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Abstract
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
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Affiliation(s)
- Jennifer Ortelt
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany
| | - Gerhard Link
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany.
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Shimmura S, Nozoe M, Kitora S, Kin S, Matsutani S, Ishizaki Y, Nakahira Y, Shiina T. Comparative Analysis of Chloroplast psbD Promoters in Terrestrial Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1186. [PMID: 28751898 PMCID: PMC5508017 DOI: 10.3389/fpls.2017.01186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/21/2017] [Indexed: 05/15/2023]
Abstract
The transcription of photosynthesis genes encoded by the plastid genome is mainly mediated by a prokaryotic-type RNA polymerase called plastid-encoded plastid RNA polymerase (PEP). Standard PEP-dependent promoters resemble bacterial sigma-70-type promoters containing the so-called -10 and -35 elements. On the other hand, an unusual light- and stress-responsive promoter (psbD LRP) that is regulated by a 19-bp AAG-box immediately upstream of the -35 element has been mapped upstream of the psbD-psbC operon in some angiosperms. However, the occurrence of the AAG-box containing psbD LRP in plant evolution remains elusive. We have mapped the psbD promoters in eleven embryophytes at different evolutionary stages from liverworts to angiosperms. The psbD promoters were mostly mapped around 500-900 bp upstream of the psbD translational start sites, indicating that the psbD mRNAs have unusually long 5'-UTR extensions in common. The -10 elements of the psbD promoter are well-conserved in all embryophytes, but not the -35 elements. We found that the AAG-box sequences are highly conserved in angiosperms and gymnosperms except for gnetaceae plants. Furthermore, partial AAG-box-like sequences have been identified in the psbD promoters of some basal embryophytes such as moss, hornwort, and lycophyte, whereas liverwort has the standard PEP promoter without the AAG-box. These results suggest that the AAG-box sequences of the psbD LRP may have evolved from a primitive type of AAG-box of basal embryophytes. On the other hand, monilophytes (ferns) use another type of psbD promoter composed of a distinct cis-element upstream of the potential -35 element. Furthermore, we found that psbD expression is not regulated by light in gymnosperms or basal angiosperms, although they have the well-conserved AAG-box sequences. Thus, it is unlikely that acquisition of the AAG-box containing psbD promoter is directly associated with light-induced transcription of the psbD-psbC operon. Light- and stress-induced transcription may have evolved independently and multiple times during terrestrial plant evolution.
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Affiliation(s)
- Shuichi Shimmura
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Mikio Nozoe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- AMITA Institute for Sustainable Economies Co., Ltd.Kyoto, Japan
| | - Shota Kitora
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Satoko Kin
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Shigeru Matsutani
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- Kyoto Botanical GardenKyoto, Japan
| | - Yoko Ishizaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Yoichi Nakahira
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- College of Agriculture, Ibaraki UniversityIbaraki, Japan
| | - Takashi Shiina
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
- *Correspondence: Takashi Shiina,
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Chi W, He B, Mao J, Jiang J, Zhang L. Plastid sigma factors: Their individual functions and regulation in transcription. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:770-8. [PMID: 25596450 DOI: 10.1016/j.bbabio.2015.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/02/2015] [Accepted: 01/06/2015] [Indexed: 11/18/2022]
Abstract
Sigma factors are the predominant factors involved in transcription regulation in bacteria. These factors can recruit the core RNA polymerase to promoters with specific DNA sequences and initiate gene transcription. The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. Although all plastid sigma factors contain sequences conserved in bacterial sigma factors, a considerable number of distinct traits have been acquired during evolution. The present review summarises recent advances concerning the regulation of the structure, function and activity of plastid sigma factors since their discovery nearly 40 years ago. We highlight the specialised roles and overlapping redundant functions of plastid sigma factors according to their promoter selectivity. We also focus on the mechanisms that modulate the activity of sigma factors to optimise plastid function in response to developmental cues and environmental signals. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Juan Mao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jingjing Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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4
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Abstract
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
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Affiliation(s)
- Jennifer Ortelt
- Plant Cell Physiology and Molecular Biology, University of Bochum, Bochum, Germany
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Jeon H, Jin YM, Choi MH, Lee H, Kim M. Chloroplast-targeted bacterial RecA proteins confer tolerance to chloroplast DNA damage by methyl viologen or UV-C radiation in tobacco (Nicotiana tabacum) plants. PHYSIOLOGIA PLANTARUM 2013; 147:218-33. [PMID: 22651245 DOI: 10.1111/j.1399-3054.2012.01658.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Indexed: 06/01/2023]
Abstract
The nature and importance of the DNA repair system in the chloroplasts of higher plants under oxidative stress or UV radiation-induced genotoxicity was investigated via gain-of-functional approaches exploiting bacterial RecAs. For this purpose, transgenic tobacco (Nicotiana tabacum) plants and cell suspensions overexpressing Escherichia coli or Pseudomonas aeruginosa RecA fused to a chloroplast-targeting transit peptide were first produced. The transgenic tobacco plants maintained higher amounts of chloroplast DNA compared with wild-type (WT) upon treatments with methyl viologen (MV), a herbicide that generates reactive oxygen species (ROS) in chloroplasts. Consistent with these results, the transgenic tobacco leaves showed less bleaching than WT following MV exposure. Similarly, the MV-treated transgenic Arabidopsis plants overexpressing the chloroplast RecA homologue RECA1 showed weak bleaching, while the recA1 mutant showed opposite results upon MV treatment. In addition, when exposed to UV-C radiation, the dark-grown E. coli RecA-overexpressing transgenic tobacco cell suspensions, but not their WT counterparts, resumed growth and greening after the recovery period under light conditions. Measurements of UV radiation-induced chloroplast DNA damage using DraI assays (Harlow et al. 1994) with the chloroplast rbcL DNA probe and quantitative PCR analyses showed that the transgenic cell suspensions better repaired their UV-C radiation-induced chloroplast DNA lesions compared with WT. Taken all together, it was concluded that RecA-overexpressing transgenic plants are endowed with an increased chloroplast DNA maintenance capacity and enhanced repair activities, and consequently have a higher survival tolerance to genotoxic stresses. These observations are made possible by the functional compatibility of the bacterial RecAs in chloroplasts.
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Affiliation(s)
- Hyesung Jeon
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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6
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Caroca R, Howell KA, Hasse C, Ruf S, Bock R. Design of chimeric expression elements that confer high-level gene activity in chromoplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:368-79. [PMID: 23004223 DOI: 10.1111/tpj.12031] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/14/2012] [Accepted: 09/17/2012] [Indexed: 05/05/2023]
Abstract
Non-green plastids, such as chromoplasts, generally have much lower activity of gene expression than chloroplasts in photosynthetically active tissues. Suppression of plastid genes in non-green tissues occurs through a complex interplay of transcriptional and translational control, with the contribution of regulation of transcript abundance versus translational activity being highly variable between genes. Here, we have investigated whether the low expression of the plastid genome in chromoplasts results from inherent limitations in gene expression capacity, or can be overcome by designing appropriate combinations of promoters and translation initiation signals in the 5' untranslated region (5'-UTR). We constructed chimeric expression elements that combine promoters and 5'-UTRs from plastid genes, which are suppressed during chloroplast-to-chromoplast conversion in Solanum lycopersicum (tomato) fruit ripening, either just at the translational level or just at the level of mRNA accumulation. These chimeric expression elements were introduced into the tomato plastid genome by stable chloroplast transformation. We report the identification of promoter-UTR combinations that confer high-level gene expression in chromoplasts of ripe tomato fruits, resulting in the accumulation of reporter protein GFP to up to 1% of total cellular protein. Our work demonstrates that non-green plastids are capable of expressing genes to high levels. Moreover, the chimeric cis-elements for chromoplasts developed here are widely applicable in basic and applied research using transplastomic methods.
