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Sotta N, Chiba Y, Aoyama H, Takamatsu S, Suzuki T, Miwa K, Yamashita Y, Naito S, Fujiwara T. Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions. PLANT & CELL PHYSIOLOGY 2022; 63:592-604. [PMID: 35166349 DOI: 10.1093/pcp/pcac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling or Ribo-seq) has enabled genome-wide analysis of translation. Sorghum is a C4 cereal important not only as food but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Yet genome-wide translational profiles in sorghum are still missing. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 4,843 main open reading frames (ORFs) annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript and translation levels. Our study revealed the translational landscape of sorghum's response to sulfur and provides datasets that could serve as a fundamental resource to extend genetic research on sorghum, including studies on translational regulation.
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Affiliation(s)
- Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Haruka Aoyama
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Seidai Takamatsu
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501 Japan
| | - Kyoko Miwa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
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2
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Nakamura M, Hibi Y, Okamoto T, Sugiura M. Cooperation between the chloroplast psbA 5'-untranslated region and coding region is important for translational initiation: the chloroplast translation machinery cannot read a human viral gene coding region. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:772-80. [PMID: 26931095 DOI: 10.1111/tpj.13150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 06/05/2023]
Abstract
Chloroplast mRNA translation is regulated by the 5'-untranslated region (5'-UTR). Chloroplast 5'-UTRs also support translation of the coding regions of heterologous genes. Using an in vitro translation system from tobacco chloroplasts, we detected no translation from a human immunodeficiency virus tat coding region fused directly to the tobacco chloroplast psbA 5'-UTR. This lack of apparent translation could have been due to rapid degradation of mRNA templates or synthesized protein products. Replacing the psbA 5'-UTR with the E. coli phage T7 gene 10 5'-UTR, a highly active 5'-UTR, and substituting synonymous codons led to some translation of the tat coding region. The Tat protein thus synthesized was stable during translation reactions. No significant degradation of the added tat mRNAs was observed after translation reactions. These results excluded the above two possibilities and confirmed that the tat coding region prevented its own translation. The tat coding region was then fused to the psbA 5'-UTR with a cognate 5'-coding segment. Significant translation was detected from the tat coding region when fused after 10 or more codons. That is, translation could be initiated from the tat coding region once translation had started, indicating that the tat coding region inhibits translational initiation but not elongation. Hence, cooperation/compatibility between the 5'-UTR and its coding region is important for translational initiation.
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Affiliation(s)
- Masayuki Nakamura
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho-ku, Nagoya, 467-8501, Japan
| | - Yurina Hibi
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Kawasumi, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Kawasumi, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho-ku, Nagoya, 467-8501, Japan
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3
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Rogalski M, do Nascimento Vieira L, Fraga HP, Guerra MP. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology. FRONTIERS IN PLANT SCIENCE 2015; 6:586. [PMID: 26284102 PMCID: PMC4520007 DOI: 10.3389/fpls.2015.00586] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/15/2015] [Indexed: 05/20/2023]
Abstract
During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.
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Affiliation(s)
- Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
| | - Hugo P. Fraga
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
| | - Miguel P. Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
- *Correspondence: Miguel P. Guerra, Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346 Florianópolis, SC 88034-000, Brazil,
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Kuroda H, Sugiura M. Processing of the 5'-UTR and existence of protein factors that regulate translation of tobacco chloroplast psbN mRNA. PLANT MOLECULAR BIOLOGY 2014; 86:585-93. [PMID: 25201100 DOI: 10.1007/s11103-014-0248-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/31/2014] [Indexed: 05/28/2023]
Abstract
The chloroplast psbB operon includes five genes encoding photosystem II and cytochrome b 6 /f complex components. The psbN gene is located on the opposite strand. PsbN is localized in the thylakoid and is present even in the dark, although its level increases upon illumination and then decreases. However, the translation mechanism of the psbN mRNA remains unclear. Using an in vitro translation system from tobacco chloroplasts and a green fluorescent protein as a reporter protein, we show that translation occurs from a tobacco primary psbN 5'-UTR of 47 nucleotides (nt). Unlike many other chloroplast 5'-UTRs, the psbN 5'-UTR has two processing sites, at -39 and -24 upstream from the initiation site. Processing at -39 enhanced the translation rate fivefold. In contrast, processing at -24 did not affect the translation rate. These observations suggest that the two distinct processing events regulate, at least in part, the level of PsbN during development. The psbN 5'-UTR has no Shine-Dalgarno (SD)-like sequence. In vitro translation assays with excess amounts of the psbN 5'-UTR or with deleted psbN 5'-UTR sequences demonstrated that protein factors are required for translation and that their binding site is an 18 nt sequence in the 5'-UTR. Mobility shift assays using 10 other chloroplast 5'-UTRs suggested that common or similar proteins are involved in translation of a set of mRNAs lacking SD-like sequences.
