093/gbe/evz227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
Microorganisms require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A prominent feature that facilitates translation initiation in bacteria is the Shine-Dalgarno (SD) sequence. However, there is much debate over its conservation in Cyanobacteria and in chloroplasts which presumably originated from endosymbiosis of ancient Cyanobacteria. Elucidating the utilization of SD sequences in Cyanobacteria and in chloroplasts is therefore important to understand whether 1) SD role in Cyanobacterial translation has been reduced prior to chloroplast endosymbiosis or 2) translation in Cyanobacteria and in plastid has been subjected to different evolutionary pressures. To test these alternatives, we employed genomic, proteomic, and transcriptomic data to trace differences in SD usage among Synechocystis species, Microcystis aeruginosa, cyanophages, Nicotiana tabacum chloroplast, and Arabidopsis thaliana chloroplast. We corrected their mis-annotated 16S rRNA 3' terminus using an RNA-Seq-based approach to determine their SD/anti-SD locational constraints using an improved measurement DtoStart. We found that cyanophages well-mimic Cyanobacteria in SD usage because both have been under the same selection pressure for SD-mediated initiation. Whereas chloroplasts lost this similarity because the need for SD-facilitated initiation has been reduced in plastids having much reduced genome size and different ribosomal proteins as a result of host-symbiont coevolution. Consequently, SD sequence significantly increases protein expression in Cyanobacteria but not in chloroplasts, and only Cyanobacterial genes compensate for a lack of SD sequence by having weaker secondary structures at the 5' UTR. Our results suggest different evolutionary pressures operate on translation initiation in Cyanobacteria and in chloroplast.
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Affiliation(s)
- Yulong Wei
- Department of Biology, University of Ottawa, Ontario, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
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4
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Hsu SC, Browne DR, Tatli M, Devarenne TP, Stern DB. N-terminal sequences affect expression of triterpene biosynthesis enzymes in Chlamydomonas chloroplasts. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Weiner I, Shahar N, Marco P, Yacoby I, Tuller T. Solving the Riddle of the Evolution of Shine-Dalgarno Based Translation in Chloroplasts. Mol Biol Evol 2019; 36:2854-2860. [DOI: 10.1093/molbev/msz210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AbstractChloroplasts originated from an ancient cyanobacterium and still harbor a bacterial-like genome. However, the centrality of Shine–Dalgarno ribosome binding, which predominantly regulates proteobacterial translation initiation, is significantly decreased in chloroplasts. As plastid ribosomal RNA anti-Shine–Dalgarno elements are similar to their bacterial counterparts, these sites alone cannot explain this decline. By computational simulation we show that upstream point mutations modulate the local structure of ribosomal RNA in chloroplasts, creating significantly tighter structures around the anti-Shine–Dalgarno locus, which in-turn reduce the probability of ribosome binding. To validate our model, we expressed two reporter genes (mCherry, hydrogenase) harboring a Shine–Dalgarno motif in the Chlamydomonas reinhardtii chloroplast. Coexpressing them with a 16S ribosomal RNA, modified according to our model, significantly enhances mCherry and hydrogenase expression compared with coexpression with an endogenous 16S gene.
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Affiliation(s)
- Iddo Weiner
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Noam Shahar
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Pini Marco
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Iftach Yacoby
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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6
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Viola S, Cavaiuolo M, Drapier D, Eberhard S, Vallon O, Wollman FA, Choquet Y. MDA1, a nucleus-encoded factor involved in the stabilization and processing of the atpA transcript in the chloroplast of Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:1033-1047. [PMID: 30809889 DOI: 10.1111/tpj.14300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 05/21/2023]
Abstract
In Chlamydomonas reinhardtii, chloroplast gene expression is tightly regulated post-transcriptionally by gene-specific trans-acting protein factors. Here, we report the molecular identification of an OctotricoPeptide Repeat (OPR) protein, MDA1, which governs the maturation and accumulation of the atpA transcript, encoding subunit α of the chloroplast ATP synthase. As does TDA1, another OPR protein required for the translation of the atpA mRNA, MDA1 targets the atpA 5'-untranslated region (UTR). Unexpectedly, it binds within a region of approximately 100 nt in the middle of the atpA 5'-UTR, at variance with the stabilization factors characterized so far, which bind to the 5'-end of their target mRNA to protect it from 5' → 3' exonucleases. It binds the same region as TDA1, with which it forms a high-molecular-weight complex that also comprises the atpA mRNA. This complex dissociates upon translation, promoting degradation of the atpA mRNA. We suggest that atpA transcripts, once translated, enter the degradation pathway because they cannot reassemble with MDA1 and TDA1, which preferentially bind to de novo transcribed mRNAs.
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Affiliation(s)
- Stefania Viola
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste -UMR7141, IBPC, CNRS-Sorbonne Université, 13, rue Pierre et Marie Curie, 75005, Paris, France
| | - Marina Cavaiuolo
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste -UMR7141, IBPC, CNRS-Sorbonne Université, 13, rue Pierre et Marie Curie, 75005, Paris, France
| | - Dominique Drapier
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste -UMR7141, IBPC, CNRS-Sorbonne Université, 13, rue Pierre et Marie Curie, 75005, Paris, France
| | - Stephan Eberhard
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste -UMR7141, IBPC, CNRS-Sorbonne Université, 13, rue Pierre et Marie Curie, 75005, Paris, France
| | - Olivier Vallon
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste -UMR7141, IBPC, CNRS-Sorbonne Université, 13, rue Pierre et Marie Curie, 75005, Paris, France
| | - Francis-André Wollman
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste -UMR7141, IBPC, CNRS-Sorbonne Université, 13, rue Pierre et Marie Curie, 75005, Paris, France
| | - Yves Choquet
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste -UMR7141, IBPC, CNRS-Sorbonne Université, 13, rue Pierre et Marie Curie, 75005, Paris, France
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7
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Trösch R, Barahimipour R, Gao Y, Badillo-Corona JA, Gotsmann VL, Zimmer D, Mühlhaus T, Zoschke R, Willmund F. Commonalities and differences of chloroplast translation in a green alga and land plants. NATURE PLANTS 2018; 4:564-575. [PMID: 30061751 DOI: 10.1038/s41477-018-0211-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Chloroplast gene expression is a fascinating and highly regulated process, which was mainly studied on specific genes in a few model organisms including the unicellular green alga Chlamydomonas (Chlamydomonas reinhardtii) and the embryophyte (land) plants tobacco (Nicotiana tabacum) and Arabidopsis (Arabidopsis thaliana). However, a direct plastid genome-wide interspecies comparison of chloroplast gene expression that includes translation was missing. We adapted a targeted chloroplast ribosome profiling approach to quantitatively compare RNA abundance and translation output between Chlamydomonas, tobacco and Arabidopsis. The re-analysis of established chloroplast mutants confirmed the capability of the approach by detecting known as well as previously undetected translation defects (including the potential photosystem II assembly-dependent regulation of PsbH). Systematic comparison of the algal and land plant wild-type gene expression showed that, for most genes, the steady-state translation output is highly conserved among the three species, while the levels of transcript accumulation are more distinct. Whereas in Chlamydomonas transcript accumulation and translation output are closely balanced, this correlation is less obvious in embryophytes, indicating more pronounced translational regulation. Altogether, this suggests that green algae and land plants evolved different strategies to achieve conserved levels of protein synthesis.
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Affiliation(s)
- Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern, Germany
| | - David Zimmer
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern, Germany.
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8
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Scharff LB, Ehrnthaler M, Janowski M, Childs LH, Hasse C, Gremmels J, Ruf S, Zoschke R, Bock R. Shine-Dalgarno Sequences Play an Essential Role in the Translation of Plastid mRNAs in Tobacco. THE PLANT CELL 2017; 29:3085-3101. [PMID: 29133466 PMCID: PMC5757275 DOI: 10.1105/tpc.17.00524] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/27/2017] [Accepted: 11/08/2017] [Indexed: 05/23/2023]
Abstract
In prokaryotic systems, the translation initiation of many, though not all, mRNAs depends on interaction between a sequence element upstream of the start codon (the Shine-Dalgarno sequence [SD]) and a complementary sequence in the 3' end of the 16S rRNA (anti-Shine-Dalgarno sequence [aSD]). Although many chloroplast mRNAs harbor putative SDs in their 5' untranslated regions and the aSD displays strong conservation, the functional relevance of SD-aSD interactions in plastid translation is unclear. Here, by generating transplastomic tobacco (Nicotiana tabacum) mutants with point mutations in the aSD coupled with genome-wide analysis of translation by ribosome profiling, we provide a global picture of SD-dependent translation in plastids. We observed a pronounced correlation between weakened predicted SD-aSD interactions and reduced translation efficiency. However, multiple lines of evidence suggest that the strength of the SD-aSD interaction is not the only determinant of the translational output of many plastid mRNAs. Finally, the translation efficiency of mRNAs with strong secondary structures around the start codon is more dependent on the SD-aSD interaction than weakly structured mRNAs. Thus, our data reveal the importance of the aSD in plastid translation initiation, uncover chloroplast genes whose translation is influenced by SD-aSD interactions, and provide insights into determinants of translation efficiency in plastids.
