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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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2
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Zhang S, Zhang H, Xia Y, Xiong L. The caseinolytic protease complex component CLPC1 in Arabidopsis maintains proteome and RNA homeostasis in chloroplasts. BMC PLANT BIOLOGY 2018; 18:192. [PMID: 30208840 PMCID: PMC6136230 DOI: 10.1186/s12870-018-1396-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 08/27/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Homeostasis of the proteome is critical to the development of chloroplasts and also affects the expression of certain nuclear genes. CLPC1 facilitates the translocation of chloroplast pre-proteins and mediates protein degradation. RESULTS We found that proteins involved in photosynthesis are dramatically decreased in their abundance in the clpc1 mutant, whereas many proteins involved in chloroplast transcription and translation were increased in the mutant. Expression of the full-length CLPC1 protein, but not of the N-terminus-deleted CLPC1 (ΔN), in the clpc1 mutant background restored the normal levels of most of these proteins. Interestingly, the ΔN complementation line could also restore some proteins affected by the mutation to normal levels. We also found that that the clpc1 mutation profoundly affects transcript levels of chloroplast genes. Sense transcripts of many chloroplast genes are up-regulated in the clpc1 mutant. The level of SVR7, a PPR protein, was affected by the clpc1 mutation. We showed that SVR7 might be a target of CLPC1 as CLPC1-SVR7 interaction was detected through co-immunoprecipitation. CONCLUSION Our study indicates that in addition to its role in maintaining proteome homeostasis, CLPC1 and likely the CLP proteasome complex also play a role in transcriptome homeostasis through its functions in maintaining proteome homeostasis.
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Affiliation(s)
- Shoudong Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region China
| | - Huoming Zhang
- Core labs, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Partner State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Shatin, Hong Kong SAR, China
- Partner State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China
| | - Liming Xiong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia
- Texas A&M AgriLife Research Center, Dallas, TX 75252 USA
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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3
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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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5
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Kanazawa T, Ishizaki K, Kohchi T, Hanaoka M, Tanaka K. Characterization of Four Nuclear-Encoded Plastid RNA Polymerase Sigma Factor Genes in the Liverwort Marchantia polymorpha: Blue-Light- and Multiple Stress-Responsive SIG5 was Acquired Early in the Emergence of Terrestrial Plants. ACTA ACUST UNITED AC 2013; 54:1736-48. [DOI: 10.1093/pcp/pct119] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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6
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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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7
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Kahlau S, Bock R. Plastid transcriptomics and translatomics of tomato fruit development and chloroplast-to-chromoplast differentiation: chromoplast gene expression largely serves the production of a single protein. THE PLANT CELL 2008; 20:856-74. [PMID: 18441214 PMCID: PMC2390737 DOI: 10.1105/tpc.107.055202] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plastid genes are expressed at high levels in photosynthetically active chloroplasts but are generally believed to be drastically downregulated in nongreen plastids. The genome-wide changes in the expression patterns of plastid genes during the development of nongreen plastid types as well as the contributions of transcriptional versus translational regulation are largely unknown. We report here a systematic transcriptomics and translatomics analysis of the tomato (Solanum lycopersicum) plastid genome during fruit development and chloroplast-to-chromoplast conversion. At the level of RNA accumulation, most but not all plastid genes are strongly downregulated in fruits compared with leaves. By contrast, chloroplast-to-chromoplast differentiation during fruit ripening is surprisingly not accompanied by large changes in plastid RNA accumulation. However, most plastid genes are translationally downregulated during chromoplast development. Both transcriptional and translational downregulation are more pronounced for photosynthesis-related genes than for genes involved in gene expression, indicating that some low-level plastid gene expression must be sustained in chromoplasts. High-level expression during chromoplast development identifies accD, the only plastid-encoded gene involved in fatty acid biosynthesis, as the target gene for which gene expression activity in chromoplasts is maintained. In addition, we have determined the developmental patterns of plastid RNA polymerase activities, intron splicing, and RNA editing and report specific developmental changes in the splicing and editing patterns of plastid transcripts.