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Affiliation(s)
- Hiroshi Kuroda
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho-ku, Nagoya, 467-8501, Japan,
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Berger H, Blifernez-Klassen O, Ballottari M, Bassi R, Wobbe L, Kruse O. Integration of carbon assimilation modes with photosynthetic light capture in the green alga Chlamydomonas reinhardtii. MOLECULAR PLANT 2014; 7:1545-1559. [PMID: 25038233 DOI: 10.1093/mp/ssu083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is capable of using organic and inorganic carbon sources simultaneously, which requires the adjustment of photosynthetic activity to the prevailing mode of carbon assimilation. We obtained novel insights into the regulation of light-harvesting at photosystem II (PSII) following altered carbon source availability. In C. reinhardtii, synthesis of PSII-associated light-harvesting proteins (LHCBMs) is controlled by the cytosolic RNA-binding protein NAB1, which represses translation of particular LHCBM isoform transcripts. This mechanism is fine-tuned via regulation of the nuclear NAB1 promoter, which is activated when linear photosynthetic electron flow is restricted by CO(2)-limitation in a photoheterotrophic context. In the wild-type, accumulation of NAB1 reduces the functional PSII antenna size, thus preventing a harmful overexcited state of PSII, as observed in a NAB1-less mutant. We further demonstrate that translation control as a newly identified long-term response to prolonged CO(2)-limitation replaces LHCII state transitions as a fast response to PSII over-excitation. Intriguingly, activation of the long-term response is perturbed in state transition mutant stt7, suggesting a regulatory link between the long- and short-term response. We depict a regulatory circuit operating on distinct timescales and in different cellular compartments to fine-tune light-harvesting in photoheterotrophic eukaryotes.
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Affiliation(s)
- Hanna Berger
- a Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Olga Blifernez-Klassen
- a Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Matteo Ballottari
- b Universita degli Studi di Verona, Department of Biotechnology, strada Le Grazie 15, 37134, Verona, Italy
| | - Roberto Bassi
- b Universita degli Studi di Verona, Department of Biotechnology, strada Le Grazie 15, 37134, Verona, Italy
| | - Lutz Wobbe
- a Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Olaf Kruse
- a Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615, Bielefeld, Germany
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6
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Ahmad T, Venkataraman S, Hefferon K, AbouHaidar MG. Viral and chloroplastic signals essential for initiation and efficiency of translation in Agrobacterium tumefaciens. Biochem Biophys Res Commun 2014; 452:14-20. [PMID: 25117444 DOI: 10.1016/j.bbrc.2014.07.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
The construction of high-level protein expression vectors using the CaMV 35S promoter in concert with highly efficient translation initiation signals for Agrobacterium tumefaciens is a relatively less explored field compared to that of Escherichia coli. In the current study, we experimentally investigated the capacity of the CaMV 35S promoter to direct GFP gene expression in A. tumefaciens in the context of different viral and chloroplastic translation initiation signals. GFP expression and concomitant translational efficiency was monitored by confocal microscopy and Western blot analysis. Among all of the constructs, the highest level of translation was observed for the construct containing the phage T7 translation initiation region followed by the chloroplastic Rubisco Large Subunit (rbcL) 58-nucleotide 5' leader region including its SD-like sequence (GGGAGGG). Replacing the SD-like (GGGAGGG) with non SD-like (TTTATTT) or replacing the remaining 52 nucleotides of rbcL with nonspecific sequence completely abolished translation. In addition, this 58 nucleotide region of rbcL serves as a translational enhancer in plants when located within the 5' UTR of mRNA corresponding to GFP. Other constructs, including those containing sequences upstream of the coat proteins of Alfalfa Mosaic Virus, or the GAGG sequence of T4 phage or the chloroplastic atpI and/or PsbA 5' UTR sequence, supported low levels of GFP expression or none at all. From these studies, we propose that we have created high expression vectors in A. tumefaciens and/or plants which contain the CaMV 35S promoter, followed by the translationally strong T7 SD plus RBS translation initiation region or the rbcL 58-nucleotide 5' leader region upstream of the gene of interest.