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Affiliation(s)
- Lars B Scharff
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Miriam Ehrnthaler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Marcin Janowski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Liam H Childs
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Claudia Hasse
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Jürgen Gremmels
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Reimo Zoschke
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
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9
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Lao YM, Jin H, Zhou J, Zhang HJ, Cai ZH. Functional Characterization of a Missing Branch Component in Haematococcus pluvialis for Control of Algal Carotenoid Biosynthesis. FRONTIERS IN PLANT SCIENCE 2017; 8:1341. [PMID: 28824677 PMCID: PMC5539077 DOI: 10.3389/fpls.2017.01341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/18/2017] [Indexed: 05/31/2023]
Abstract
Cyclization of acyclic lycopene by cyclases marks an important regulatory point in carotenoid biosynthesis. Though some algal lycopene epsilon cyclases (LCYEs) have been predicted computationally, very few have been functionally identified. Little is known about the regulation mechanisms of algal LCYEs. Recent comparative genomic analysis suggested that Haematococcus pluvialis contained only the β type cyclase (HpLCYB). However, in this study, carotenoid profiling found trace α-carotene in the salt-treated cells, indicating the in vivo activity of HpLCYE, a missing component for α-branch carotenoids. Thus, genes coding for HpLCYB and HpLCYE were isolated and functionally complemented in Escherichia coli. Substrate specificity assays revealed an exclusive cyclization order of HpLCYE to HpLCYB for the biosynthesis of heterocyclic carotenoids. Expression pattern studies and bioinformatic analysis of promoter regions showed that both cyclases were differentially regulated by the regulatory cis-acting elements in promoters to correlate with primary and secondary carotenoid biosynthesis under environmental stresses. Characterization of the branch components in algal carotenoid biosynthesis revealed a mechanism for control of metabolic flux into α- and β-branch by the competition and cooperation between HpLCYE and HpLCYB; and supplied a promising route for molecular breeding of cyclic carotenoid biosynthesis.
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Affiliation(s)
- Yong M. Lao
- Shenzhen Public Platform of Screening and Application of Marine Microbial ResourcesGuangdong, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China
| | - Hui Jin
- Shenzhen Public Platform of Screening and Application of Marine Microbial ResourcesGuangdong, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China
- School of Life Sciences, Tsinghua UniversityBeijing, China
| | - Jin Zhou
- Shenzhen Public Platform of Screening and Application of Marine Microbial ResourcesGuangdong, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China
| | - Huai J. Zhang
- School of Life Sciences, Tsinghua UniversityBeijing, China
| | - Zhong H. Cai
- Shenzhen Public Platform of Screening and Application of Marine Microbial ResourcesGuangdong, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China
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10
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Kang S, Odom OW, Thangamani S, Herrin DL. Toward mosquito control with a green alga: Expression of Cry toxins of Bacillus thuringiensis subsp. israelensis (Bti) in the chloroplast of Chlamydomonas. JOURNAL OF APPLIED PHYCOLOGY 2017; 29:1377-1389. [PMID: 28713202 PMCID: PMC5509220 DOI: 10.1007/s10811-016-1008-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We are developing Chlamydomonas strains that can be used for safe and sustainable control of mosquitoes, because they produce proteins from Bacillus thuringiensis subsp. israelensis (Bti) in the chloroplast. Chlamydomonas has a number of advantages for this approach, including genetic controls that are not generally available with industrial algae. The Bti toxin has been used for mosquito control for > 30 years and does not engender resistance; it contains three Cry proteins, Cry4Aa (135 kDa), Cry4Ba (128 kDa) and Cry11Aa (72 kDa), and Cyt1Aa (25 kDa). To express the Cry proteins in the chloroplast, the three genes were resynthesized and cry4Aa was truncated to the first 700 amino acids (cry4Aa700 ); also, since they can be toxic to host cells, the inducible Cyc6:Nac2-psbD expression system was used. Western blots of total protein from the chloroplast transformants showed accumulation of the intact polypeptides, and the relative expression level was Cry11Aa > Cry4Aa700 > Cry4Ba. Quantitative western blots with purified Cry11Aa as a standard showed that Cry11Aa accumulated to 0.35% of total cell protein. Live cell bioassays in dH20 demonstrated toxicity of the cry4Aa700 and cry11Aa transformants to larvae of Aedes aegypti and Culex quinquefasciatus. These results demonstrate that the Cry proteins that are most toxic to Aedes and Culex mosquitoes, Cry4Aa and Cry11Aa, can be successfully expressed in the chloroplast of Chlamydomonas.
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Affiliation(s)
- Seongjoon Kang
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Pond Life Technologies LLC, Cedar Park, TX 78613, USA
| | - Obed W. Odom
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Saravanan Thangamani
- Dept. of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - David L. Herrin
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Pond Life Technologies LLC, Cedar Park, TX 78613, USA
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11
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Douchi D, Qu Y, Longoni P, Legendre-Lefebvre L, Johnson X, Schmitz-Linneweber C, Goldschmidt-Clermont M. A Nucleus-Encoded Chloroplast Phosphoprotein Governs Expression of the Photosystem I Subunit PsaC in Chlamydomonas reinhardtii. THE PLANT CELL 2016; 28:1182-99. [PMID: 27113776 PMCID: PMC4904667 DOI: 10.1105/tpc.15.00725] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 04/25/2016] [Indexed: 05/05/2023]
Abstract
The nucleo-cytoplasmic compartment exerts anterograde control on chloroplast gene expression through numerous proteins that intervene at posttranscriptional steps. Here, we show that the maturation of psaC mutant (mac1) of Chlamydomonas reinhardtii is defective in photosystem I and fails to accumulate psaC mRNA. The MAC1 locus encodes a member of the Half-A-Tetratricopeptide (HAT) family of super-helical repeat proteins, some of which are involved in RNA transactions. The Mac1 protein localizes to the chloroplast in the soluble fraction. MAC1 acts through the 5' untranslated region of psaC transcripts and is required for their stability. Small RNAs that map to the 5'end of psaC RNA in the wild type but not in the mac1 mutant are inferred to represent footprints of MAC1-dependent protein binding, and Mac1 expressed in bacteria binds RNA in vitro. A coordinate response to iron deficiency, which leads to dismantling of the photosynthetic electron transfer chain and in particular of photosystem I, also causes a decrease of Mac1. Overexpression of Mac1 leads to a parallel increase in psaC mRNA but not in PsaC protein, suggesting that Mac1 may be limiting for psaC mRNA accumulation but that other processes regulate protein accumulation. Furthermore, Mac 1 is differentially phosphorylated in response to iron availability and to conditions that alter the redox balance of the electron transfer chain.
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Affiliation(s)
- Damien Douchi
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Yujiao Qu
- Institute of Biology, Molecular Genetics, Humboldt University of Berlin, D-10115 Berlin, Germany
| | - Paolo Longoni
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Linnka Legendre-Lefebvre
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Xenie Johnson
- Unité Mixte de Recherche 7141, CNRS/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | | | - Michel Goldschmidt-Clermont
- Department of Botany and Plant Biology and Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland
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12
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Sun Y, Zerges W. Translational regulation in chloroplasts for development and homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:809-20. [PMID: 25988717 DOI: 10.1016/j.bbabio.2015.05.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/13/2015] [Accepted: 05/10/2015] [Indexed: 11/16/2022]
Abstract
Chloroplast genomes encode 100-200 proteins which function in photosynthesis, the organellar genetic system, and other pathways and processes. These proteins are synthesized by a complete translation system within the chloroplast, with bacterial-type ribosomes and translation factors. Here, we review translational regulation in chloroplasts, focusing on changes in translation rates which occur in response to requirements for proteins encoded by the chloroplast genome for development and homeostasis. In addition, we delineate the developmental and physiological contexts and model organisms in which translational regulation in chloroplasts has been studied. This article is part of a Special Issue entitled: Chloroplast biogenesis.
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Affiliation(s)
- Yi Sun
- Biology Department and Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W., Montreal, Quebec H4B 1R6, Canada
| | - William Zerges
- Biology Department and Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W., Montreal, Quebec H4B 1R6, Canada.
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13
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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.
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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.)
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14
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Bock R. Engineering plastid genomes: methods, tools, and applications in basic research and biotechnology. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:211-41. [PMID: 25494465 DOI: 10.1146/annurev-arplant-050213-040212] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The small bacterial-type genome of the plastid (chloroplast) can be engineered by genetic transformation, generating cells and plants with transgenic plastid genomes, also referred to as transplastomic plants. The transformation process relies on homologous recombination, thereby facilitating the site-specific alteration of endogenous plastid genes as well as the precisely targeted insertion of foreign genes into the plastid DNA. The technology has been used extensively to analyze chloroplast gene functions and study plastid gene expression at all levels in vivo. Over the years, a large toolbox has been assembled that is now nearly comparable to the techniques available for plant nuclear transformation and that has enabled new applications of transplastomic technology in basic and applied research. This review describes the state of the art in engineering the plastid genomes of algae and land plants (Embryophyta). It provides an overview of the existing tools for plastid genome engineering, discusses current technological limitations, and highlights selected applications that demonstrate the immense potential of chloroplast transformation in several key areas of plant biotechnology.