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Affiliation(s)
- Rodrigo Caroca
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
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Wang Y, Ding J, Daniell H, Hu H, Li X. Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins. PLANT MOLECULAR BIOLOGY 2012; 80:177-87. [PMID: 22733202 DOI: 10.1007/s11103-012-9938-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/15/2012] [Indexed: 06/01/2023]
Abstract
Chloroplasts play critical roles in land plant cells. Despite their importance and the availability of at least 200 sequenced chloroplast genomes, the number of known DNA regulatory sequences in chloroplast genomes are limited. In this paper, we designed computational methods to systematically study putative DNA regulatory sequences in intergenic regions near chloroplast genes in seven plant species and in promoter sequences of nuclear genes in Arabidopsis and rice. We found that -35/-10 elements alone cannot explain the transcriptional regulation of chloroplast genes. We also concluded that there are unlikely motifs shared by intergenic sequences of most of chloroplast genes, indicating that these genes are regulated differently. Finally and surprisingly, we found five conserved motifs, each of which occurs in no more than six chloroplast intergenic sequences, are significantly shared by promoters of nuclear-genes encoding chloroplast proteins. By integrating information from gene function annotation, protein subcellular localization analyses, protein-protein interaction data, and gene expression data, we further showed support of the functionality of these conserved motifs. Our study implies the existence of unknown nuclear-encoded transcription factors that regulate both chloroplast genes and nuclear genes encoding chloroplast protein, which sheds light on the understanding of the transcriptional regulation of chloroplast genes.
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Affiliation(s)
- Ying Wang
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA
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Liere K, Weihe A, Börner T. The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1345-60. [PMID: 21316793 DOI: 10.1016/j.jplph.2011.01.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 01/07/2011] [Accepted: 01/10/2011] [Indexed: 05/04/2023]
Abstract
Although genomes of mitochondria and plastids are very small compared to those of their bacterial ancestors, the transcription machineries of these organelles are of surprising complexity. With respect to the number of different RNA polymerases per organelle, the extremes are represented on one hand by chloroplasts of eudicots which use one bacterial-type RNA polymerase and two phage-type RNA polymerases to transcribe their genes, and on the other hand by Physcomitrella possessing three mitochondrial RNA polymerases of the phage type. Transcription of genes/operons is often driven by multiple promoters in both organelles. This review describes the principle components of the transcription machineries (RNA polymerases, transcription factors, promoters) and the division of labor between the different RNA polymerases. While regulation of transcription in mitochondria seems to be only of limited importance, the plastid genes of higher plants respond to exogenous and endogenous cues rather individually by altering their transcriptional activities.
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Affiliation(s)
- Karsten Liere
- Institut für Biologie/Genetik, Humboldt-Universität zu Berlin, Chausseestrasse 117, Berlin, Germany
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Newell CA, Gray JC. Binding of lac repressor-GFP fusion protein to lac operator sites inserted in the tobacco chloroplast genome examined by chromatin immunoprecipitation. Nucleic Acids Res 2010; 38:e145. [PMID: 20484380 PMCID: PMC2919732 DOI: 10.1093/nar/gkq413] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 04/29/2010] [Accepted: 05/04/2010] [Indexed: 11/12/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) has been used to detect binding of DNA-binding proteins to sites in nuclear and mitochondrial genomes. Here, we describe a method for detecting protein-binding sites on chloroplast DNA, using modifications to the nuclear ChIP procedures. The method was developed using the lac operator (lacO)/lac repressor (LacI) system from Escherichia coli. The lacO sequences were integrated into a single site between the rbcL and accD genes in tobacco plastid DNA and homoplasmic transplastomic plants were crossed with transgenic tobacco plants expressing a nuclear-encoded plastid-targeted GFP-LacI fusion protein. In the progeny, the GFP-LacI fusion protein could be visualized in living tissues using confocal microscopy, and was found to co-localize with plastid nucleoids. Isolated chloroplasts from the lacO/GFP-LacI plants were lysed, treated with micrococcal nuclease to digest the DNA to fragments of approximately 600 bp and incubated with antibodies to GFP and protein A-Sepharose. PCR analysis on DNA extracted from the immunoprecipitate demonstrated IPTG (isopropylthiogalactoside)-sensitive binding of GFP-LacI to lacO. Binding of GFP-LacI to endogenous sites in plastid DNA showing sequence similarity to lacO was also detected, but required reversible cross-linking with formaldehyde. This may provide a general method for the detection of binding sites on plastid DNA for specific proteins.
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Affiliation(s)
| | - John C. Gray
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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10
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Onda Y, Yagi Y, Saito Y, Takenaka N, Toyoshima Y. Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:968-78. [PMID: 18532976 DOI: 10.1111/j.1365-313x.2008.03567.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In higher plants, multiple nuclear-encoded sigma factors activate select subsets of plastid gene promoters in a partially redundant manner. We analysed the light induction profiles of transcripts from six Arabidopsis sigma factor (AtSIG) genes in mature leaves, focusing on the effects of wavelength and intensity. Red-light illumination (660 nm) of dark-adapted plants strongly induced AtSIG1 transcripts, while blue-light illumination (470 nm) caused strong and rapid induction of AtSIG1 and AtSIG5 transcripts. The fluence response differed in blue-light-responsive rapid induction in AtSIG1 and AtSIG5. AtSIG1 transcripts increased to plateau with a threshold of 2 micromol m(-2) sec(-1) under all fluences examined (1-50 micromol m(-2) sec(-1)), and AtSIG5 transcripts were induced with a distinct two-phase profile, with the lower-fluence induction similar to that of AtSIG1 and further enhancement with increasing fluences greater than 10 micromol m(-2) sec(-1). Blue-light-receptor mutational analysis revealed that AtSIG5-specific two-phase induction is mediated through cryptochrome 1 and cryptochrome 2 at lower fluences and more significantly through cryptochrome 1 at higher fluences. In mature chloroplasts, the promoters of psbA and psbD are predominantly recognized by AtSIG5 among six sigma factors. Using a protoplast transient expression assay with AtSIG5-AtSIG1 chimeric genes, we present evidence that AtSIG5 contains determinants for activating the psbD blue-light-responsive promoter (BLRP) in region 4.2 rather than region 2.4. Amino acid scanning within AtSIG5 region 4.2 revealed that Asn484, but not Arg493, functions as a key residue for psbD BLRP activation. Arginine 493 may be involved in psbA promoter recognition.
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Affiliation(s)
- Yayoi Onda
- Department of Bioscience and Nano-biotechnology Research Centre, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
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11
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Lysenko EA. Plant sigma factors and their role in plastid transcription. PLANT CELL REPORTS 2007; 26:845-59. [PMID: 17356883 DOI: 10.1007/s00299-007-0318-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/13/2007] [Accepted: 02/09/2007] [Indexed: 05/08/2023]
Abstract
Plant sigma factors determine the promoter specificity of the major RNA polymerase of plastids and thus regulate the first level of plastome gene expression. In plants, sigma factors are encoded by a small family of nuclear genes, and it is not yet clear if the family members are functionally redundant or each paralog plays a particular role. The review presents the analysis of the information on plant sigma factors obtained since their discovery a decade ago and focuses on similarities and differences in structure and functions of various paralogs. Special attention is paid to their interaction with promoters, the regulation of their expression, and their role in the development of a whole plant. The analysis suggests that though plant sigma factors are basically similar, at least some of them perform distinct functions. Finally, the work presents the scheme of this gene family evolution in higher plants.
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Affiliation(s)
- Eugene A Lysenko
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya ul. 35, 127276 Moscow, Russia.
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12
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Transcription and transcriptional regulation in plastids. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0232] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Demarsy E, Courtois F, Azevedo J, Buhot L, Lerbs-Mache S. Building up of the plastid transcriptional machinery during germination and early plant development. PLANT PHYSIOLOGY 2006; 142:993-1003. [PMID: 16963522 PMCID: PMC1630747 DOI: 10.1104/pp.106.085043] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 08/30/2006] [Indexed: 05/11/2023]
Abstract
The plastid genome is transcribed by three different RNA polymerases, one is called plastid-encoded RNA polymerase (PEP) and two are called nucleus-encoded RNA polymerases (NEPs). PEP transcribes preferentially photosynthesis-related genes in mature chloroplasts while NEP transcribes preferentially housekeeping genes during early phases of plant development, and it was generally thought that during plastid differentiation the building up of the NEP transcription system precedes the building up of the PEP transcription system. We have now analyzed in detail the establishment of the two different transcription systems, NEP and PEP, during germination and early seedling development on the mRNA and protein level. Experiments have been performed with two different plant species, Arabidopsis (Arabidopsis thaliana) and spinach (Spinacia oleracea). Results show that the building up of the two different transcription systems is different in the two species. However, in both species NEP as well as PEP are already present in seeds, and results using Tagetin as a specific inhibitor of PEP activity demonstrate that PEP is important for efficient germination, i.e. PEP is already active in not yet photosynthetically active seed plastids.