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Affiliation(s)
- Tauqeer Ahmad
- Department of Cell and Systems Biology, University of Toronto, St. George Campus, 25 Willcocks Street, Toronto, ON M5S3B2, Canada
| | - Srividhya Venkataraman
- Department of Cell and Systems Biology, University of Toronto, St. George Campus, 25 Willcocks Street, Toronto, ON M5S3B2, Canada
| | - Kathleen Hefferon
- Department of Cell and Systems Biology, University of Toronto, St. George Campus, 25 Willcocks Street, Toronto, ON M5S3B2, Canada
| | - Mounir G AbouHaidar
- Department of Cell and Systems Biology, University of Toronto, St. George Campus, 25 Willcocks Street, Toronto, ON M5S3B2, Canada.
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7
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Abstract
Overall translational machinery in plastids is similar to that of E. coli. Initiation is the crucial step for translation and this step in plastids is somewhat different from that of E. coli. Unlike the Shine-Dalgarno sequence in E. coli, cis-elements for translation initiation are not well conserved in plastid mRNAs. Specific trans-acting factors are generally required for translation initiation and its regulation in plastids. During translation elongation, ribosomes pause sometimes on photosynthesis-related mRNAs due probably to proper insertion of nascent polypeptides into membrane complexes. Codon usage of plastid mRNAs is different from that of E. coli and mammalian cells. Plastid mRNAs do not have the so-called rare codons. Translation efficiencies of several synonymous codons are not always correlated with codon usage in plastid mRNAs.
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8
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Berry JO, Yerramsetty P, Zielinski AM, Mure CM. Photosynthetic gene expression in higher plants. PHOTOSYNTHESIS RESEARCH 2013; 117:91-120. [PMID: 23839301 DOI: 10.1007/s11120-013-9880-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/26/2013] [Indexed: 05/08/2023]
Abstract
Within the chloroplasts of higher plants and algae, photosynthesis converts light into biological energy, fueling the assimilation of atmospheric carbon dioxide into biologically useful molecules. Two major steps, photosynthetic electron transport and the Calvin-Benson cycle, require many gene products encoded from chloroplast as well as nuclear genomes. The expression of genes in both cellular compartments is highly dynamic and influenced by a diverse range of factors. Light is the primary environmental determinant of photosynthetic gene expression. Working through photoreceptors such as phytochrome, light regulates photosynthetic genes at transcriptional and posttranscriptional levels. Other processes that affect photosynthetic gene expression include photosynthetic activity, development, and biotic and abiotic stress. Anterograde (from nucleus to chloroplast) and retrograde (from chloroplast to nucleus) signaling insures the highly coordinated expression of the many photosynthetic genes between these different compartments. Anterograde signaling incorporates nuclear-encoded transcriptional and posttranscriptional regulators, such as sigma factors and RNA-binding proteins, respectively. Retrograde signaling utilizes photosynthetic processes such as photosynthetic electron transport and redox signaling to influence the expression of photosynthetic genes in the nucleus. The basic C3 photosynthetic pathway serves as the default form used by most of the plant species on earth. High temperature and water stress associated with arid environments have led to the development of specialized C4 and CAM photosynthesis, which evolved as modifications of the basic default expression program. The goal of this article is to explain and summarize the many gene expression and regulatory processes that work together to support photosynthetic function in plants.