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Affiliation(s)
- Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany;
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15
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Young REB, Purton S. Cytosine deaminase as a negative selectable marker for the microalgal chloroplast: a strategy for the isolation of nuclear mutations that affect chloroplast gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:915-25. [PMID: 25234691 PMCID: PMC4282525 DOI: 10.1111/tpj.12675] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/04/2014] [Accepted: 09/16/2014] [Indexed: 05/09/2023]
Abstract
Negative selectable markers are useful tools for forward-genetic screens aimed at identifying trans-acting factors that are required for expression of specific genes. Transgenic lines harbouring the marker fused to a gene element, such as a promoter, may be mutagenized to isolate loss-of-function mutants able to survive under selection. Such a strategy allows the molecular dissection of factors that are essential for expression of the gene. Expression of individual chloroplast genes in plants and algae typically requires one or more nuclear-encoded factors that act at the post-transcriptional level, often through interaction with the 5' UTR of the mRNA. To study such nuclear control further, we have developed the Escherichia coli cytosine deaminase gene codA as a conditional negative selectable marker for use in the model green alga Chlamydomonas reinhardtii. We show that a codon-optimized variant of codA with three amino acid substitutions confers sensitivity to 5-fluorocytosine (5-FC) when expressed in the chloroplast under the control of endogenous promoter/5' UTR elements from the photosynthetic genes psaA or petA. UV mutagenesis of the psaA transgenic line allowed recovery of 5-FC-resistant, photosynthetically deficient lines harbouring mutations in the nuclear gene for the factor TAA1 that is required for psaA translation. Similarly, the petA line was used to isolate mutants of the petA mRNA stability factor MCA1 and the translation factor TCA1. The codA marker may be used to identify critical residues in known nuclear factors and to aid the discovery of additional factors required for expression of chloroplast genes.
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Affiliation(s)
- Rosanna E B Young
- Algal Research Group, Institute of Structural and Molecular Biology, University College LondonGower Street, London, WC1E 6BT, UK
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College LondonGower Street, London, WC1E 6BT, UK
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16
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Lefebvre-Legendre L, Merendino L, Rivier C, Goldschmidt-Clermont M. On the Complexity of Chloroplast RNA Metabolism: psaA Trans-splicing Can be Bypassed in Chlamydomonas. Mol Biol Evol 2014; 31:2697-707. [DOI: 10.1093/molbev/msu215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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17
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Wu CS, Chen DY, Chang CF, Li MJ, Hung KY, Chen LJ, Chen PW. The promoter and the 5'-untranslated region of rice metallothionein OsMT2b gene are capable of directing high-level gene expression in germinated rice embryos. PLANT CELL REPORTS 2014; 33:793-806. [PMID: 24381099 DOI: 10.1007/s00299-013-1555-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/18/2013] [Indexed: 06/03/2023]
Abstract
Critical regions within the rice metallothionein OsMT2b gene promoter are identified and the 5'-untranslated region (5'-UTR) is found essential for the high-level promoter activity in germinated transgenic rice embryos. Many metallothionein (MT) genes are highly expressed in plant tissues. A rice subfamily p2 (type 2) MT gene, OsMT2b, has been shown previously to exhibit the most abundant gene expression in young rice seedling. In the present study, transient expression assays and a transgenic approach were employed to characterize the expression of the OsMT2b gene in rice. We found that the OsMT2b gene is strongly and differentially expressed in germinated rice embryos during seed germination and seedling development. Histochemical staining analysis of transgenic rice carrying OsMT2b::GUS chimeric gene showed that high-level GUS activity was detected in germinated embryos and at the meristematic part of other tissues during germination. Deletion analysis of the OsMT2b promoter revealed that the 5'-flanking region of the OsMT2b between nucleotides -351 and -121 relative to the transcriptional initiation site is important for promoter activity in rice embryos, and this region contains the consensus sequences of G box and TA box. Our study demonstrates that the 5'-untranslated region (5'-UTR) of OsMT2b gene is not only necessary for the OsMT2b promoter activity, but also sufficient to augment the activity of a minimal promoter in both transformed cell cultures and germinated transgenic embryos in rice. We also found that addition of the maize Ubi intron 1 significantly enhanced the OsMT2b promoter activity in rice embryos. Our studies reveal that OsMT2b351-ubi(In) promoter can be applied in plant transformation and represents potential for driving high-level production of foreign proteins in transgenic rice.
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Affiliation(s)
- Chung-Shen Wu
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 60004, Taiwan, ROC
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18
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Loizeau K, Qu Y, Depp S, Fiechter V, Ruwe H, Lefebvre-Legendre L, Schmitz-Linneweber C, Goldschmidt-Clermont M. Small RNAs reveal two target sites of the RNA-maturation factor Mbb1 in the chloroplast of Chlamydomonas. Nucleic Acids Res 2013; 42:3286-97. [PMID: 24335082 PMCID: PMC3950674 DOI: 10.1093/nar/gkt1272] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Many chloroplast transcripts are protected against exonucleolytic degradation by RNA-binding proteins. Such interactions can lead to the accumulation of short RNAs (sRNAs) that represent footprints of the protein partner. By mining existing data sets of Chlamydomonas reinhardtii small RNAs, we identify chloroplast sRNAs. Two of these correspond to the 5′-ends of the mature psbB and psbH messenger RNAs (mRNAs), which are both stabilized by the nucleus-encoded protein Mbb1, a member of the tetratricopeptide repeat family. Accordingly, we find that the two sRNAs are absent from the mbb1 mutant. Using chloroplast transformation and site-directed mutagenesis to survey the psbB 5′ UTR, we identify a cis-acting element that is essential for mRNA accumulation. This sequence is also found in the 5′ UTR of psbH, where it plays a role in RNA processing. The two sRNAs are centered on these cis-acting elements. Furthermore, RNA binding assays in vitro show that Mbb1 associates with the two elements specifically. Taken together, our data identify a conserved cis-acting element at the extremity of the psbH and psbB 5′ UTRs that plays a role in the processing and stability of the respective mRNAs through interactions with the tetratricopeptide repeat protein Mbb1 and leads to the accumulation of protected sRNAs.
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Affiliation(s)
- Karen Loizeau
- Department of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva University of Geneva, CH-1211 Geneva 4, Switzerland and Institute of Biology, Molecular Genetics, Humboldt University of Berlin, D-10115 Berlin, Germany
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19
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Bohne AV, Schwarz C, Schottkowski M, Lidschreiber M, Piotrowski M, Zerges W, Nickelsen J. Reciprocal regulation of protein synthesis and carbon metabolism for thylakoid membrane biogenesis. PLoS Biol 2013; 11:e1001482. [PMID: 23424285 PMCID: PMC3570535 DOI: 10.1371/journal.pbio.1001482] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/04/2013] [Indexed: 11/19/2022] Open
Abstract
A subunit of the chloroplast pyruvate dehydrogenase complex, which serves as a metabolic enzyme, also has a dual function as an RNA-binding protein and influences mRNA translation. Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities. This control can be exerted by metabolites acting as regulatory signals and/or a class of metabolic enzymes with dual functions as regulators of gene expression. However, little is known about how metabolic signals affect the balance between enzymatic and regulatory roles of these dual functional proteins. We previously described the RNA binding activity of a 63 kDa chloroplast protein from Chlamydomonas reinhardtii, which has been implicated in expression of the psbA mRNA, encoding the D1 protein of photosystem II. Here, we identify this factor as dihydrolipoamide acetyltransferase (DLA2), a subunit of the chloroplast pyruvate dehydrogenase complex (cpPDC), which is known to provide acetyl-CoA for fatty acid synthesis. Analyses of RNAi lines revealed that DLA2 is involved in the synthesis of both D1 and acetyl-CoA. Gel filtration analyses demonstrated an RNP complex containing DLA2 and the chloroplast psbA mRNA specifically in cells metabolizing acetate. An intrinsic RNA binding activity of DLA2 was confirmed by in vitro RNA binding assays. Results of fluorescence microscopy and subcellular fractionation experiments support a role of DLA2 in acetate-dependent localization of the psbA mRNA to a translation zone within the chloroplast. Reciprocally, the activity of the cpPDC was specifically affected by binding of psbA mRNA. Beyond that, in silico analysis and in vitro RNA binding studies using recombinant proteins support the possibility that RNA binding is an ancient feature of dihydrolipoamide acetyltransferases. Our results suggest a regulatory function of DLA2 in response to growth on reduced carbon energy sources. This raises the intriguing possibility that this regulation functions to coordinate the synthesis of lipids and proteins for the biogenesis of photosynthetic membranes. Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities. This control can be exerted by metabolites acting as regulatory signals on a class of metabolic enzymes with dual functions as regulators of gene expression. However, little is known about how metabolic signals affect the balance between enzymatic and regulatory roles of these proteins. Here, we report an example of a protein with dual functions in gene expression and carbon metabolism. The chloroplast pyruvate dehydrogenase complex is well-known to produce activated di-carbon precursors for fatty acid, which is required for lipid synthesis. Our results show that a subunit of this enzyme forms ribonucleoprotein particles and influences chloroplast mRNA translation. Conversely, RNA binding affects pyruvate dehydrogenase (metabolic) activity. These findings offer insight into how intracellular metabolic signaling and gene expression are reciprocally regulated during membrane biogenesis. In addition, our results suggest that these dual roles of the protein might exist in evolutionary distant organisms ranging from cyanobacteria to humans.