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Affiliation(s)
- Sabine Kahlau
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
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8
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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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9
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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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10
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Zghidi W, Merendino L, Cottet A, Mache R, Lerbs-Mache S. Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids. Nucleic Acids Res 2006; 35:455-64. [PMID: 17175536 PMCID: PMC1802608 DOI: 10.1093/nar/gkl1067] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have investigated the function of one of the six plastid sigma-like transcription factors, sigma 3 (SIG3), by analysing two different Arabidopsis T-DNA insertion lines having disrupted SIG3 genes. Hybridization of wild-type and sig3 plant RNA to a plastid specific microarray revealed a strong reduction of the plastid psbN mRNA. The microarray result has been confirmed by northern blot analysis. The SIG3-specific promoter region has been localized on the DNA by primer extension and mRNA capping experiments. Results suggest tight regulation of psbN gene expression by a SIG3-PEP holoenzyme. The psbN gene is localized on the opposite strand of the psbB operon, between the psbT and psbH genes, and the SIG3-dependent psbN transcription produces antisense RNA to the psbT-psbH intergenic region. We show that this antisense RNA is not limited to the intergenic region, i.e. it does not terminate at the end of the psbN gene but extends as antisense transcript to cover the whole psbT coding region. Thus, by specific transcription initiation at the psbN gene promoter, SIG3-PEP holoenzyme could also influence the expression of the psbB operon by producing psbT antisense RNA.
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Affiliation(s)
| | | | | | | | - Silva Lerbs-Mache
- To whom correspondence should be addressed. Tel: +33 0 4 76 63 57 44; Fax: +33 0 4 76 63 55 86;
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11
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Bohne AV, Irihimovitch V, Weihe A, Stern DB. Chlamydomonas reinhardtii encodes a single sigma70-like factor which likely functions in chloroplast transcription. Curr Genet 2006; 49:333-40. [PMID: 16453112 DOI: 10.1007/s00294-006-0060-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 01/13/2006] [Accepted: 01/17/2006] [Indexed: 11/30/2022]
Abstract
Chlamydomonas reinhardtii EST clones encoding a protein highly similar to prokaryotic sigma factors and plant sigma-like factors (SLFs) were used to isolate a BAC clone containing the full-length gene CrRpoD. The gene is likely to be single-copy, in contrast to small gene families encoding SLFs in plants. The CrRpoD mRNA comprises 3,033 nt with an open reading frame of 2,256 nt, encoding a putative protein of 752 amino acids with a molecular mass of 80.2 kDa. The sequence contains conserved regions 2-4 typically found in sigma factors, and an unusually long amino terminal extension, which by in silico analysis has properties of a chloroplast transit peptide. Expression of CrRpoD was confirmed by immunodetection of a 85 kDa polypeptide in a preparation enriched for chloroplast proteins. To demonstrate functionality in transcription initiation, a recombinant CrRpoD-thioredoxin fusion protein was reconstituted with E. coli RNA polymerase core enzyme and tested in vitro. This chimeric holoenzyme specifically bound the spinach psbA and Chlamydomonas rrn16 promoters in gel mobility shift assays and exhibited specific transcription initiation from the same two promoters, providing evidence for the role of CrRpoD as a functional transcription factor.