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Affiliation(s)
- James O Berry
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA,
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Roy B, von Arnim AG. Translational Regulation of Cytoplasmic mRNAs. THE ARABIDOPSIS BOOK 2013; 11:e0165. [PMID: 23908601 PMCID: PMC3727577 DOI: 10.1199/tab.0165] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Translation of the coding potential of a messenger RNA into a protein molecule is a fundamental process in all living cells and consumes a large fraction of metabolites and energy resources in growing cells. Moreover, translation has emerged as an important control point in the regulation of gene expression. At the level of gene regulation, translational control is utilized to support the specific life histories of plants, in particular their responses to the abiotic environment and to metabolites. This review summarizes the diversity of translational control mechanisms in the plant cytoplasm, focusing on specific cases where mechanisms of translational control have evolved to complement or eclipse other levels of gene regulation. We begin by introducing essential features of the translation apparatus. We summarize early evidence for translational control from the pre-Arabidopsis era. Next, we review evidence for translation control in response to stress, to metabolites, and in development. The following section emphasizes RNA sequence elements and biochemical processes that regulate translation. We close with a chapter on the role of signaling pathways that impinge on translation.
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Affiliation(s)
- Bijoyita Roy
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Current address: University of Massachussetts Medical School, Worcester, MA 01655-0122, USA
| | - Albrecht G. von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
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10
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Floris M, Bassi R, Robaglia C, Alboresi A, Lanet E. Post-transcriptional control of light-harvesting genes expression under light stress. PLANT MOLECULAR BIOLOGY 2013; 82:147-54. [PMID: 23526054 DOI: 10.1007/s11103-013-0046-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 03/12/2013] [Indexed: 05/20/2023]
Abstract
Plants have to deal with fluctuating light environment and the regulation of the photosynthetic apparatus is crucial for their survival. The large multigenic family of nuclear encoded chloroplastic proteins called light harvesting complex (LHC) is involved in both light harvesting and photoprotection. Changes in light intensity induce a complex set of molecular events within both the chloroplast and the cytoplasmic compartments of the cell leading to reorganization of the photosynthetic apparatus in order to optimize photosynthesis to the new conditions. In this study we have investigated the occurrence of translational regulations during light stress in Arabidopsis thaliana by using polysomes profiling. We have observed a strong effect of light on global translation activity of the cell. We show that individual LHC genes are translationally regulated in response to light conditions by changing the ratio between polysomal versus total messenger RNA. In addition, we found that cytoplasmic translational regulation can precede nuclear transcriptional regulation. Thus translational control appears as an important component of the crosstalk between chloroplast and the nucleus in plant cells.
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Affiliation(s)
- Maïna Floris
- Laboratoire de Génétique et Biophysique des Plantes, Service de Biologie Végétale et de Microbiologie Environnementale, Unite Mixte de Recherche 7225, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Faculte des Sciences de Luminy, Aix Marseille Universite, 13009, Marseille, France
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11
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Zoschke R, Qu Y, Zubo YO, Börner T, Schmitz-Linneweber C. Mutation of the pentatricopeptide repeat-SMR protein SVR7 impairs accumulation and translation of chloroplast ATP synthase subunits in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2013; 126:403-14. [PMID: 23076438 DOI: 10.1007/s10265-012-0527-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 09/19/2012] [Indexed: 05/21/2023]
Abstract
RNA processing, RNA editing, RNA splicing and translational activation of RNAs are essential post-transcriptional steps in chloroplast gene expression. Typically, the factors mediating those processes are nuclear encoded and post-translationally imported into the chloroplasts. In land plants, members of the large pentatricopeptide repeat (PPR) protein family are required for individual steps in chloroplast RNA processing. Interestingly, a subgroup of PPR proteins carries a C-terminal small MutS related (SMR) domain. Here we analyzed the consequences of mutations in the SVR7 gene, which encodes a PPR-SMR protein, in Arabidopsis thaliana. We demonstrate that SVR7 mutations lead to a specific reduction in chloroplast ATP synthase levels. Furthermore, we found aberrant transcript patterns for ATP synthase coding mRNAs in svr7 mutants. Finally, a reduced ribosome association of atpB/E and rbcL mRNAs in svr7 mutants suggests the involvement of the PPR-SMR protein SVR7 in translational activation of these mRNAs. We describe that the function of SVR7 in translation has expanded relative to its maize ortholog ATP4. The results provide evidence for a relaxed functional conservation of this PPR-SMR protein in eudicotyledonous and monocotyledonous plants, thus adding to the knowledge about the function and evolution of PPR-SMR proteins.