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Affiliation(s)
- Alexandra-Viola Bohne
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Christian Schwarz
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Marco Schottkowski
- Biology Department and Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Michael Lidschreiber
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Markus Piotrowski
- Department of Plant Physiology, Ruhr-University Bochum, Bochum, Germany
| | - William Zerges
- Biology Department and Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Jörg Nickelsen
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
- * E-mail:
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20
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Lyska D, Meierhoff K, Westhoff P. How to build functional thylakoid membranes: from plastid transcription to protein complex assembly. PLANTA 2013; 237:413-28. [PMID: 22976450 PMCID: PMC3555230 DOI: 10.1007/s00425-012-1752-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/10/2012] [Indexed: 05/06/2023]
Abstract
Chloroplasts are the endosymbiotic descendants of cyanobacterium-like prokaryotes. Present genomes of plant and green algae chloroplasts (plastomes) contain ~100 genes mainly encoding for their transcription-/translation-machinery, subunits of the thylakoid membrane complexes (photosystems II and I, cytochrome b (6) f, ATP synthase), and the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Nevertheless, proteomic studies have identified several thousand proteins in chloroplasts indicating that the majority of the plastid proteome is not encoded by the plastome. Indeed, plastid and host cell genomes have been massively rearranged in the course of their co-evolution, mainly through gene loss, horizontal gene transfer from the cyanobacterium/chloroplast to the nucleus of the host cell, and the emergence of new nuclear genes. Besides structural components of thylakoid membrane complexes and other (enzymatic) complexes, the nucleus provides essential factors that are involved in a variety of processes inside the chloroplast, like gene expression (transcription, RNA-maturation and translation), complex assembly, and protein import. Here, we provide an overview on regulatory factors that have been described and characterized in the past years, putting emphasis on mechanisms regulating the expression and assembly of the photosynthetic thylakoid membrane complexes.
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Affiliation(s)
- Dagmar Lyska
- Entwicklungs- und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany.
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21
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Specht EA, Mayfield SP. Synthetic oligonucleotide libraries reveal novel regulatory elements in Chlamydomonas chloroplast mRNAs. ACS Synth Biol 2013; 2:34-46. [PMID: 23656324 DOI: 10.1021/sb300069k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene expression in chloroplasts is highly regulated during translation by sequence and secondary-structure elements in the 5' untranslated region (UTR) of mRNAs. These chloroplast mRNA 5' UTRs interact with nuclear-encoded factors to regulate mRNA processing, stability, and translation initiation. Although several UTR elements in chloroplast mRNAs have been identified by site-directed mutagenesis, the complete set of elements required for expression of plastid mRNAs remains undefined. Here we present a synthetic biology approach using an arrayed oligonucleotide library to examine in vivo hundreds of designed variants of endogenous UTRs from Chlamydomonas reinhardtii and quantitatively identify essential regions through next-generation sequencing of thousands of mutants. We validate this strategy by characterizing the relatively well-studied 5' UTR of the psbD mRNA encoding the D2 protein in photosystem II and find that our analysis generally agrees with previous work identifying regions of importance but significantly expands and clarifies the boundaries of these regulatory regions. We then use this strategy to characterize the previously unstudied psaA 5' UTR and obtain a detailed map of regions essential for both positive and negative regulation. This analysis can be performed in a high-throughput manner relative to previous site-directed mutagenesis methods, enabling compilation of a large unbiased data set of regulatory elements of chloroplast gene expression. Finally, we create a novel synthetic UTR based on aggregate sequence analysis from the libraries and demonstrate that it significantly increases accumulation of an exogenous protein, attesting to the utility of this strategy for enhancing protein production in algal chloroplasts.
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Affiliation(s)
- Elizabeth A. Specht
- The San Diego Center for Algae Biotechnology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Stephen P. Mayfield
- The San Diego Center for Algae Biotechnology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
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22
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Meierhoff K, Westhoff P. The Biogenesis of the Thylakoid Membrane: Photosystem II, a Case Study. PLASTID DEVELOPMENT IN LEAVES DURING GROWTH AND SENESCENCE 2013. [DOI: 10.1007/978-94-007-5724-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Schwarz C, Bohne AV, Wang F, Cejudo FJ, Nickelsen J. An intermolecular disulfide-based light switch for chloroplast psbD gene expression in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:378-89. [PMID: 22725132 DOI: 10.1111/j.1365-313x.2012.05083.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Expression of the chloroplast psbD gene encoding the D2 protein of the photosystem II reaction center is regulated by light. In the green alga Chlamydomonas reinhardtii, D2 synthesis requires a high-molecular-weight complex containing the RNA stabilization factor Nac2 and the translational activator RBP40. Based on size exclusion chromatography analyses, we provide evidence that light control of D2 synthesis depends on dynamic formation of the Nac2/RBP40 complex. Furthermore, 2D redox SDS-PAGE assays suggest an intermolecular disulfide bridge between Nac2 and Cys11 of RBP40 as the putative molecular basis for attachment of RBP40 to the complex in light-grown cells. This covalent link is reduced in the dark, most likely via NADPH-dependent thioredoxin reductase C, supporting the idea of a direct relationship between chloroplast gene expression and chloroplast carbon metabolism during dark adaption of algal cells.
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Affiliation(s)
- Christian Schwarz
- Molekulare Pflanzenwissenschaften, Biozentrum Ludwig Maximilian University Munich, Grosshaderner Strasse, Planegg-Martinsried, Germany
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24
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Suzuki Y, Makino A. Availability of Rubisco small subunit up-regulates the transcript levels of large subunit for stoichiometric assembly of its holoenzyme in rice. PLANT PHYSIOLOGY 2012; 160:533-40. [PMID: 22811433 PMCID: PMC3440226 DOI: 10.1104/pp.112.201459] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/15/2012] [Indexed: 05/20/2023]
Abstract
Rubisco is composed of eight small subunits coded for by the nuclear RBCS multigene family and eight large subunits coded for by the rbcL gene in the plastome. For synthesis of the Rubisco holoenzyme, both genes need to be expressed coordinately. To investigate this molecular mechanism, the protein synthesis of two subunits of Rubisco was characterized in transgenic rice (Oryza sativa) plants with overexpression or antisense suppression of the RBCS gene. Total RBCS and rbcL messenger RNA (mRNA) levels and RBCS and RbcL synthesis simultaneously increased in RBCS-sense plants, although the increase in total RBCS mRNA level was greater. In RBCS-antisense plants, the levels of these mRNAs and the synthesis of the corresponding proteins declined to a similar extent. The amount of RBCS synthesized was tightly correlated with rbcL mRNA level among genotypes but not associated with changes in mRNA levels of other major chloroplast-encoded photosynthetic genes. The level of rbcL mRNA, in turn, was tightly correlated with the amount of RbcL synthesized, the molar ratio of RBCS synthesis to RbcL synthesis being identical irrespective of genotype. Polysome loading of rbcL mRNA was not changed. These results demonstrate that the availability of RBCS protein up-regulates the gene expression of rbcL primarily at the transcript level in a quantitative manner for stoichiometric assembly of Rubisco holoenzyme.
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MESH Headings
- Cell Culture Techniques/methods
- Chloroplasts/enzymology
- Chloroplasts/genetics
- Enzyme Activation
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes, Plant
- Holoenzymes/genetics
- Holoenzymes/metabolism
- Oryza/enzymology
- Oryza/genetics
- Photosynthesis
- Plant Leaves/enzymology
- Plant Leaves/genetics
- Plant Proteins/genetics
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Polyribosomes/metabolism
- Protein Biosynthesis
- Protein Subunits/genetics
- Protein Subunits/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/analysis
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Ribulose-Bisphosphate Carboxylase/genetics
- Ribulose-Bisphosphate Carboxylase/metabolism
- Transcription, Genetic
- Up-Regulation
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Affiliation(s)
- Yuji Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.