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Affiliation(s)
- Emilie Demarsy
- Laboratoire Plastes et Differenciation Cellulaire, Université Joseph Fourier and Centre National de la Recherche Scientifique, F-38041 Grenoble, France
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Wagner R, Pfannschmidt T. Eukaryotic transcription factors in plastids--Bioinformatic assessment and implications for the evolution of gene expression machineries in plants. Gene 2006; 381:62-70. [PMID: 16934950 DOI: 10.1016/j.gene.2006.06.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 06/01/2006] [Accepted: 06/19/2006] [Indexed: 10/24/2022]
Abstract
The expression of genes in higher plant chloroplasts includes a complex transcriptional regulation which can be explained only in part with the action of the actually known components of the transcriptional machinery. This suggests the existence of still unknown important regulatory factors which influence chloroplast transcription. In order to test if such factors could exist we performed in silico analyses of Arabidopsis genes encoding putative transcription factors looking for putative N-terminal chloroplast transit peptides in the amino acid sequences. Our results suggest that 48 (and maybe up to 100) transcription factors of eukaryotic origin are likely to be imported into plastids. None of them has been described yet. This set of transcription factors highly expands the actually known regulation capacity of the chloroplast transcription machinery and provides a possible explanation for the complex initiation patterns of chloroplast transcripts. As consequence of a massive import of eukaryotic transcription factors a comprehensive reconstruction of the ancient prokaryotic gene expression machinery must be assumed resulting in a novel compatible combination of eukaryotic and prokaryotic protein components. In turn, the opposite process has been induced in the nucleus by the integration of prokaryotic components of the plastid ancestor via its loss of genes during endosymbiosis. Thus, a mutual exchange of regulatory factors, i.e. transcription factors occurred which resulted in the unique signalling network of today's plants. An evolutionary model of how this could have emerged during endosymbiosis in a timely coordinated manner is proposed.
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Affiliation(s)
- Raik Wagner
- Junior Research Group Plant acclimation to environmental changes: Protein analysis by MS, Department for Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
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Shiina T, Tsunoyama Y, Nakahira Y, Khan MS. Plastid RNA polymerases, promoters, and transcription regulators in higher plants. INTERNATIONAL REVIEW OF CYTOLOGY 2005; 244:1-68. [PMID: 16157177 DOI: 10.1016/s0074-7696(05)44001-2] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Plastids are semiautonomous plant organelles exhibiting their own transcription-translation systems that originated from a cyanobacteria-related endosymbiotic prokaryote. As a consequence of massive gene transfer to nuclei and gene disappearance during evolution, the extant plastid genome is a small circular DNA encoding only ca. 120 genes (less than 5% of cyanobacterial genes). Therefore, it was assumed that plastids have a simple transcription-regulatory system. Later, however, it was revealed that plastid transcription is a multistep gene regulation system and plays a crucial role in developmental and environmental regulation of plastid gene expression. Recent molecular and genetic approaches have identified several new players involved in transcriptional regulation in plastids, such as multiple RNA polymerases, plastid sigma factors, transcription regulators, nucleoid proteins, and various signaling factors. They have provided novel insights into the molecular basis of plastid transcription in higher plants. This review summarizes state-of-the-art knowledge of molecular mechanisms that regulate plastid transcription in higher plants.
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Affiliation(s)
- Takashi Shiina
- Faculty of Human Environment, Kyoto Prefectural University, Kyoto 606-8522, Japan
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Mochizuki T, Onda Y, Fujiwara E, Wada M, Toyoshima Y. Two independent light signals cooperate in the activation of the plastid psbD blue light-responsive promoter in Arabidopsis. FEBS Lett 2004; 571:26-30. [PMID: 15280012 DOI: 10.1016/j.febslet.2004.06.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 06/21/2004] [Accepted: 06/21/2004] [Indexed: 10/26/2022]
Abstract
The psbD blue light-responsive promoter (BLRP), whose activation has been considered to require strong blue light, is recognized only by SIG5 among six sigma factors of plastid RNA polymerase in Arabidopsis. We found SIG5 transcript accumulation was rapidly induced after a 30-min induction time by blue light (470 nm) with an intensity threshold of 5 micromol m(-2)s(-1) through cryptochromes. Besides this weak blue light, the psbD BLRP activation required the stronger light such as 50 micromol m(-2)s(-1) irrespective of blue or red light (660 nm). Thus, the two independent light signalings, the cryptochrome-mediated signaling to induce SIG5 transcription and the stronger light-dependent signaling, cooperate to activate the psbD BLRP.
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Affiliation(s)
- Takateru Mochizuki
- Department of Bioscience and Nano-biotechnology Research Center, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan
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Nagashima A, Hanaoka M, Shikanai T, Fujiwara M, Kanamaru K, Takahashi H, Tanaka K. The Multiple-Stress Responsive Plastid Sigma Factor, SIG5, Directs Activation of the psbD Blue Light-Responsive Promoter (BLRP) in Arabidopsis thaliana. ACTA ACUST UNITED AC 2004; 45:357-68. [PMID: 15111710 DOI: 10.1093/pcp/pch050] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Transcription in higher plant plastids is performed by two types of RNA polymerases called NEP and PEP, and expression of photosynthesis genes in chloroplasts is largely dependent on PEP, a eubacteria-type multi-subunit enzyme. The transcription specificity of PEP is modulated by six nuclear-encoded sigma factors (SIG1 to SIG6) in Arabidopsis thaliana. Here, we show that one of the six sigma factors, SIG5, is induced under various stress conditions, such as high light, low temperature, high salt and high osmotic conditions. Interestingly, transcription from the psbD blue light-responsive promoter (psbD-BLRP) was activated by not only light but also various stresses, and the transcription and the transcriptional activation of psbD-BLRP were abolished in a sig5-2 mutant. This suggests that the PEP holoenzyme containing SIG5 transcribes the psbD-BLRP in response to multiple stresses. Since the seed germination under saline conditions and recovery from damage to the PSII induced by high light were delayed in the sig5-2 mutant, we postulate that SIG5 protects plants from stresses by enhancing repair of the PSII reaction center.
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Affiliation(s)
- Akitomo Nagashima
- Laboratory of Molecular Genetics, Department of Molecular Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
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19
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Tsunoyama Y, Ishizaki Y, Morikawa K, Kobori M, Nakahira Y, Takeba G, Toyoshima Y, Shiina T. Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. Proc Natl Acad Sci U S A 2004; 101:3304-9. [PMID: 14976253 PMCID: PMC365785 DOI: 10.1073/pnas.0308362101] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Indexed: 11/18/2022] Open
Abstract
Light is one of the most important environmental factors regulating expression of photosynthesis genes. The plastid psbD gene encoding the photosystem II reaction center protein D2 is under the control of a unique blue light responsive promoter (BLRP) that is transcribed by a bacterial-type plastid RNA polymerase (PEP). Promoter recognition of PEP is mediated by one of the six nuclear-encoded sigma factors in Arabidopsis. The replacement of the plastid sigma factor associated with PEP may be the major mechanism for switching of plastid transcription pattern in response to environmental and developmental signals. This study demonstrates that AtSig5 is a unique sigma factor that is essential for psbD BLRP activity. A T-DNA insertional mutant with reduced AtSIG5 expression resulted in loss of primary transcripts from the psbD BLRP. Furthermore, transient overexpression of AtSig5 in dark-adapted protoplasts specifically elevated psbD and psbA transcription activities. On the other hand, overproduction of AtSig2 enhanced the transcription of psbA gene and trnE operon, but not psbD transcription. The AtSIG5 gene is phylogenetically distinct from other plastid sigma factors, and its expression is induced exclusively by blue light. We propose that AtSig5 acts as a mediator of blue light signaling that specifically activates the psbD BLRP in response to blue light in Arabidopsis.