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Affiliation(s)
- Reimo Zoschke
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.
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12
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Yukawa M, Sugiura M. Additional pathway to translate the downstream ndhK cistron in partially overlapping ndhC-ndhK mRNAs in chloroplasts. Proc Natl Acad Sci U S A 2013; 110:5701-6. [PMID: 23509265 PMCID: PMC3619338 DOI: 10.1073/pnas.1219914110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The chloroplast NAD(P)H dehydrogenase (NDH) C (ndhC) and ndhK genes partially overlap and are cotranscribed in many plants. We previously reported that the tobacco ndhC/K genes are translationally coupled but produce NdhC and NdhK, subunits of the NDH complex, in similar amounts. Generally, translation of the downstream cistron in overlapping mRNAs is very low. Hence, these findings suggested that the ndhK cistron is translated not only from the ndhC 5'UTR but also by an additional pathway. Using an in vitro translation system from tobacco chloroplasts, we report here that free ribosomes enter, with formylmethionyl-tRNA(fMet), at an internal AUG start codon that is located in frame in the middle of the upstream ndhC cistron, translate the 3' half of the ndhC cistron, reach the ndhK start codon, and that, at that point, some ribosomes resume ndhK translation. We detected a peptide corresponding to a 57-amino-acid product encoded by the sequence from the internal AUG to the ndhC stop codon. We propose a model in which the internal initiation site AUG is not designed for synthesizing a functional isoform but for delivering additional ribosomes to the ndhK cistron to produce NdhK in the amount required for the assembly of the NDH complex. This pathway is a unique type of translation to produce protein in the needed amount with the cost of peptide synthesis.
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Affiliation(s)
- Maki Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan; and
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan; and
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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13
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Pfalz J, Pfannschmidt T. Essential nucleoid proteins in early chloroplast development. TRENDS IN PLANT SCIENCE 2013; 18:186-94. [PMID: 23246438 DOI: 10.1016/j.tplants.2012.11.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 11/01/2012] [Accepted: 11/12/2012] [Indexed: 05/04/2023]
Abstract
The plastid transcription machinery can be biochemically purified at different organisational levels as soluble RNA polymerase, transcriptionally active chromosome, or nucleoid. Recent proteomic studies have uncovered several novel proteins in these structures and functional genomic studies have indicated that a lack of many of these proteins results in chlorotic phenotypes of varying degree. The most severe cases exhibit complete albino phenotypes, which led to the conclusion that the proteins that were lacking had important regulatory roles in plastid gene expression and chloroplast development. In this opinion article, we propose an alternative model in which the structural establishment of a transcriptional subdomain within the nucleoid represents an early developmental bottleneck that leads to abortion of proper chloroplast biogenesis if disturbed.
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Affiliation(s)
- Jeannette Pfalz
- Department of Plant Physiology, Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, D-07743 Jena, Germany
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14
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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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Formighieri C, Franck F, Bassi R. Regulation of the pigment optical density of an algal cell: Filling the gap between photosynthetic productivity in the laboratory and in mass culture. J Biotechnol 2012; 162:115-23. [DOI: 10.1016/j.jbiotec.2012.02.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 02/27/2012] [Accepted: 02/29/2012] [Indexed: 11/26/2022]
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16
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Adachi Y, Kuroda H, Yukawa Y, Sugiura M. Translation of partially overlapping psbD-psbC mRNAs in chloroplasts: the role of 5'-processing and translational coupling. Nucleic Acids Res 2012; 40:3152-8. [PMID: 22156163 PMCID: PMC3326318 DOI: 10.1093/nar/gkr1185] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/14/2011] [Accepted: 11/14/2011] [Indexed: 11/24/2022] Open
Abstract
The chloroplast psbD and psbC genes encode the D2 and CP43 proteins of the photosystem II complex, and they are generally cotranscribed. We report studies on the basic translation process of tobacco psbD-psbC mRNAs using an in vitro translation system from tobacco chloroplasts. The primary transcript has an unusually long 5'-UTR (905 nt). We show that it is translatable. Processing of the 5'-UTR greatly enhances the translation efficiency of the psbD cistron. A striking feature is that psbD and psbC cistrons overlap by 14 nt. Removal of the psbD 5'-UTR plus the start codon and introduction of a premature termination codon in the psbD cistron considerably reduce the translation efficiency of the downstream psbC cistron. These results indicate that translation of the psbC cistron depends largely on that of the upstream psbD cistron and thus shows translational coupling; however, a portion is independently translated. These observations, together with the presence of monocistronic psbC mRNAs, suggest that the psbD and psbC cistrons are translated via multiple processes to produce necessary amounts of D2 and CP43 proteins.