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25
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Sharwood RE, Halpert M, Luro S, Schuster G, Stern DB. Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA. RNA (NEW YORK, N.Y.) 2011; 17:2165-76. [PMID: 22033332 PMCID: PMC3222129 DOI: 10.1261/rna.028043.111] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 09/13/2011] [Indexed: 05/20/2023]
Abstract
Ribonuclease J is an essential enzyme, and the Bacillus subtilis ortholog possesses both endoribonuclease and 5' → 3' exoribonuclease activities. Chloroplasts also contain RNase J, which has been postulated to participate, as both an exo- and endonuclease, in the maturation of polycistronic mRNAs. Here we have examined recombinant Arabidopsis RNase J and found both 5' → 3' exoribonuclease and endonucleolytic activities. Virus-induced gene silencing was used to reduce RNase J expression in Arabidopsis and Nicotiana benthamiana, leading to chlorosis but surprisingly few disruptions in the cleavage of polycistronic rRNA and mRNA precursors. In contrast, antisense RNAs accumulated massively, suggesting that the failure of chloroplast RNA polymerase to terminate effectively leads to extensive symmetric transcription products that are normally eliminated by RNase J. Mung bean nuclease digestion and polysome analysis revealed that this antisense RNA forms duplexes with sense strand transcripts and prevents their translation. We conclude that a major role of chloroplast RNase J is RNA surveillance to prevent overaccumulation of antisense RNA, which would otherwise exert deleterious effects on chloroplast gene expression.
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Affiliation(s)
- Robert E. Sharwood
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Michal Halpert
- Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Scott Luro
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Gadi Schuster
- Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - David B. Stern
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
- Corresponding author.E-mail .
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26
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Light-dependent attenuation of phycoerythrin gene expression reveals convergent evolution of green light sensing in cyanobacteria. Proc Natl Acad Sci U S A 2011; 108:18542-7. [PMID: 22042852 DOI: 10.1073/pnas.1107427108] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The colorful process of chromatic acclimation allows many cyanobacteria to change their pigmentation in response to ambient light color changes. In red light, cells produce red-absorbing phycocyanin (PC), whereas in green light, green-absorbing phycoerythrin (PE) is made. Controlling these pigment levels increases fitness by optimizing photosynthetic activity in different light color environments. The light color sensory system controlling PC expression is well understood, but PE regulation has not been resolved. In the filamentous cyanobacterium Fremyella diplosiphon UTEX 481, two systems control PE synthesis in response to light color. The first is the Rca pathway, a two-component system controlled by a phytochrome-class photoreceptor, which transcriptionally represses cpeCDESTR (cpeC) expression during growth in red light. The second is the Cgi pathway, which has not been characterized. We determined that the Cgi system also regulates PE synthesis by repressing cpeC expression in red light, but acts posttranscriptionally, requiring the region upstream of the CpeC translation start codon. cpeC RNA stability was comparable in F. diplosiphon cells grown in red and green light, and a short transcript that included the 5' region of cpeC was detected, suggesting that the Cgi system operates by transcription attenuation. The roles of four predicted stem-loop structures within the 5' region of cpeC RNA were analyzed. The putative stem-loop 31 nucleotides upstream of the translation start site was required for Cgi system function. Thus, the Cgi system appears to be a unique type of signal transduction pathway in which the attenuation of cpeC transcription is regulated by light color.
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27
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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.
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Affiliation(s)
- Jessica Jacobs
- Department for General and Molecular Biology, Ruhr-University Bochum, Universitätsstraße 150, Bochum, Germany.
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Boulouis A, Raynaud C, Bujaldon S, Aznar A, Wollman FA, Choquet Y. The nucleus-encoded trans-acting factor MCA1 plays a critical role in the regulation of cytochrome f synthesis in Chlamydomonas chloroplasts. THE PLANT CELL 2011; 23:333-49. [PMID: 21216944 PMCID: PMC3051260 DOI: 10.1105/tpc.110.078170] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/26/2010] [Accepted: 12/07/2010] [Indexed: 05/18/2023]
Abstract
Organelle gene expression is characterized by nucleus-encoded trans-acting factors that control posttranscriptional steps in a gene-specific manner. As a typical example, in Chlamydomonas reinhardtii, expression of the chloroplast petA gene encoding cytochrome f, a major subunit of the cytochrome b(6)f complex, depends on MCA1 and TCA1, required for the accumulation and translation of the petA mRNA. Here, we show that these two proteins associate in high molecular mass complexes that also contain the petA mRNA. We demonstrate that MCA1 is degraded upon interaction with unassembled cytochrome f that transiently accumulates during the biogenesis of the cytochrome b(6)f complex. Strikingly, this interaction relies on the very same residues that form the repressor motif involved in the Control by Epistasy of cytochrome f Synthesis (CES), a negative feedback mechanism that downregulates cytochrome f synthesis when its assembly within the cytochrome b(6)f complex is compromised. Based on these new findings, we present a revised picture for the CES regulation of petA mRNA translation that involves proteolysis of the translation enhancer MCA1, triggered by its interaction with unassembled cytochrome f.
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Affiliation(s)
| | | | | | | | | | - Yves Choquet
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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Chloroplast DnaJ-like proteins 3 and 4 (CDJ3/4) from Chlamydomonas reinhardtii contain redox-active Fe–S clusters and interact with stromal HSP70B. Biochem J 2010; 427:205-15. [DOI: 10.1042/bj20091412] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the present study we report on the identification and characterization of three novel chloroplast-targeted DnaJ-like proteins CDJ3–5, which in addition to their J-domains contain bacterial-type ferredoxin domains. In sequence databases we could identify homologues of CDJ3–5 in green algae, moss and higher plants, but not in cyanobacteria. Phylogenetic analyses allowed us to distinguish two clades containing CDJ3/4 and CDJ5 that must have diverged early in the ancestor of the ‘green lineage’ and have further diversified later on. Molecular and biochemical analysis of CDJ3 and CDJ4 from Chlamydomonas reinhardtii revealed that both proteins are weakly expressed and appear to be localized to the stroma and to thylakoid membranes respectively. The low transcript levels of the CDJ3 and CDJ4 genes declined even further in the initial phase of heat shock, but CDJ3 transcript levels strongly increased after a dark-to-light shift. Accordingly, the Arabidopsis orthologue of CDJ5 was also found to be light-inducible and to be under strong circadian control. CDJ3 and CDJ4 proteins could both be expressed in Escherichia coli and had redox-active Fe–S clusters. In vitro cross-linking studies demonstrated that CDJ3 and CDJ4 interact with chloroplast ATP-bound HSP70B (heat-shock protein 70B), presumably as dimers, and immunoprecipitation studies showed that CDJ3/4 were also in a complex with HSP70B in Chlamydomonas cell extracts. Finally, CDJ3 was found in complexes with apparent molecular masses of approx. 550–2800 kDa, which appeared to contain RNA. We speculate that the CDJ3–5 proteins might represent redox switches that act by recruiting HSP70B for the reorganization of regulatory protein complexes.
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Alizadeh D, Cohen A. Red light and calmodulin regulate the expression of the psbA binding protein genes in Chlamydomonas reinhardtii. PLANT & CELL PHYSIOLOGY 2010; 51:312-22. [PMID: 20061301 PMCID: PMC2817094 DOI: 10.1093/pcp/pcq002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 12/25/2009] [Indexed: 05/23/2023]
Abstract
In the unicellular green alga Chlamydomonas reinhardtii, translation of the chloroplast-encoded psbA mRNA is regulated by the light-dependent binding of a nuclear-encoded protein complex (RB38, RB47, RB55 and RB60) to the 5'-untranslated region of the RNA. Despite the absence of any report identifying a red light photoreceptor within this alga, we show that the expression of the rb38, rb47 and rb60 genes, as well as the nuclear-encoded psbO gene that directs the synthesis of OEE1 (oxygen evolving enhancer 1), is differentially regulated by red light. Further elucidation of the signal transduction pathway shows that calmodulin is an important messenger in the signaling cascade that leads to the expression of rb38, rb60 and psbO, and that a chloroplast signal affects rb47 at the translational level. While there may be several factors involved in the cascade of events from the perception of red light to the expression of the rb and psbO genes, our data suggest the involvement of a red light photoreceptor. Future studies will elucidate this receptor and the additional components of this red light signaling expression pathway in C. reinhardtii.