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Affiliation(s)
- Yuichi Tsunoyama
- Radioisotope Research Center, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku Kyoto 606-8502, Japan
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20
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Abstract
Chloroplasts are the important plant cell organelles where photosynthesis takes place. Throughout this process, reaction center proteins are degraded and subsequently replenished by redox-responsive gene expression. In addition to well defined posttranscriptional mechanisms at the RNA and protein level, the transcription of chloroplast DNA into RNA precursors has been a focal point of studies in this area. Evidence has become available for a central role of a redox-responsive protein kinase named plastid transcription kinase (PTK) because of its association with the chloroplast transcription complex. The recent cloning of the PTK gene has resulted in a full-length cDNA for a protein related to the catalytic alpha subunit of nucleocytoplasmic casein kinase (CK2), yet with an additional chloroplast transit peptide. The corresponding protein, termed cpCK2alpha, was shown to be associated with the major organellar RNA polymerase, PEP-A. Both authentic PTK and recombinant cpCK2alpha have comparable general properties in vitro, and both are subject to regulation by the redox-reactive reagent glutathione. Based on the physical and functional equivalence, it is anticipated that the cloned protein can help clarify the functional role of the transcription kinase in vivo, including the identification of interaction partners at the interface between photosynthetic redox signaling and gene expression.
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Affiliation(s)
- Gerhard Link
- Department of Plant Cell Physiology and Molecular Biology, University of Bochum, D-44780 Bochum, Germany.
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21
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Suzuki JY, Sriraman P, Svab Z, Maliga P. Unique architecture of the plastid ribosomal RNA operon promoter recognized by the multisubunit RNA polymerase in tobacco and other higher plants. THE PLANT CELL 2003; 15:195-205. [PMID: 12509531 PMCID: PMC143491 DOI: 10.1105/tpc.007914] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Accepted: 10/24/2002] [Indexed: 05/20/2023]
Abstract
Expression of the plastid rRNA operon (rrn) during development is highly regulated at the level of transcription. The plastid rrn operon in most higher plants is transcribed by the plastid-encoded RNA polymerase (PEP), the multisubunit plastid RNA polymerase from PrrnP1, a sigma(70)-type promoter with conserved -10 and -35 core promoter elements. To identify functionally important sequences, the tobacco PrrnP1 was dissected in vivo and in vitro. Based on in vivo deletion analysis, sequences upstream of nucleotide -83 do not significantly contribute to promoter function. The in vitro analyses identified an essential hexameric sequence upstream of the -35 element (GTGGGA; the rRNA operon upstream activator [RUA]) that is conserved in monocot and dicot species and suggested that the -10 element plays only a limited role in PrrnP1 recognition. Mutations in the initial transcribed sequence (+9 to +14) enhanced transcription, the characteristic of strong promoters in prokaryotes. We propose that sigma interaction with the -10 element in PrrnP1 is replaced in part by direct PEP-RUA (protein-DNA) interaction or by protein-protein interaction between the PEP and an RUA binding transcription factor.
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Affiliation(s)
- Jon Y Suzuki
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020, USA
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22
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Tsunoyama Y, Morikawa K, Shiina T, Toyoshima Y. Blue light specific and differential expression of a plastid sigma factor, Sig5 in Arabidopsis thaliana. FEBS Lett 2002; 516:225-8. [PMID: 11959137 DOI: 10.1016/s0014-5793(02)02538-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The transcription of plastid gene psbD is under the control of the BLRP (blue-light-responsive promoter) recognized by plastid-encoded RNA polymerase, in which nuclear-encoded sigma factors play a crucial role in the promoter recognition. We examined the effects of light on mRNA levels of six different SIG genes in Arabidopsis and found that blue light extensively induced the accumulation of SIG5 transcripts, but red light did not. The blue light specificity was not observed in the accumulations of remaining five SIG genes. The blue light dependency of the SIG5 expression well explains the light-dependent behavior of the psbD BLRP.
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Affiliation(s)
- Yuichi Tsunoyama
- Radioisotope Research Center, Kyoto University, Kitashirakawa-oiwake-cho, Kyoto 606-8502, Sakyo-ku, Japan
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23
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Thum KE, Kim M, Christopher DA, Mullet JE. Cryptochrome 1, cryptochrome 2, and phytochrome a co-activate the chloroplast psbD blue light-responsive promoter. THE PLANT CELL 2001; 13:2747-60. [PMID: 11752385 PMCID: PMC139486 DOI: 10.1105/tpc.010345] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2001] [Accepted: 09/07/2001] [Indexed: 05/20/2023]
Abstract
The reaction center core of photosystem II is composed of two chlorophyll binding proteins, D1 and D2, that are encoded by the chloroplast genes psbA and psbD. These chlorophyll binding proteins are damaged during photochemistry, especially under high irradiance. Photosystem II function is maintained under these conditions through turnover and resynthesis of D1 and D2. Blue light-activated transcription of psbD from a special light-responsive promoter is part of the repair system. In this study, light-activated chloroplast and psbD transcription were studied after dark adaptation of 21-day-old light-grown Arabidopsis plants. Illumination of dark-adapted plants with red light increased chloroplast transcription activity and transcription from the psbD light-responsive promoter. Blue light further increased chloroplast transcription activity and stimulated differential transcription from the psbD light-responsive promoter. Photoreceptor mutants showed that blue light-specific activation of chloroplast transcription and the psbD light-responsive promoter involve cryptochrome 1 (cry1) or cryptochrome 2 (cry2) and phytochrome A (phyA). Blue light-induced activation of the psbD light-responsive promoter was normal in det2-1 and hy5-1 but attenuated in det3-1. Therefore, cry1/cry2/phyA-mediated blue light activation of the psbD light-responsive promoter in 21-day-old Arabidopsis plants does not involve hy5, a transcription factor that mediates other phyA and blue light-induced responses.
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Affiliation(s)
- K E Thum
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas 77843, USA
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24
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Thum KE, Kim M, Christopher DA, Mullet JE. Cryptochrome 1, cryptochrome 2, and phytochrome a co-activate the chloroplast psbD blue light-responsive promoter. THE PLANT CELL 2001. [PMID: 11752385 DOI: 10.1105/tpc.13.12.2747] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The reaction center core of photosystem II is composed of two chlorophyll binding proteins, D1 and D2, that are encoded by the chloroplast genes psbA and psbD. These chlorophyll binding proteins are damaged during photochemistry, especially under high irradiance. Photosystem II function is maintained under these conditions through turnover and resynthesis of D1 and D2. Blue light-activated transcription of psbD from a special light-responsive promoter is part of the repair system. In this study, light-activated chloroplast and psbD transcription were studied after dark adaptation of 21-day-old light-grown Arabidopsis plants. Illumination of dark-adapted plants with red light increased chloroplast transcription activity and transcription from the psbD light-responsive promoter. Blue light further increased chloroplast transcription activity and stimulated differential transcription from the psbD light-responsive promoter. Photoreceptor mutants showed that blue light-specific activation of chloroplast transcription and the psbD light-responsive promoter involve cryptochrome 1 (cry1) or cryptochrome 2 (cry2) and phytochrome A (phyA). Blue light-induced activation of the psbD light-responsive promoter was normal in det2-1 and hy5-1 but attenuated in det3-1. Therefore, cry1/cry2/phyA-mediated blue light activation of the psbD light-responsive promoter in 21-day-old Arabidopsis plants does not involve hy5, a transcription factor that mediates other phyA and blue light-induced responses.