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Affiliation(s)
- Yuka Adachi
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Hiroshi Kuroda
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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17
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Suzuki H, Kuroda H, Yukawa Y, Sugiura M. The downstream atpE cistron is efficiently translated via its own cis-element in partially overlapping atpB-atpE dicistronic mRNAs in chloroplasts. Nucleic Acids Res 2011; 39:9405-12. [PMID: 21846772 PMCID: PMC3241655 DOI: 10.1093/nar/gkr644] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/22/2011] [Accepted: 07/22/2011] [Indexed: 11/12/2022] Open
Abstract
The chloroplast atpB and atpE genes encode subunits β and ε of the ATP synthase, respectively. They are co-transcribed as dicistronic mRNAs in flowering plants. An unusual feature is an overlap (AUGA) of the atpB stop codon (UGA) with the atpE start codon (AUG). Hence, atpE translation has been believed to depend on atpB translation (i.e. translational coupling). Using an in vitro translation system from tobacco chloroplasts, we showed that both atpB and atpE cistrons are translated from the tobacco dicistronic mRNA, and that the efficiency of atpB translation is higher than that of atpE translation. When the atpB 5'-UTR was replaced with lower efficiency 5'-UTRs, atpE translation was higher than atpB translation. Removal of the entire atpB 5'-UTR arrested atpB translation but atpE translation still proceeded. Introduction of a premature stop codon in the atpB cistron did not abolish atpE translation. These results indicate that atpE translation is independent of atpB translation. Mutation analysis showed that the atpE cistron possesses its own cis-element(s) for translation, located ~25 nt upstream from the start codon.
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Affiliation(s)
- Haruka Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Sugiyama Human Research Center, Sugiyama Jogakuen University, Nagoya 464-8662, Japan
| | - Hiroshi Kuroda
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Sugiyama Human Research Center, Sugiyama Jogakuen University, Nagoya 464-8662, Japan
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Sugiyama Human Research Center, Sugiyama Jogakuen University, Nagoya 464-8662, Japan
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467-8501 and Sugiyama Human Research Center, Sugiyama Jogakuen University, Nagoya 464-8662, Japan
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18
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Johnson X. Manipulating RuBisCO accumulation in the green alga, Chlamydomonas reinhardtii. PLANT MOLECULAR BIOLOGY 2011; 76:397-405. [PMID: 21607658 DOI: 10.1007/s11103-011-9783-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 04/27/2011] [Indexed: 05/03/2023]
Abstract
The nuclear factor, Maturation/stability of RbcL (MRL1), regulates the accumulation of the chloroplast rbcL gene transcript in Chlamydomonas reinhardtii by stabilising the mRNA via its 5' UTR. An absence of MRL1 in algal mrl1 mutants leads to a complete absence of RuBisCO large subunit protein and thus a lack of accumulation of the RuBisCO holoenzyme. By complementing mrl1 mutants by random transformation of the nuclear genome with the MRL1 cDNA, different levels of rbcL transcript accumulate. We also observe that RuBisCO Large Subunit accumulation is perturbed. Complemented strains accumulating as little as 15% RuBisCO protein can grow phototrophically while RuBisCO in this range is limiting for phototrophic growth. We also observe that photosynthetic activity, here measured by the quantum yield of PSII, appears to be a determinant for phototrophic growth. In some strains that accumulate less RuBisCO, a strong production of reactive oxygen species is detected. In the absence of RuBisCO, oxygen possibly acts as the PSI terminal electron acceptor. These results show that random transformation of MRL1 into mrl1 mutants can change RuBisCO accumulation allowing a range of phototrophic growth phenotypes. Furthermore, this technique allows for the isolation of strains with low RuBisCO, within the range of acceptable photosynthetic growth and reasonably low ROS production. MRL1 is thus a potential tool for applications to divert electrons away from photosynthetic carbon metabolism towards alternative pathways.