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Affiliation(s)
- Alexandra-V Bohne
- Institut für Biologie, Humboldt-Universität, Chausseestr. 117, 10115, Berlin, Germany
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12
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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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13
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Carter ML, Smith AC, Kobayashi H, Purton S, Herrin DL. Structure, circadian regulation and bioinformatic analysis of the unique sigma factor gene in Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 2004; 82:339-49. [PMID: 16143845 DOI: 10.1007/s11120-004-4213-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2003] [Accepted: 07/19/2004] [Indexed: 05/04/2023]
Abstract
In higher plants, the transcription of plastid genes is mediated by at least two types of RNA polymerase (RNAP); a plastid-encoded bacterial RNAP in which promoter specificity is conferred by nuclear-encoded sigma factors, and a nuclear-encoded phage-like RNAP. Green algae, however, appear to possess only the bacterial enzyme. Since transcription of much, if not most, of the chloroplast genome in Chlamydomonas reinhardtii is regulated by the circadian clock and the nucleus, we sought to identify sigma factor genes that might be responsible for this regulation. We describe a nuclear gene (RPOD) that is predicted to encode an 80 kDa protein that, in addition to a predicted chloroplast transit peptide at the N-terminus, has the conserved motifs (2.1- 4.2) diagnostic of bacterial sigma-70 factors. We also identified two motifs not previously recognized for sigma factors, adjacent PEST sequences and a leucine zipper, both suggested to be involved in protein-protein interactions. PEST sequences were also found in approximately 40% of sigma factors examined, indicating they may be of general significance. Southern blot hybridization and BLAST searches of the genome and EST databases suggest that RPODmay be the only sigma factor gene in C. reinhardtii. The levels of RPODmRNA increased 2- 3-fold in the mid-to-late dark period of light-dark cycling cells, just prior to, or coincident with, the peak in chloroplast transcription. Also, the dark-period peak in RPOD mRNA persisted in cells shifted to continuous light or continuous dark for at least one cycle, indicating that RPODis under circadian clock control. These results suggest that regulation of RPODexpression contributes to the circadian clock's control of chloroplast transcription.
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Affiliation(s)
- Matthew L Carter
- Section Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A6700, Austin, TX, 78712, USA,
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14
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Yao J, Roy-Chowdhury S, Allison LA. AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like factor. PLANT PHYSIOLOGY 2003; 132:739-47. [PMID: 12805603 PMCID: PMC167013 DOI: 10.1104/pp.102.017913] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 01/13/2003] [Accepted: 02/23/2003] [Indexed: 05/20/2023]
Abstract
Transcription of chloroplast genes is subject to control by nucleus-encoded proteins. The chloroplast-encoded RNA polymerase (PEP) is a eubacterial-type RNA polymerase that is presumed to assemble with nucleus-encoded sigma-factors mediating promoter recognition. Recently, families of sigma-factor genes have been identified in several plants including Arabidopsis. One of these genes, Arabidopsis SIG5, encodes a sigma-factor, AtSig5, which is phylogenetically distinct from the other family members. To investigate the role of this plant sigma-factor, two different insertional alleles of the SIG5 gene were identified and characterized. Heterozygous mutant plants showed no visible leaf phenotype, but exhibited siliques containing aborted embryos and unfertilized ovules. Our inability to recover plants homozygous for a SIG5 gene disruption indicates that SIG5 is an essential gene. SIG5 transcripts accumulate in flower tissues, consistent with a role for AtSig5 protein in reproduction. Therefore, SIG5 encodes an essential member of the Arabidopsis sigma-factor family that plays a role in plant reproduction in addition to its previously proposed role in leaf chloroplast gene expression.
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Affiliation(s)
- Junlan Yao
- Department of Biochemistry, University of Nebraska-Lincoln, N250 Beadle Center, 68588-0664, USA
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15
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Sawers RJH, Linley PJ, Farmer PR, Hanley NP, Costich DE, Terry MJ, Brutnell TP. Elongated mesocotyl1, a phytochrome-deficient mutant of maize. PLANT PHYSIOLOGY 2002; 130:155-63. [PMID: 12226496 PMCID: PMC166549 DOI: 10.1104/pp.006411] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2002] [Revised: 04/28/2002] [Accepted: 05/05/2002] [Indexed: 05/20/2023]
Abstract
To begin the functional dissection of light signal transduction pathways of maize (Zea mays), we have identified and characterized the light-sensing mutant elm1 (elongated mesocotyl1). Seedlings homozygous for elm1 are pale green, show pronounced elongation of the mesocotyl, and fail to de-etiolate under red or far-red light. Etiolated elm1 mutants contain no spectrally active phytochrome and do not deplete levels of phytochrome A after red-light treatment. High-performance liquid chromatography analyses show that elm1 mutants are unable to convert biliverdin IX alpha to 3Z-phytochromobilin, preventing synthesis of the phytochrome chromophore. Despite the impairment of the phytochrome photoreceptors, elm1 mutants can be grown to maturity in the field. Mature plants retain aspects of the seedling phenotype and flower earlier than wild-type plants under long days. Thus, the elm1 mutant of maize provides the first direct evidence for phytochrome-mediated modulation of flowering time in this agronomically important species.