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Affiliation(s)
- K E Thum
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas 77843, USA
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25
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Thum KE, Kim M, Morishige DT, Eibl C, Koop HU, Mullet JE. Analysis of barley chloroplast psbD light-responsive promoter elements in transplastomic tobacco. PLANT MOLECULAR BIOLOGY 2001; 47:353-66. [PMID: 11587507 DOI: 10.1023/a:1011616400264] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The plastid gene psbD encodes D2, a photosystem II reaction center chlorophyll-binding protein. psbD is transcribed from a conserved chloroplast promoter that is activated by blue, white, or UV-A light. In this study, various forms of the barley (Hordeum vulgare L.) chloroplast psbD-LRP were fused to the uidA reporter gene and introduced into the tobacco (Nicotiana tabacum L.) plastid genome through homologous recombination. Primer extension analysis of transcripts from the psbD-LRP-uidA construct showed that the barley psbD-LRP was activated in tobacco by blue or white light. Transcription from this construct was also regulated by circadian cycling indicating that the barley psbD-LRP could respond to light modulated regulatory pathways in tobacco. Mutation of the psbD-LRP prokaryotic -10 promoter element reduced transcription to very low levels in all light regimes. In contrast, mutation of a prokaryotic -35 promoter element had no effect on transcription from the psbD-LRP. Deletion or mutation of an upstream activating element, the AAG-box (-36 to -64), also reduced transcription from the construct to very low levels. In contrast, deletion of the upstream PGT-box (-71 to -100) did not alter promoter activation by blue light, or responsiveness to circadian cycling. These in vivo studies confirm the importance of the psbD-LRP -10 promoter element and AAG-box in light regulation and demonstrate that these elements are sufficient to mediate circadian cycling of the barley psbD promoter.
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Affiliation(s)
- K E Thum
- Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843, USA
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26
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Sato N, Ohta N. DNA-binding specificity and dimerization of the DNA-binding domain of the PEND protein in the chloroplast envelope membrane. Nucleic Acids Res 2001; 29:2244-50. [PMID: 11376142 PMCID: PMC55719 DOI: 10.1093/nar/29.11.2244] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The PEND protein is a DNA-binding protein in the inner envelope membrane of a developing chloroplast, which may anchor chloroplast nucleoids. Here we report the DNA-binding characteristics of the N-terminal basic region plus leucine zipper (bZIP)-like domain of the PEND protein that we call cbZIP domain. The basic region of the cbZIP domain diverges significantly from the basic region of known bZIP proteins that contain a bipartite nuclear localization signal. However, the cbZIP domain has the ability to dimerize in vitro. Selection of binding sites from a random sequence pool indicated that the cbZIP domain preferentially binds to a canonical sequence, TAAGAAGT. The binding site was also confirmed by gel mobility shift analysis using a representative binding site within the chloroplast DNA. These results suggest that the cbZIP domain is a unique DNA-binding domain of the chloroplast protein.
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Affiliation(s)
- N Sato
- Department of Molecular Biology, Faculty of Science, Saitama University, 255 Shimo-Ohkubo, Saitama, Saitama Prefecture 338-8570, Japan.
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27
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Baba K, Nakano T, Yamagishi K, Yoshida S. Involvement of a nuclear-encoded basic helix-loop-helix protein in transcription of the light-responsive promoter of psbD. PLANT PHYSIOLOGY 2001; 125:595-603. [PMID: 11161017 PMCID: PMC64861 DOI: 10.1104/pp.125.2.595] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2000] [Revised: 06/18/2000] [Accepted: 10/03/2000] [Indexed: 05/20/2023]
Abstract
In the chloroplast psbD light-responsive promoter (LRP), a highly conserved sequence exists upstream from the bacterial -10/-35 elements. Multiple sequence-specific DNA binding proteins are predicted to bind to the conserved sequence as transcription factors. Using yeast one-hybrid screening of an Arabidopsis cDNA library, a possible DNA binding protein of the psbD LRP upstream sequence was identified. The protein, designated PTF1, is a novel protein of 355 amino acids (estimated molecular weight of 39.6) that contains a basic helix-loop-helix DNA binding motif in the predicted N-terminal region of the mature protein. Transient expression assay of PTF1-GFP fusion protein showed that PTF1 was localized in chloroplasts. Using the modified DNA sequence in the one-hybrid system, the ACC repeat was shown to be essential for PTF1 binding. The rate of psbD LRP mRNA accumulation was reduced in a T-DNA-inserted Arabidopsis ptf1 mutant. Compared with wild-type plants, the mutant had pale green cotyledons and its growth was inhibited under short-day conditions. These results suggest that PTF1 is a trans-acting factor of the psbD LRP.
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Affiliation(s)
- K Baba
- RIKEN, The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan.
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28
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29
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Abstract
Expression of plastid genes is controlled at both transcriptional and post-transcriptional levels in response to developmental and environmental signals. In many cases this regulation is mediated by nuclear-encoded proteins acting in concert with the endogenous plastid gene expression machinery. Transcription in plastids is accomplished by two distinct RNA polymerase enzymes, one of which resembles eubacterial RNA polymerases in both subunit structure and promoter recognition properties. The holoenzyme contains a catalytic core composed of plastid-encoded subunits, assembled with a nuclear-encoded promoter-specificity factor, sigma. Based on examples of transcriptional regulation in bacteria, it is proposed that differential activation of sigma factors may provide the nucleus with a mechanism to control expression of groups of plastid genes. Hence, much effort has focused on identifying and characterizing sigma-like factors in plants. While fractionation studies had identified several candidate sigma factors in purified RNA polymerase preparations, it was only 4 years ago that the first sigma factor genes were cloned from two photosynthetic eukaryotes, both of which were red algae. More recently this achievement has extended to the identification of families of sigma-like factor genes from several species of vascular plants. Now, efforts in the field are directed at understanding the roles in plastid transcription of each member of the rapidly expanding plant sigma factor gene family. Recent results suggest that accumulation of individual sigma-like factors is controlled by light, by plastid type and/or by a particular stage of chloroplast development. These data mesh nicely with accumulating evidence that the core sigma-binding regions of plastid promoters mediate regulated transcription in response to light-regime and plastid type or developmental state. In this review I will outline progress made to date in identifying and characterizing the sigma-like factors of plants, and in dissecting their potential roles in chloroplast gene expression.
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Affiliation(s)
- L A Allison
- Department of Biochemistry, University of Nebraska, NE 68588-0664, Lincoln, USA.
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30
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Bligny M, Courtois F, Thaminy S, Chang CC, Lagrange T, Baruah-Wolff J, Stern D, Lerbs-Mache S. Regulation of plastid rDNA transcription by interaction of CDF2 with two different RNA polymerases. EMBO J 2000; 19:1851-60. [PMID: 10775269 PMCID: PMC302015 DOI: 10.1093/emboj/19.8.1851] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The plastid genome is known to be transcribed by a plastid-encoded prokaryotic-type RNA polymerase (PEP) and by a nucleus-encoded phage-type RNA polymerase (NEP). The spinach plastid rrn operon promoter region harbours three different, overlapping promoters. Two of them are of the prokaryotic type. The third promoter is a non-consensus-type NEP promoter. We separated three different transcriptional activities from spinach chloroplasts: PEP, the phage-type RNA polymerase NEP-1, and a third, hitherto undescribed transcriptional activity (NEP-2). NEP-2 specifically transcribes the rrn operon in the presence of the transcription factor CDF2. CDF2 was previously shown to recruit PEP to the rrn promoter to repress transcription. Together, our results suggest the existence of a third RNA polymerase in plastids and a mechanism of rDNA transcriptional regulation that is based on the interaction of the transcription factor CDF2 with two different transcriptional systems.
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Affiliation(s)
- M Bligny
- Laboratoire de Génétique Moléculaire des Plantes, Université Joseph Fourier and Centre National de la Recherche Scientifique, BP 53X, F-38041 Grenoble, France
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31
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Morikawa K, Ito S, Tsunoyama Y, Nakahira Y, Shiina T, Toyoshima Y. Circadian-regulated expression of a nuclear-encoded plastid sigma factor gene (sigA) in wheat seedlings. FEBS Lett 1999; 451:275-8. [PMID: 10371204 DOI: 10.1016/s0014-5793(99)00593-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The activity of a light-responsive psbD promoter in plastids is known to be regulated by a circadian clock. However, the mechanism of the circadian regulation of the psbD light-responsive promotor, which is recognized by an Escherichia coli-type RNA polymerase, is not yet known. We examined the time course of mRNA accumulation of two E. coli-type RNA polymerase subunit genes, sigA and rpoA, under a continuous light condition after 12 h light/12 h dark entrainment. Accumulation of the sigA mRNA was found to be regulated by a circadian clock, while rpoA mRNA did not show any significant oscillation throughout the experiment.