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Affiliation(s)
- Xenie Johnson
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141/Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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19
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Stephens E, Ross IL, Mussgnug JH, Wagner LD, Borowitzka MA, Posten C, Kruse O, Hankamer B. Future prospects of microalgal biofuel production systems. TRENDS IN PLANT SCIENCE 2010; 15:554-64. [PMID: 20655798 DOI: 10.1016/j.tplants.2010.06.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 06/11/2010] [Accepted: 06/24/2010] [Indexed: 05/09/2023]
Abstract
Climate change mitigation, economic growth and stability, and the ongoing depletion of oil reserves are all major drivers for the development of economically rational, renewable energy technology platforms. Microalgae have re-emerged as a popular feedstock for the production of biofuels and other more valuable products. Even though integrated microalgal production systems have some clear advantages and present a promising alternative to highly controversial first generation biofuel systems, the associated hype has often exceeded the boundaries of reality. With a growing number of recent analyses demonstrating that despite the hype, these systems are conceptually sound and potentially sustainable given the available inputs, we review the research areas that are key to attaining economic reality and the future development of the industry.
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Affiliation(s)
- Evan Stephens
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Qld 4072, Australia
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20
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Beckmann J, Lehr F, Finazzi G, Hankamer B, Posten C, Wobbe L, Kruse O. Improvement of light to biomass conversion by de-regulation of light-harvesting protein translation in Chlamydomonas reinhardtii. J Biotechnol 2009; 142:70-7. [DOI: 10.1016/j.jbiotec.2009.02.015] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 02/09/2009] [Accepted: 02/17/2009] [Indexed: 11/29/2022]
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21
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Foyer CH, Noctor G. Redox regulation in photosynthetic organisms: signaling, acclimation, and practical implications. Antioxid Redox Signal 2009; 11:861-905. [PMID: 19239350 DOI: 10.1089/ars.2008.2177] [Citation(s) in RCA: 729] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Reactive oxygen species (ROS) have multifaceted roles in the orchestration of plant gene expression and gene-product regulation. Cellular redox homeostasis is considered to be an "integrator" of information from metabolism and the environment controlling plant growth and acclimation responses, as well as cell suicide events. The different ROS forms influence gene expression in specific and sometimes antagonistic ways. Low molecular antioxidants (e.g., ascorbate, glutathione) serve not only to limit the lifetime of the ROS signals but also to participate in an extensive range of other redox signaling and regulatory functions. In contrast to the low molecular weight antioxidants, the "redox" states of components involved in photosynthesis such as plastoquinone show rapid and often transient shifts in response to changes in light and other environmental signals. Whereas both types of "redox regulation" are intimately linked through the thioredoxin, peroxiredoxin, and pyridine nucleotide pools, they also act independently of each other to achieve overall energy balance between energy-producing and energy-utilizing pathways. This review focuses on current knowledge of the pathways of redox regulation, with discussion of the somewhat juxtaposed hypotheses of "oxidative damage" versus "oxidative signaling," within the wider context of physiological function, from plant cell biology to potential applications.
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Affiliation(s)
- Christine H Foyer
- School of Agriculture, Food and Rural Development, Agriculture Building, University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom.