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Affiliation(s)
- Darya Alizadeh
- Department of Biological Science, California State University, Fullerton, PO Box 6850, Fullerton, CA 92834-6850, USA
- City of Hope, Division of Neurosurgery, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Amybeth Cohen
- Department of Biological Science, California State University, Fullerton, PO Box 6850, Fullerton, CA 92834-6850, USA
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31
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Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts. EMBO J 2009; 28:2042-52. [PMID: 19424177 DOI: 10.1038/emboj.2009.121] [Citation(s) in RCA: 272] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 03/26/2009] [Indexed: 12/30/2022] Open
Abstract
Chloroplast mRNA populations are characterized by overlapping transcripts derived by processing from polycistronic precursors. The mechanisms and functional significance of these processing events are poorly understood. We describe a pentatricopeptide repeat (PPR) protein, PPR10, whose binding defines mRNA segments derived from two transcription units in maize chloroplasts. PPR10 interacts in vivo and in vitro with two intergenic RNA regions of similar sequence. The processed 5' and 3' RNA termini in these regions overlap by approximately 25 nucleotides. The PPR10-binding sites map precisely to these overlapping sequences, and PPR10 is required specifically for the accumulation of RNAs with these termini. These findings show that PPR10 serves as a barrier to RNA decay from either the 5' or 3' direction and that a bound protein provides an alternative to an RNA hairpin as a barrier to 3' exonucleases. The results imply that protein 'caps' at both 5' and 3' ends can define the termini of chloroplast mRNA segments. These results, together with recent insights into bacterial RNA decay, suggest a unifying model for the biogenesis of chloroplast transcript populations and for the determinants of chloroplast mRNA stability.
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Loiselay C, Gumpel NJ, Girard-Bascou J, Watson AT, Purton S, Wollman FA, Choquet Y. Molecular identification and function of cis- and trans-acting determinants for petA transcript stability in Chlamydomonas reinhardtii chloroplasts. Mol Cell Biol 2008; 28:5529-42. [PMID: 18573878 PMCID: PMC2519735 DOI: 10.1128/mcb.02056-07] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 02/25/2008] [Accepted: 06/13/2008] [Indexed: 11/20/2022] Open
Abstract
In organelles, the posttranscriptional steps of gene expression are tightly controlled by nucleus-encoded factors, most often acting in a gene-specific manner. Despite the molecular identification of a growing number of factors, their mode of action remains largely unknown. In the green alga Chlamydomonas reinhardtii, expression of the chloroplast petA gene, which codes for cytochrome f, depends on two specific nucleus-encoded factors. MCA1 controls the accumulation of the transcript, while TCA1 is required for its translation. We report here the cloning of MCA1, the first pentatricopeptide repeat protein functionally identified in this organism. By chloroplast transformation with modified petA genes, we investigated the function of MCA1 in vivo. We demonstrate that MCA1 acts on the very first 21 nucleotides of the petA 5' untranslated region to protect the whole transcript from 5'-->3' degradation but does not process the 5' end of the petA mRNA. MCA1 and TCA1 recognize adjacent targets and probably interact together for efficient expression of petA mRNA. MCA1, although not strictly required for translation, shows features of a translational enhancer, presumably by assisting the binding of TCA1 to its own target. Conversely, TCA1 participates to the full stabilization of the transcript through its interaction with MCA1.
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Affiliation(s)
- Christelle Loiselay
- UMR 7141 CNRS/UPMC, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, F-75005 Paris, France
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Zhou F, Karcher D, Bock R. Identification of a plastid intercistronic expression element (IEE) facilitating the expression of stable translatable monocistronic mRNAs from operons. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:961-72. [PMID: 17825052 PMCID: PMC2230500 DOI: 10.1111/j.1365-313x.2007.03261.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 07/12/2007] [Indexed: 05/17/2023]
Abstract
Most plastid genes are part of operons and expressed as polycistronic mRNAs. Many primary polycistronic transcripts undergo post-transcriptional processing in monocistronic or oligocistronic units. At least some polycistronic transcripts are not translatable, and endonucleolytic processing may therefore be a prerequisite for translation to occur. As the requirements for intercistronic mRNA processing into stable monocistronic transcript are not well understood, we have sought to define minimum sequence elements that trigger processing and thus are capable of generating stable translatable monocistronic mRNAs. We describe here the in vivo identification of a small intercistronic expression element that mediates intercistronic cleavage into stable monocistronic transcripts. Separation of foreign genes by this element facilitates transgene stacking in operons, and thus will help to expand the range of applications of transplastomic technology.
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Affiliation(s)
- Fei Zhou
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP)Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP)Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP)Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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Schwarz C, Elles I, Kortmann J, Piotrowski M, Nickelsen J. Synthesis of the D2 protein of photosystem II in Chlamydomonas is controlled by a high molecular mass complex containing the RNA stabilization factor Nac2 and the translational activator RBP40. THE PLANT CELL 2007; 19:3627-39. [PMID: 18055611 PMCID: PMC2174876 DOI: 10.1105/tpc.107.051722] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 10/31/2007] [Accepted: 11/05/2007] [Indexed: 05/19/2023]
Abstract
Gene expression in chloroplasts is regulated mainly at the posttranscriptional level. In the green alga Chlamydomonas reinhardtii, synthesis of the D2 protein (PsbD), which is the rate-determining subunit for the assembly of photosystem II, depends on the RNA stability factor Nac2. In addition, the RNA binding protein RBP40 has been implicated in translational control via a U-rich element in the 5' untranslated region (5'UTR) of the psbD mRNA. Here, we report the identification of the RBP40 gene based on mass spectrometric analysis of its purified product. Unexpectedly, this was found to be identical to the previously described RNA binding protein RB38, which had been suggested to be involved in the regulation of D1 protein synthesis. However, we show that RBP40 binds to the psbD 5'UTR in a Nac2-dependent fashion both in vitro and in vivo. Molecular characterization of RBP40 RNA interference lines confirmed that RBP40 specifically affects the initiation of D2 synthesis. Native polyacrylamide gel electrophoresis, coimmunoprecipitation, and sedimentation analyses revealed that Nac2 and RBP40 form parts of a complex of 550 kD that is displaced from the psbD mRNA prior to polysome assembly. Together, these data indicate that the processes of 5'UTR-mediated RNA stabilization and translation initiation are tightly coupled in Chlamydomonas.
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Affiliation(s)
- Christian Schwarz
- Molekulare Pflanzenwissenschaften, Ludwig-Maximilians Universität München, 80638 Munich, Germany
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35
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Marín-Navarro J, Manuell AL, Wu J, P Mayfield S. Chloroplast translation regulation. PHOTOSYNTHESIS RESEARCH 2007; 94:359-74. [PMID: 17661159 DOI: 10.1007/s11120-007-9183-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 04/19/2007] [Indexed: 05/16/2023]
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 of bacteria, but has adopted novel mechanisms in order to execute the specific roles that this organelle performs within a eukaryotic cell. Accordingly, plastid ribosomes contain a number of chloroplast-unique proteins and domains that may function in translational regulation. Chloroplast translation regulation involves cis-acting RNA elements (located in the mRNA 5' UTR) as well as a set of corresponding trans-acting protein factors. While regulation of chloroplast translation is primarily controlled at the initiation steps through these RNA-protein interactions, elongation steps are also targets for modulating chloroplast gene expression. Translation of chloroplast mRNAs is regulated in response to light, and the molecular mechanisms underlying this response involve changes in the redox state of key elements related to the photosynthetic electron chain, fluctuations of the ADP/ATP ratio and the generation of a proton gradient. Photosynthetic complexes also experience assembly-related autoinhibition of translation to coordinate the expression of different subunits of the same complex. Finally, the localization of all these molecular events among the different chloroplast subcompartments appear to be a crucial component of the regulatory mechanisms of chloroplast gene expression.
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Affiliation(s)
- Julia Marín-Navarro
- Department of Cell Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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36
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Mathur S, Dasgupta I. Downstream promoter sequence of an Indian isolate of Rice tungro bacilliform virus alters tissue-specific expression in host rice and acts differentially in heterologous system. PLANT MOLECULAR BIOLOGY 2007; 65:259-75. [PMID: 17721744 DOI: 10.1007/s11103-007-9214-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 07/20/2007] [Indexed: 05/16/2023]
Abstract
An Indian isolate of Rice tungro bacilliform virus from West Bengal (RTBV-WB) showed significant nucleotide differences in its putative promoter region when compared with a previously characterized isolate from Philippines. The transcription start site of RTBV-WB was mapped followed by assessing the activity and tissue-specificity of the full-length (FL) promoter (-231 to +645) and several of its upstream and downstream deletions by studying the expression of beta-Glucuronidase (GUS) reporter gene in transgenic rice (Oryza sativa L. subsp. indica) plants at various stages of development. In addition to the expected vascular-specific expression pattern, studied by histochemical staining, GUS enzymatic assay and northern and RT-PCR analysis, two novel patterns were revealed in some of the downstream deleted versions; a non-expressing type, representing no expression at any stage in any tissue and constitutive type, representing constitutive expression at all stages in most tissues. This indicated the presence of previously unreported positive and negative cis-regulatory elements in the downstream region. The negative element and a putative enhancer region in the upstream region specifically bound to rice nuclear proteins in vitro. The FL and its deletion derivatives were also active in heterologous systems like tobacco (Nicotiana tabacum) and wheat (Triticum durum). Expression patterns in tobacco were different from those observed in rice suggesting the importance of upstream elements in those systems and host-specific regulation of the promoter in diverse organisms. Thus, the RTBV-WB FL promoter and its derivatives contain an array of cis-elements, which control constitutive or tissue- and development-specific gene expression in a combinatorial fashion.