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Affiliation(s)
- K Morikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Japan
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32
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Abstract
The nuclear genome of the model plant Arabidopsis thaliana contains a small gene family consisting of three genes encoding RNA polymerases of the single-subunit bacteriophage type. There is evidence that similar gene families also exist in other plants. Two of these RNA polymerases are putative mitochondrial enzymes, whereas the third one may represent the nuclear-encoded RNA polymerase (NEP) active in plastids. In addition, plastid genes are transcribed from another, entirely different multisubunit eubacterial-type RNA polymerase, the core subunits of which are encoded by plastid genes [plastid-encoded RNA polymerase (PEP)]. This core enzyme is complemented by one of several nuclear-encoded sigma-like factors. The development of photosynthetically active chloroplasts requires both PEP and NEP. Most NEP promoters show certain similarities to mitochondrial promoters in that they include the sequence motif 5'-YRTA-3' near the transcription initiation site. PEP promoters are similar to bacterial promoters of the -10/-35 sigma 70 type.
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Affiliation(s)
- W R Hess
- Institute of Biology, Humboldt University, Berlin, Germany
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33
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Chang CC, Sheen J, Bligny M, Niwa Y, Lerbs-Mache S, Stern DB. Functional analysis of two maize cDNAs encoding T7-like RNA polymerases. THE PLANT CELL 1999; 11:911-26. [PMID: 10330475 PMCID: PMC144232 DOI: 10.1105/tpc.11.5.911] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have characterized two maize cDNAs, rpoTm and rpoTp, that encode putative T7-like RNA polymerases. In vivo cellular localization experiments using transient expression of the green fluorescent protein suggest that their encoded proteins are targeted exclusively to mitochondria and plastids, respectively. An antibody raised against the C terminus of the rpoTp gene product identified mitochondrial polypeptides of approximately 100 kD. Their presence was correlated with RNA polymerase activity, and the antibody inhibited mitochondrial in vitro transcription activity. Together, these results strongly suggest that the product of rpoTm is involved in maize mitochondrial transcription. By contrast, immunoblot analysis and an antibody-linked polymerase assay indicated that rpoTp specifies a plastid RNA polymerase component. A quantitative reverse transcription-polymerase chain reaction assay was used to study the transcription of rpoTp and rpoTm in different tissues and under different environmental conditions. Although both genes were constitutively expressed, rpoTm transcripts were generally more prevalent in nonphotosynthetic tissues, whereas an increase in rpoTp transcripts paralleled chloroplast development. We suggest that these two genes encode constitutive components of the organelle transcription machinery but that their expression is nonetheless subject to modulation during plant development.
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Affiliation(s)
- C C Chang
- Boyce Thompson Institute for Plant Research, Tower Road, Cornell University, Ithaca, New York 14853-1801, USA
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34
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Satoh J, Baba K, Nakahira Y, Tsunoyama Y, Shiina T, Toyoshima Y. Developmental stage-specific multi-subunit plastid RNA polymerases (PEP) in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 18:407-415. [PMID: 10406124 DOI: 10.1046/j.1365-313x.1999.00465.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Most photosystem I and II plastid genes are transcribed by a plastid encoded Escherichia coli-like RNA polymerase (PEP). In this study, we show that both promoter selectivity and light-dependency of PEP change dramatically during development in wheat leaves. In the leaf tip, psbA and psbD promoter activities are light induced, whilst psbC, psbE and 16S rRNA promoters do not function efficiently irrespective of light conditions. In contrast to the leaf tip, in the basal portion all PEP promoters studied function in the dark as well as the light, except for psbD. Using in vitro transcription, we found that PEP in the illuminated leaf tip can initiate transcription from the -35 destructed psbA promoter, but the -35 element is essential for transcription in the basal portion. There is an extended -10 element in the psbA promoter, recognized by the PEP in the illuminated leaf tip or purified sigma 70-type Escherichia coli RNA polymerase but not by the PEP in the leaf base. These results suggest that during wheat leaf development, PEP in the leaf base that is functional for most PEP promoters even in the dark is replaced by the light-dependent PEP selectively transcribing the psbA and psbD promoters.
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Affiliation(s)
- J Satoh
- Graduate School of Human and Environmental Studies, Kyoto University, Japan
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35
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Tan S, Troxler RF. Characterization of two chloroplast RNA polymerase sigma factors from Zea mays: photoregulation and differential expression. Proc Natl Acad Sci U S A 1999; 96:5316-21. [PMID: 10220463 PMCID: PMC21861 DOI: 10.1073/pnas.96.9.5316] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two distinct cDNAs encoding putative sigma factors of plastid RNA polymerase were isolated from Zea mays, a C4 plant. The deduced amino acid sequences of both cDNAs possess all four highly conserved domains proposed for recognition of -10 and -35 promoter elements, core complex binding, DNA binding, and melting. These two cDNAs are designated sig1 and sig2. Phylogenetic analysis of available plastid sigma factors indicated that they were probably the descendants of cyanobacterial principal sigma factors. Southern blots probed with sig1 and sig2 revealed that both genes exist in the maize nuclear genome as single-copy genes, but low-stringency hybridization suggested the presence of a multigene family of maize plastid sigma factors. Transcription of sig1 and sig2 is light inducible and tissue specific. Transcripts of sig1 and sig2 were abundant in greening leaf tissues; sig2 (but not sig1) was barely detectable in etiolated leaves and neither was detectable in roots. Immunological studies using a peptide antibody against an epitope in subdomain 2.4 of Sig1 revealed 50-kDa and 60-kDa immunoreactive proteins in maize chloroplasts. Reduced levels of the 60-kDa immunoreactive protein were detected in etioplasts, and no immunoreactive proteins were observed in roots. Collectively, the data suggest that the nuclear genes, sig1 and sig2, may play a role in differential expression of plastid genes during chloroplast biogenesis.
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Affiliation(s)
- S Tan
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
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36
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Kim M, Christopher DA, Mullet JE. ADP-Dependent phosphorylation regulates association of a DNA-binding complex with the barley chloroplast psbD blue-light-responsive promoter. PLANT PHYSIOLOGY 1999; 119:663-70. [PMID: 9952463 PMCID: PMC32144 DOI: 10.1104/pp.119.2.663] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/1998] [Accepted: 11/06/1998] [Indexed: 05/20/2023]
Abstract
The chloroplast gene psbD encodes D2, a chlorophyll-binding protein located in the photosystem II reaction center. Transcription of psbD in higher plants involves at least three promoters, one of which is regulated by blue light. The psbD blue-light-regulated promoter (BLRP) consists of a -10 promoter element and an activating complex, AGF, that binds immediately upstream of -35. A second sequence-specific DNA-binding complex, PGTF, binds upstream of AGF between -71 and -100 in the barley (Hordeum vulgare) psbD BLRP. In this study we report that ADP-dependent phosphorylation selectively inhibits the binding of PGTF to the barley psbD BLRP. ATP at high concentrations (1-5 mM) inhibits PGTF binding, but in the presence of phosphocreatine and phosphocreatine kinase, this capacity is lost, presumably due to scavenging of ADP. ADP inhibits PGTF binding at relatively low concentrations (0.1 mM), whereas other nucleotides are unable to mediate this response. ADP-mediated inhibition of PGTF binding is reduced in the presence of the protein kinase inhibitor K252a. This and other results suggest that ADP-dependent phosphorylation of PGTF (or some associated protein) inhibits binding of PGTF to the psbD BLRP and reduces transcription. ADP-dependent phosphorylation is expected to increase in darkness in parallel with the rise in ADP levels in chloroplasts. ADP-dependent phosphorylation in chloroplasts may, therefore, in coordination, inactivate enzymes involved in carbon assimilation, protein synthesis, and transcription during diurnal light/dark cycles.