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22
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Baecker JJ, Sneddon JC, Hollingsworth MJ. Efficient translation in chloroplasts requires element(s) upstream of the putative ribosome binding site from atpI. AMERICAN JOURNAL OF BOTANY 2009; 96:627-636. [PMID: 21628219 DOI: 10.3732/ajb.0800259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Thousands of proteins make up a chloroplast, but fewer than 100 are encoded by the chloroplast genome. Despite this low number, expression of chloroplast-encoded genes is essential for plant survival. Every chloroplast has its own gene expression system with a major regulatory point at the initiation of protein synthesis (translation). In chloroplasts, most protein-encoding genes contain elements resembling the ribosome binding sites (RBS) found in prokaryotes. In vitro, these putative chloroplast ribosome binding sequences vary in their ability to support translation. Here we report results from an investigation into effects of the predicted RBS for the tobacco chloroplast atpI gene on translation in vivo. Two reporter constructs, differing only in their 5'-untranslated regions (5'UTRs) were stably incorporated into tobacco chloroplast genomes and their expression analyzed. One 5'UTR was derived from the wild-type (WT) atpI gene. The second, Holo-substitution (Holo-sub), had nonchloroplast sequence replacing all wild-type nucleotides, except for the putative RBS. The abundance of reporter RNA was the same for both 5'UTRs. However, translation controlled by Holo-sub was less than 4% that controlled by WT. These in vivo experiments support the idea that translation initiation in land plant chloroplasts depends on 5'UTR elements outside the putative RBS.
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Affiliation(s)
- Joshua J Baecker
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, New York 14260 USA
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23
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Abstract
Despite recent elucidation of the three-dimensional structure of major photosynthetic complexes, our understanding of light energy conversion in plant chloroplasts and microalgae under physiological conditions requires exploring the dynamics of photosynthesis. The photosynthetic apparatus is a flexible molecular machine that can acclimate to metabolic and light fluctuations in a matter of seconds and minutes. On a longer time scale, changes in environmental cues trigger acclimation responses that elicit intracellular signaling between the nucleo-cytosol and chloroplast resulting in modification of the biogenesis of the photosynthetic machinery. Here we attempt to integrate well-established knowledge on the functional flexibility of light-harvesting and electron transfer processes, which has greatly benefited from genetic approaches, with data derived from the wealth of recent transcriptomic and proteomic studies of acclimation responses in photosynthetic eukaroytes.
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Affiliation(s)
- Stephan Eberhard
- Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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24
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Yukawa M, Sugiura M. Termination codon-dependent translation of partially overlapping ndhC-ndhK transcripts in chloroplasts. Proc Natl Acad Sci U S A 2008; 105:19550-4. [PMID: 19033452 PMCID: PMC2614798 DOI: 10.1073/pnas.0809240105] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Indexed: 11/18/2022] Open
Abstract
The chloroplast NAD(P)H dehydrogenase complex, a homologue of mitochondrial complex I, consists of >15 subunits, of which 11 are encoded by the chloroplast genome (ndhA-K). The ndhC and ndhK genes are partially overlapped and cotranscribed in many land plants. The downstream ndhK mRNA possesses 4 possible AUG initiation codons in many dicot plants. By using an efficient in vitro translation system from tobacco chloroplasts, we defined that the major initiation site of tobacco ndhK mRNAs is the third AUG that is located 4 nt upstream from the ndhC stop codon. Mutation of the ndhC stop codon (UAG) arrested translation of the ndhK cistron. Frameshift of the ndhC coding strand inhibited also translation of the distal cistron. The results indicated that ndhK translation depends on termination of the preceding cistron, namely translational coupling. Surprisingly, removal of the ndhC 5'-UTR and its AUG still supported substantial translation of the ndhK cistron. This translation was abolished again by removing the ndhC stop codon. Although translation of the downstream cistron of an overlapping mRNA is generally very low, we found that the ndhC/K mRNA produces NdhK and NdhC in similar amounts. Based on subunit compositions of the bacterial complex I, the stoichiometry of NdhK and NdhC is suggested to be 1:1 in chloroplasts. To meet this stoichiometry, the ndhC/K mRNA is translated not only by a translational coupling event but also by a termination codon-dependent pathway.
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Affiliation(s)
- Maki Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan; and
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan; and
- Sugiyama Human Research Center, Sugiyama Jogakuen University, Nagoya 464-8662, Japan
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