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Affiliation(s)
- Saloni Mathur
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
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Schult K, Meierhoff K, Paradies S, Töller T, Wolff P, Westhoff P. The nuclear-encoded factor HCF173 is involved in the initiation of translation of the psbA mRNA in Arabidopsis thaliana. THE PLANT CELL 2007; 19:1329-46. [PMID: 17435084 PMCID: PMC1913763 DOI: 10.1105/tpc.106.042895] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2006] [Revised: 03/08/2007] [Accepted: 03/22/2007] [Indexed: 05/14/2023]
Abstract
To gain insight into the biogenesis of photosystem II (PSII) and to identify auxiliary factors required for this process, we characterized the mutant hcf173 of Arabidopsis thaliana. The mutant shows a high chlorophyll fluorescence phenotype (hcf) and is severely affected in the accumulation of PSII subunits. In vivo labeling experiments revealed a drastically decreased synthesis of the reaction center protein D1. Polysome association experiments suggest that this is primarily caused by reduced translation initiation of the corresponding psbA mRNA. Comparison of mRNA steady state levels indicated that the psbA mRNA is significantly reduced in hcf173. Furthermore, the determination of the psbA mRNA half-life revealed an impaired RNA stability. The HCF173 gene was identified by map-based cloning, and its identity was confirmed by complementation of the hcf phenotype. HCF173 encodes a protein with weak similarities to the superfamily of the short-chain dehydrogenases/reductases. The protein HCF173 is localized in the chloroplast, where it is mainly associated with the membrane system and is part of a higher molecular weight complex. Affinity chromatography of an HCF173 fusion protein uncovered the psbA mRNA as a component of this complex.
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Affiliation(s)
- Kerstin Schult
- Institut für Entwicklungs und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
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Zicker AA, Kadakia CS, Herrin DL. Distinct roles for the 5' and 3' untranslated regions in the degradation and accumulation of chloroplast tufA mRNA: identification of an early intermediate in the in vivo degradation pathway. PLANT MOLECULAR BIOLOGY 2007; 63:689-702. [PMID: 17180456 DOI: 10.1007/s11103-006-9117-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 11/13/2006] [Indexed: 05/13/2023]
Abstract
Elongation factor Tu in Chlamydomonas reinhardtii is a chloroplast-encoded gene (tufA) whose 1.7-kb mRNA has a relatively short half-life. In the presence of chloramphenicol (CAP), which freezes translating chloroplast ribosomes, a 1.5-kb tufA RNA becomes prominent. Rifampicin-chase analysis indicates that the 1.5-kb RNA is a degradation intermediate, and mapping studies show that it is missing 176-180 nucleotides from the 5' end of tufA. The 5' terminus of the intermediate maps to a section of the untranslated region (UTR) predicted to be highly structured and to encode a small ORF. The intermediate could be detected in older cultures in the absence of CAP, indicating that it is not an artifact of drug treatment. Also, it did not overaccumulate in the chloroplast ribosome-deficient mutant, ac20 cr1, indicating its stabilization is specific to elongation-arrested ribosomes. To determine if the 5' UTR of tufA is destabilizing, the corresponding region of the atpA-aadA-rbcL gene was replaced with the tufA sequence, and introduced into the chloroplast genome; the 3' UTR was also substituted for comparison. Analysis of these transformants showed that the transcripts containing the tufA 3'-UTR accumulate to significantly lower levels. Data from constructs based on the vital reporter, Renilla luciferase, confirmed the importance of the tufA 3'-UTR in determining RNA levels, and suggested that the 5' UTR of tufA affects translation efficiency. These data indicate that the in vivo degradation of tufA mRNA begins in the 5' UTR, and is promoted by translation. The data also suggest, however, that the level of the mature RNA is determined more by the 3' UTR than the 5' UTR.
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Affiliation(s)
- Alicia A Zicker
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, School of Biological Sciences, University of Texas at Austin, 1 University Station A6700, Austin, TX 78712, USA
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Rochaix JD. The Role of Nucleus- and Chloroplast-Encoded Factors in the Synthesis of the Photosynthetic Apparatus. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/978-1-4020-4061-0_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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40
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Processing, degradation, and polyadenylation of chloroplast transcripts. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0235] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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41
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Translation and translational regulation in chloroplasts. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0234] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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42
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Xiao H, Zhang F, Zheng Y. The 5' stem-loop and its role in mRNA stability in maize S cytoplasmic male sterility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 47:864-72. [PMID: 16961731 DOI: 10.1111/j.1365-313x.2006.02838.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The co-transcribed orf355-orf77 region of the mitochondrial genome is associated with S cytoplasmic male sterility (CMS-S) in maize; the amounts of its 1.6- and 2.8-kb transcripts were previously shown to be greatly reduced in fertility-restored microspores relative to the amounts in sterile plants. To investigate the mechanism underlying this reduction, detailed analysis of the 5' and 3' termini of these transcripts was conducted. Using 3' RACE analysis, the polyadenylation sites of the 1.6- and 2.8-kb transcripts were mapped adjacent to a 3' stem-loop, which may play an important role in stabilizing their 3' ends. No difference was found between the polyadenylation sites in sterile and fertility-restored microspores that could account for the differences in orf355-orf77 transcript levels. The 5' terminus of the 1.6-kb transcript was further studied by primer extension; the result revealed that there was a deletion of nine nucleotides only in fertility-restored microspores, and that this deletion eliminated a 5' stem-loop sequence. We propose that the elimination of the 5' stem-loop in the fertility-restored microspores could be the cause of the degradation of the 1.6-kb transcript. Because the 2.8-kb transcript can be cleaved to generate the 1.6-kb transcript, the amount of the 2.8-kb transcript is also reduced in fertility-restored microspores.
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Affiliation(s)
- Hailin Xiao
- State Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Rymarquis LA, Higgs DC, Stern DB. Nuclear suppressors define three factors that participate in both 5' and 3' end processing of mRNAs in Chlamydomonas chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 46:448-61. [PMID: 16623905 DOI: 10.1111/j.1365-313x.2006.02711.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Chloroplast RNA processing and degradation are orchestrated by nucleus-encoded factors. Although several transcript-specific factors have been identified, those involved in global RNA metabolism have mostly remained elusive. Using Chlamydomonas reinhardtii, we have identified three pleiotropic nuclear mutations, mcd3, mcd4 and mcd5, which cause quantitative variation between polycistronic transcripts and accumulation of transcripts with novel 3' ends. The mcd3, mcd4 and mcd5 mutants were initially isolated as photoautotrophic suppressors of the petD 5' mutants LS2 and LS6, which harbour four nucleotide linker-scanning mutations near the 5' end of the mature transcript. The LS mutants accumulate 1-3% of the wild-type (WT) petD mRNA level and no cytochrome b6/f complex subunit IV, which is the petD gene product and required for photosynthesis. Each suppressor restores approximately 15% of the WT petD mRNA and subunit IV levels. Genetic analysis showed mcd4 to be recessive, and suggested that MCD4 interacts with the petD mRNA stability factor MCD1. To assess the specificity of mcd3, mcd4 and mcd5, transcripts from 32 chloroplast genes were analysed by RNA filter hybridizations. mcd3 and mcd4 displayed aberrant transcript patterns for 17 genes, whereas only three were altered in mcd5. Since the mutations affect multiple RNAs in a variety of ways, our data suggest that MCD3, MCD4 and MCD5 may participate in a series of multiprotein complexes responsible for RNA maturation and degradation in Chlamydomonas chloroplasts.
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Kramzar LM, Mueller T, Erickson B, Higgs DC. Regulatory sequences of orthologous petD chloroplast mRNAs are highly specific among Chlamydomonas species. PLANT MOLECULAR BIOLOGY 2006; 60:405-22. [PMID: 16514563 DOI: 10.1007/s11103-005-4477-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2005] [Accepted: 10/24/2005] [Indexed: 05/06/2023]
Abstract
The 5' untranslated regions (UTR) of chloroplast mRNAs often contain regulatory sequences that control RNA stability and/or translation. The petD chloroplast mRNA in Chlamydomonas reinhardtii has three such essential regulatory elements in its 362-nt long 5' UTR. To further analyze these elements, we compared 5' UTR sequences from four Chlamydomonas species (C. reinhardtii, C. incerta, C. moewusii and C. eugametos) and five independent strains of C. reinhardtii. Overall, these petD 5' UTRs have relatively low sequence conservation across these species. In contrast, sequences of the three regulatory elements and their relative positions appear partially conserved. Functionality of the 5' UTRs was tested in C. reinhardtii chloroplasts using beta-glucuronidase reporter genes, and the nearly identical C. incerta petD functioned for mRNA stability and translation in C. reinhardtii chloroplasts while the more divergent C. eugametos petD did not. This identified what may be key features in these elements. We conclude that these petD regulatory elements, and possibly the corresponding trans-acting factors, function via mechanisms highly specific and surprisingly sensitive to minor sequence changes. This provides a new and broader perspective of these important regulatory sequences that affect photosynthesis in these algae.