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Affiliation(s)
- M Kim
- Department of Biochemistry and Biophysics, Crop Biotechnology Center, Texas A&M University, College Station, Texas 77843, USA
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37
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Nakahira Y, Baba K, Yoneda A, Shiina T, Toyoshima Y. Circadian-regulated transcription of the psbD light-responsive promoter in wheat chloroplasts. PLANT PHYSIOLOGY 1998; 118:1079-88. [PMID: 9808753 PMCID: PMC34781 DOI: 10.1104/pp.118.3.1079] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/1998] [Accepted: 08/17/1998] [Indexed: 05/20/2023]
Abstract
The level of mRNAs derived from the plastid-encoded psbD light-responsive promoter (LRP) is controlled by a circadian clock(s) in wheat (Triticum aestivum). The circadian oscillations in the psbD LRP mRNA level persisted for at least three cycles in continuous light and for one cycle in continuous dark, with maxima in subjective morning and minima in subjective early night. In vitro transcription in chloroplast extracts revealed that the circadian cycles in the psbD LRP mRNA level were dominantly attributed to the circadian-regulated transcription of the psbD LRP. The effects of various mutations introduced into the promoter region on the psbD LRP activity in vitro suggest the existence of two positive elements located between -54 and -36, which generally enhance the transcription activity, and an anomalous core promoter structure lacking the functional "-35" element, which plays a crucial role in the circadian fluctuation and light dependency of psbD LRP transcription activity.
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Affiliation(s)
- Y Nakahira
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatu-cho, Sakyo-ku, Kyoto 606-8501, Japan
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38
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Shiina T, Allison L, Maliga P. rbcL Transcript levels in tobacco plastids are independent of light: reduced dark transcription rate is compensated by increased mRNA stability. THE PLANT CELL 1998; 10:1713-22. [PMID: 9761797 PMCID: PMC143938 DOI: 10.1105/tpc.10.10.1713] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The plastid rbcL gene, encoding the large subunit of ribulose-1, 5-bisphosphate carboxylase, in higher plants is transcribed from a sigma70 promoter by the eubacterial-type RNA polymerase. To identify regulatory elements outside of the rbcL -10/-35 promoter core, we constructed transplastomic tobacco plants with uidA reporter genes expressed from rbcL promoter derivatives. Promoter activity was characterized by measuring steady state levels of uidA mRNA on RNA gel blots and by measuring promoter strength in run-on transcription assays. We report here that the rbcL core promoter is sufficient to obtain wild-type rates of transcription. Furthermore, the rates of transcription were up to 10-fold higher in light-grown leaves than in dark-adapted plants. Although the rates of transcription were lower in the dark, rbcL mRNA accumulated to similar levels in light-grown and dark-adapted leaves. Accumulation of uidA mRNA from most rbcL promoter deletion derivatives directly reflected the relative rates of transcription: high in the light-grown and low in the dark-adapted leaves. However, uidA mRNA accumulated to high levels in a light-independent fashion as long as a segment encoding a stem-loop structure in the 5' untranslated region was included in the promoter construct. This finding indicates that lower rates of rbcL transcription in the dark are compensated by increased mRNA stability.
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MESH Headings
- Base Sequence
- DNA Primers/genetics
- DNA, Plant/genetics
- Darkness
- Drug Stability
- Gene Expression
- Genes, Plant
- Genes, Reporter
- Light
- Molecular Sequence Data
- Plant Proteins/genetics
- Plants, Genetically Modified
- Plants, Toxic
- Plastids/genetics
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Ribulose-Bisphosphate Carboxylase/genetics
- Sequence Homology, Nucleic Acid
- Nicotiana/genetics
- Nicotiana/metabolism
- Nicotiana/radiation effects
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Affiliation(s)
- T Shiina
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, New Jersey 08854-8020, USA
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Leon P, Arroyo A, Mackenzie S. NUCLEAR CONTROL OF PLASTID AND MITOCHONDRIAL DEVELOPMENT IN HIGHER PLANTS. ACTA ACUST UNITED AC 1998; 49:453-480. [PMID: 15012242 DOI: 10.1146/annurev.arplant.49.1.453] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nucleus must coordinate organelle biogenesis and function on a cell and tissue-specific basis throughout plant development. The vast majority of plastid and mitochondrial proteins and components involved in organelle biogenesis are encoded by nuclear genes. Molecular characterization of nuclear mutants has illuminated chloroplast development and function. Fewer mutants exist that affect mitochondria, but molecular and biochemical approaches have contributed to a greater understanding of this organelle. Similarities between organelles and prokaryotic regulatory molecules have been found, supporting the prokaryotic origin of chloroplasts and mitochondria. A striking characteristic for both mitochondria and chloroplast is that most regulation is posttranscriptional.
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Affiliation(s)
- P. Leon
- Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia UNAM, Cuernavaca, Morelos 62250 Mexico; e-mail: , Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana 47907
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40
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Hong S, Spreitzer RJ. Nuclear-gene mutations suppress a defect in the expression of the chloroplast-encoded large subunit of ribulose-1,5-bisphosphate Carboxylase/Oxygenase. PLANT PHYSIOLOGY 1998; 116:1387-1392. [PMID: 9536056 PMCID: PMC35046 DOI: 10.1104/pp.116.4.1387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/1997] [Accepted: 12/15/1997] [Indexed: 05/22/2023]
Abstract
The green alga Chlamydomonas reinhardtii mutant 76-5EN lacks photosynthesis because of a nuclear-gene mutation that specifically inhibits expression of the chloroplast gene encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39). Photosynthesis-competent revertants were selected from mutant 76-5EN to explore the possibility of increasing Rubisco expression. Genetic analysis of 10 revertants revealed that most arose from suppressor mutations in nuclear genes distinct from the original 76-5EN mutant gene. The revertant strains have regained various levels of Rubisco holoenzyme, but none of the suppressor mutations increased Rubisco expression above the wild-type level in either the presence or absence of the 76-5EN mutation. One suppressor mutation, S107-4B, caused a temperature-conditional, photosynthesis-deficient phenotype in the absence of the original 76-5EN mutation. The S107-4B strain was unable to grow photosynthetically at 35 degreesC, but it expressed a substantial level of Rubisco holoenzyme. Whereas the 76-5EN gene encodes a nuclear factor that appears to be required for the transcription of the Rubisco large-subunit gene, the S107-4B nuclear gene may be required for the expression of other chloroplast genes.
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Affiliation(s)
- S Hong
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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41
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Christopher DA, Hoffer PH. DET1 represses a chloroplast blue light-responsive promoter in a developmental and tissue-specific manner in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 14:1-11. [PMID: 9681024 DOI: 10.1046/j.1365-313x.1998.00078.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The chloroplast psbD-psbC loci, which encode the D2 and CP43 subunits of the photosystem II reaction center, respectively, are regulated by a blue light-responsive promoter (BLRP). It has recently been shown in barley seedlings that activation of psbD-psbC transcription by blue light involves inhibition of a protein kinase that represses the BLRP in the dark. To elucidate further the photosensory pathways regulating the psbD BLRP, the effects of three nuclear mutations on the expression of the BLRP in chloroplasts of Arabidopsis thaliana were examined. The mutants used included the det1-1 and det1-6 alleles for the nuclear protein DET1, involved in repressing photomorphogenesis, and the cry1 gene for the blue light photoreceptor, cryptochrome (CRY1), involved in hypocotyl elongation. The BLRP was not significantly expressed in cotyledons of light-grown wild-type seedlings, unlike the light-responsive expression of the chloroplast, psbA and rbcL, and nuclear, Lhcb and Chs, genes. Analysis of the mutants revealed that DET1 represses transcription from the BLRP in a developmental and tissue-specific manner, which is unique from the effects that DET1 has on other light-regulated promoters. In addition, the cry1 mutation did not reduce the expression of the BLRP in response to blue light. This suggests that the BLRP is regulated by a different photosensory system relative to CRY1. A model is proposed involving blue light, DET1 and phytochrome in regulating transcription from the psbD BLRP.
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Affiliation(s)
- D A Christopher
- Department of Plant Molecular Physiology, University of Hawaii at Manoa, Honolulu 96822, USA.
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42
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Goldschmidt-Clermont M. Coordination of nuclear and chloroplast gene expression in plant cells. INTERNATIONAL REVIEW OF CYTOLOGY 1997; 177:115-80. [PMID: 9378616 DOI: 10.1016/s0074-7696(08)62232-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Plastid proteins are encoded in two genomes, one in the nucleus and the other in the organelle. The expression of genes in these two compartments in coordinated during development and in response to environmental parameters such as light. Two converging approaches reveal features of this coordination: the biochemical analysis of proteins involved in gene expression, and the genetic analysis of mutants affected in plastid function or development. Because the majority of proteins implicated in plastid gene expression are encoded in the nucleus, regulatory processes in the nucleus and in the cytoplasm control plastid gene expression, in particular during development. Many nucleus-encoded factors involved in transcriptional and posttranscriptional steps of plastid gene expression have been characterized. We are also beginning to understand whether and how certain developmental or environmental signals perceived in one compartment may be transduced to the other.
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43
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Hajdukiewicz PT, Allison LA, Maliga P. The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J 1997; 16:4041-8. [PMID: 9233813 PMCID: PMC1170027 DOI: 10.1093/emboj/16.13.4041] [Citation(s) in RCA: 348] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The plastid genome in photosynthetic higher plants encodes subunits of an Escherichia coli-like RNA polymerase (PEP) which initiates transcription from E.coli sigma70-type promoters. We have previously established the existence of a second nuclear-encoded plastid RNA polymerase (NEP) in photosynthetic higher plants. We report here that many plastid genes and operons have at least one promoter each for PEP and NEP (Class II transcription unit). However, a subset of plastid genes, including photosystem I and II genes, are transcribed from PEP promoters only (Class I genes), while in some instances (e.g. accD) genes are transcribed exclusively by NEP (Class III genes). Sequence alignment identified a 10 nucleotide NEP promoter consensus around the transcription initiation site. Distinct NEP and PEP promoters reported here provide a general mechanism for group-specific gene expression through recognition by the two RNA polymerases.
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Affiliation(s)
- P T Hajdukiewicz
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway 08855-0759, USA
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Christopher DA, Li X, Kim M, Mullet JE. Involvement of protein kinase and extraplastidic serine/threonine protein phosphatases in signaling pathways regulating plastid transcription and the psbD blue light-responsive promoter in barley. PLANT PHYSIOLOGY 1997; 113:1273-82. [PMID: 9112776 PMCID: PMC158250 DOI: 10.1104/pp.113.4.1273] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We investigated the signaling pathways that control changes in plastid transcription in response to development and light. Plastid gene expression was analyzed in dark-grown barley (Hordeum vulgare L.) seedlings treated in vivo with an inhibitor of protein phosphatases 1 and 2A, okadaic acid (OA), or an inhibitor of protein kinases (K252a), followed by exposure of the seedlings to either red, blue, or white light. OA prevented blue light from activating the plastid pshD blue-light-responsive promoter (BLRP) and prevented red and blue light from activating the expression of the plastid-encoded rbcl and psbA and the nuclear-encoded RbcS and Lhcb genes. OA reduced total plastid transcription activity in dark- and light-grown seedlings by 77 to 80%, indicating that OA prevented light-responsive transcription by reducing total plastid transcription. In contrast, K252a activated the accumulation of mRNAs arising from the BLRP. Blue light in combination with K252a increased psbD mRNA levels in an additive manner. The results indicate that protein phosphatases 1 and/or 2A, which reside external to the organelle, are required for proper function of plastid transcription and chloroplast development, whereas a protein kinase represses the BLRP in plants grown in the dark.
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Affiliation(s)
- D A Christopher
- Department of Plant Molecular Physiology, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA.
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45
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Satoh J, Baba K, Nakahira Y, Shiina T, Toyoshima Y. Characterization of dynamics of the psbD light-induced transcription in mature wheat chloroplasts. PLANT MOLECULAR BIOLOGY 1997; 33:267-278. [PMID: 9037145 DOI: 10.1023/a:1005799001271] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Dynamical aspects of three chloroplast promoters responding to change in light condition were examined in mature chloroplasts of wheat (Triticum aestivum) by in vitro transcription. The wheat psbD/C operon has four distinct promoters, two of which named as D/C-3 and D/C-4 promoters dominantly function in mature chloroplasts to produce the mRNAs encoding D2/CP43 and CP43 alone, respectively. Activity of the D/C-3 promoter in mature chloroplasts was reduced to less than 30% by 24 h dark adaptation and recovered by re-illumination to the original level within 30 to 60 min. The activation of the D/C-3 promoter which requires de novo cytoplasmic protein synthesis was induced by low fluence of light (e.g. 16 microE m(-2) s(-1)), but the extent of activation increased with increasing light fluence. The accumulation of mRNAs from the D/C-3 promoter saturated at 2- to 3-fold higher level within 2 h when the dark-adapted seedlings were transferred to the light at 72 microE m(-2) s(-1), concomitant with the increase in rate of D2 synthesis, suggesting that synthesis of D2 in mature chloroplasts is controlled via the D/C-3 promoter activity in a light-dependent way. Activity of the D/C-4 promoter slightly increased in the dark and decreased in the light. Effect of light on the psbA promoter activity was not observed at all in mature chloroplasts. In vitro transcriptional analysis of the D/C-3 promoter with 5' deletion mutations revealed that at least two cis elements which are located within the sequences of -78 to -47 and -46 to -29 of the transcription initiation site, respectively, act as enhancing elements in the D/C-3 promoter. The light-switching element of the transcription, however, was suggested to be located in the core promoter sequence downstream of the -35 element.
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Affiliation(s)
- J Satoh
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Japan
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46
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Allison LA, Simon LD, Maliga P. Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J 1996; 15:2802-9. [PMID: 8654377 PMCID: PMC450217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The plastid genome in higher plants encodes subunits of an Escherichia coli-like RNA polymerase which initiates transcription of plastid genes from sequences resembling E.coli sigma70-type promoters. By deleting the gene for the essential beta subunit of the tobacco E.coli-like RNA polymerase, we have established the existence of a second plastid transcription system which does not utilize E.coli-like promoters. In contrast to the E.coli-like RNA polymerase, the novel transcription machinery preferentially transcribes genetic system genes rather than photosynthetic genes. Although the mutant plants are photosynthetically defective, transcription by this polymerase is sufficient for plastid maintenance and plant development.
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Affiliation(s)
- L A Allison
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08855-0759, USA
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47
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48
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Christopher DA. Leaf development and phytochrome modulate the activation ofpsbD-psbC transcription by high-fluence blue light in barley chloroplasts. PHOTOSYNTHESIS RESEARCH 1996; 47:239-251. [PMID: 24301991 DOI: 10.1007/bf02184285] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/1995] [Accepted: 02/26/1996] [Indexed: 06/02/2023]
Abstract
Activation ofpsbD transcription by light assists in maintaining the synthesis of the PS II reaction center protein, D2, which is photodamaged in plants exposed to high light. In this study, the photosensory pathways and mechanisms that regulate the expression of thepsbD-psbC light-responsive promoter, LRP, were investigated during barley (Hordeum vulgare L.) seedling development. Accumulation ofpsbD-psbC mRNAs in response to light was observed in apical sections of primary leaves with little or no increase in mRNAs in basal sections. In both 4.5- and 7.5-day-old etiolated seedlings, blue light was most effective for activating mRNA accumulation from thepsbD-psbC LRP. However, the response of the LRP to red light increased 7-fold in 7.5-day relative to 4.5-day-old seedlings. Blue light preferentially activatedpsbD-psbC transcription, while red light was most effective for activating total plastid transcription and the expression of genes encoding the small (RbcS) and large (rbcL) subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase and Chl-a/b-binding protein (Lhcb). The stimulatory effects of red light onpsbD-psbC expression were partially reversed, and of blue light were not reversed, by subsequent pulses of far-red light. In contrast, continuous far-red light given together with blue light enhancedpsbD-psbC transcription in a synergistic manner. These observations indicate that phytochrome modulates the effects of high-fluence blue light onpsbD-psbC transcription by affecting total plastid transcription.
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Affiliation(s)
- D A Christopher
- Department of Plant Molecular Physiology, University of Hawaii, 3190 Maile Way, 96822, Honolulu, HI, USA
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