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Affiliation(s)
- Lynn M Kramzar
- Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha, WI 53141, USA
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Klinkert B, Elles I, Nickelsen J. Translation of chloroplast psbD mRNA in Chlamydomonas is controlled by a secondary RNA structure blocking the AUG start codon. Nucleic Acids Res 2006; 34:386-94. [PMID: 16410618 PMCID: PMC1331992 DOI: 10.1093/nar/gkj433] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 12/21/2005] [Accepted: 12/21/2005] [Indexed: 11/28/2022] Open
Abstract
Translation initiation represents a key step during regulation of gene expression in chloroplasts. Here, we report on the identification and characterization of three suppressor point mutations which overcome a translational defect caused by the deletion of a U-rich element in the 5'-untranslated region (5'-UTR) of the psbD mRNA in the green alga Chlamydomonas reinhardtii. All three suppressors affect a secondary RNA structure encompassing the psbD AUG initiation codon within a double-stranded region as judged by the analysis of site-directed chloroplast mutants as well as in vitro RNA mapping experiments using RNase H. In conclusion, the data suggest that these new element serves as a negative regulator which mediates a rapid shut-down of D2 synthesis.
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Affiliation(s)
- Birgit Klinkert
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150D-44780 Bochum, Germany
| | - Ingolf Elles
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150D-44780 Bochum, Germany
| | - Jörg Nickelsen
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150D-44780 Bochum, Germany
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Klinkert B, Schwarz C, Pohlmann S, Pierre Y, Girard-Bascou J, Nickelsen J. Relationship between mRNA levels and protein accumulation in a chloroplast promoter-mutant of Chlamydomonas reinhardtii. Mol Genet Genomics 2005; 274:637-43. [PMID: 16244871 DOI: 10.1007/s00438-005-0056-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Accepted: 09/27/2005] [Indexed: 10/25/2022]
Abstract
The photosynthetic chloroplast mutant G64 of Chlamydomonas reinhardtii was shown to contain a single point mutation within the 5' region of the psbD gene encoding the D2 protein of the photosystem II reaction center. The mutation affects the sequence element TATAATAT which has previously been hypothesized to function as the psbD promoter. Run-on analysis confirmed that transcription of psbD in the mutant was reduced to approximately 10% of the wild-type level. However, psbD mRNA accumulated to approximately 35%, despite the prominent decrease in RNA synthesis. This suggests that RNA-stabilization effects can compensate to some extent for a reduction in transcriptional activity. Interestingly, a direct correlation between transcript levels and the accumulation of the psbD gene product, the D2-protein, was observed in G64. The data suggest that posttranscriptionally acting regulatory factors determine the rate-limiting steps of chloroplast psbD gene expression.
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Affiliation(s)
- Birgit Klinkert
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany
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Barnes D, Franklin S, Schultz J, Henry R, Brown E, Coragliotti A, Mayfield SP. Contribution of 5′- and 3′-untranslated regions of plastid mRNAs to the expression of Chlamydomonas reinhardtii chloroplast genes. Mol Genet Genomics 2005; 274:625-36. [PMID: 16231149 DOI: 10.1007/s00438-005-0055-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Accepted: 09/05/2005] [Indexed: 10/25/2022]
Abstract
Expression of chloroplast genes is primarily regulated posttranscriptionally, and a number of RNA elements, found in either the 5'- or 3'-untranslated regions (UTRs) of plastid mRNAs, that impact gene expression have been identified. Complex regulatory and feedback mechanisms influence both translation and protein accumulation, making assignment of roles for specific RNA elements difficult. To identify specific contributions made by various UTRs on translation of plastid mRNAs, we used a heterologous gfp reporter gene that is fused combinatorially to chloroplast 5'- and 3'-UTRs. In general, the 5'-UTR, including the promoter, of the plastid atpA and psbD genes produced the highest levels of chimeric mRNA and protein accumulation, while the 5'-UTR of the rbcL and psbA genes produced less mRNA and protein. Varying the 3'-UTR had little impact on mRNA and protein accumulation, as long as a 3'-UTR was present. Overall, accumulation of chimeric mRNAs was proportional to protein accumulation, with a few notable exceptions. Light-regulated translation continues to operate in chimeric mRNAs containing the 5'-UTR of either the psbA or psbD mRNAs, despite translation of these two chimeric mRNAs at very different efficiencies, suggesting that translational efficiency and light-regulated translation are separate events. Translation of some chimeric mRNAs was much more efficient than others, suggesting that interactions between the untranslated and coding sequences can dramatically impact translational efficiency.
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Affiliation(s)
- Dwight Barnes
- Department of Cell Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Suay L, Salvador ML, Abesha E, Klein U. Specific roles of 5' RNA secondary structures in stabilizing transcripts in chloroplasts. Nucleic Acids Res 2005; 33:4754-61. [PMID: 16116040 PMCID: PMC1188514 DOI: 10.1093/nar/gki760] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNA secondary structures, e.g. stem–loops that are often found at the 5′ and 3′ ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study 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 sequence around its base into a specific RNA conformation, consisting of a helical and single-stranded region, i.e. the real structure required for longevity of rbcL transcripts in chloroplasts. Disturbing this structure renders transcripts completely unstable, even if the sequence of this element is not altered. The requirement of a specific 5′ sequence and structure for RNA longevity suggests an interaction of this element with a trans-acting factor that protects transcripts from rapid degradation in chloroplasts.
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Affiliation(s)
| | | | - Emnet Abesha
- Department of Molecular Biosciences, University of OsloPO Box 1041 Blindern, 0316 Oslo, Norway
| | - Uwe Klein
- Department of Molecular Biosciences, University of OsloPO Box 1041 Blindern, 0316 Oslo, Norway
- To whom correspondence should be addressed. Tel: +34 47 22854662; Fax +34 47 22854726;
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Murakami S, Kuehnle K, Stern DB. A spontaneous tRNA suppressor of a mutation in the Chlamydomonas reinhardtii nuclear MCD1 gene required for stability of the chloroplast petD mRNA. Nucleic Acids Res 2005; 33:3372-80. [PMID: 15947135 PMCID: PMC1148173 DOI: 10.1093/nar/gki651] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Numerous nuclear gene products are required for the correct expression of organellar genes. One such gene in the green alga Chlamydomonas reinhardtii is MCD1, whose product is required for stability of the chloroplast-encoded petD mRNA. In mcd1 mutants, which are non-photosynthetic, petD mRNA is degraded by a 5′–3′ exonuclease activity, resulting in a failure to synthesize its product, subunit IV of the cytochrome b6/f complex. Here, we report the sequence of the wild-type MCD1 gene, which encodes a large and novel putative protein. Analysis of three mutant alleles showed that two harbored large deletions, but that one allele, mcd1-2, had a single base change resulting in a nonsense codon near the N-terminus. This same mutant allele can be suppressed by a second-site mutation in the nuclear MCD2 gene, whereas mcd2-1 cannot suppress the deletion in mcd1-1 (Esposito,D. Higgs,D.C. Drager,R.G. Stern, D.B. and Girard-Bascou,J. (2001) Curr. Genet., 39, 40–48). We report the cloning of mcd2-1, and show that the mutation lies in a tRNASer(CGA), which has been modified to translate the nonsense codon in mcd1-2. We discuss how the existence of a large tRNASer gene family may permit this suppression without pleiotropic consequences.
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Affiliation(s)
| | | | - David B. Stern
- To whom correspondence should be addressed. Tel: +1 607 254 1306; Fax: +1 607 255 6695;
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Ossenbühl F, Göhre V, Meurer J, Krieger-Liszkay A, Rochaix JD, Eichacker LA. Efficient assembly of photosystem II in Chlamydomonas reinhardtii requires Alb3.1p, a homolog of Arabidopsis ALBINO3. THE PLANT CELL 2004; 16:1790-800. [PMID: 15208384 PMCID: PMC514161 DOI: 10.1105/tpc.023226] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Accepted: 04/16/2004] [Indexed: 05/18/2023]
Abstract
Alb3 homologs Oxa1 and YidC have been shown to be required for the integration of newly synthesized proteins into membranes. Here, we show that although Alb3.1p is not required for integration of the plastid-encoded photosystem II core subunit D1 into the thylakoid membrane of Chlamydomonas reinhardtii, the insertion of D1 into functional photosystem II complexes is retarded in the Alb3.1 deletion mutant ac29. Alb3.1p is associated with D1 upon its insertion into the membrane, indicating that Alb3.1p is essential for the efficient assembly of photosystem II. Furthermore, levels of nucleus-encoded light-harvesting proteins are vastly reduced in ac29; however, the remaining antenna systems are still connected to photosystem II reaction centers. Thus, Alb3.1p has a dual function and is required for the accumulation of both nucleus- and plastid-encoded protein subunits in photosynthetic complexes of C. reinhardtii.
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Affiliation(s)
- Friedrich Ossenbühl
- Department for Biology I, Ludwig-Maximilians-University Munich, D-80638, Germany
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