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Affiliation(s)
- Ruairidh J H Sawers
- Boyce Thompson Institute, Cornell University, Tower Road, Ithaca, New York 14853, USA
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16
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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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17
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Hara K, Morita M, Takahashi R, Sugita M, Kato S, Aoki S. Characterization of two genes, Sig1 and Sig2, encoding distinct plastid sigma factors(1) in the moss Physcomitrella patens: phylogenetic relationships to plastid sigma factors in higher plants. FEBS Lett 2001; 499:87-91. [PMID: 11418118 DOI: 10.1016/s0014-5793(01)02530-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We isolated the cDNA for a sigma factor from the moss Physcomitrella patens, which possesses unusually large N-terminal extension and the conserved subdomains 1.2-4.2. Phylogenetic analyses indicated that this novel sigma factor and PpSIG1*(2), a plastid sigma factor previously identified from Physcomitrella, were classified into SigA and SigB groups, two major classes of higher plant plastid sigma factors, respectively. According to the nomenclature recently proposed, we renamed PpSIG1* into PpSIG2, and named the novel sigma factor PpSIG1. A transient expression assay using a green fluorescent protein showed that the N-terminal region of PpSIG1 acts as a chloroplast-targeting signal. Reverse transcription-PCR experiments showed that light induces the expression of the Sig1 and Sig2 genes encoding PpSIG1 and PpSIG2, respectively. Thus, PpSIG1 and PpSIG2 are likely plastid sigma factors regulating plastid gene expression in response to light signals.
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Affiliation(s)
- K Hara
- Division of Biological Informatics, Graduate School of Human Informatics, Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Japan
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18
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Hara K, Sugita M, Aoki S. Cloning and characterization of the cDNA for a plastid sigma factor from the moss Physcomitrella patens. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1517:302-6. [PMID: 11342113 DOI: 10.1016/s0167-4781(00)00250-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We isolated a cDNA PpSig1 encoding a plastid sigma factor from the moss Physcomitrella patens. The PpSIG1 protein is composed of the conserved subdomains for recognition of -10 and -35 promoter elements, core complex binding and DNA melting. Southern blot analysis showed that the moss sig1 gene is likely a member of a small gene family. Transient expression assay using green fluorescent protein demonstrated that the N-terminal region of PpSIG1 functions as a chloroplast-targeting signal peptide. These observations suggest that multiple nuclear-encoded sigma factors regulate chloroplast gene expression in P. patens.
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Affiliation(s)
- K Hara
- Division of Biological Informatics, Graduate School of Human Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Oikawa K, Fujiwara M, Nakazato E, Tanaka K, Takahashi H. Characterization of two plastid sigma factors, SigA1 and SigA2, that mainly function in matured chloroplasts in Nicotiana tabacum. Gene 2000; 261:221-8. [PMID: 11167008 DOI: 10.1016/s0378-1119(00)00505-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have isolated and characterized two genes from Nicotiana tabacum, whose products function as putative sigma factors for plastid RNA polymerase. Since the amino acid sequence deduced from the DNA sequences of both genes showed highly similar to that of the SigA protein of Arabidopsis thaliana, we termed the corresponding genes sigA1 and sigA2, respectively. Transient expression assay using a green fluorescent protein (GFP) fusion construct indicated that the N-terminal region of the sigA2 gene product could function as a transit peptide for import into chloroplasts. The gel-blot analysis of RNAs revealed that the sum of the sigA1 and sigA2 transcripts fluctuated apparently with an endogenous rhythm after 12-h-light, 12-h-dark entrainment in photomixotrophically cultured tobacco cells. RT-PCR based northern analysis revealed that the sigA1 and sigA2 transcripts increased along with the cell growth in cultured cells, and were most abundant in mature leaves and shoot meristems with very young leaves in tobacco plants. Immunoblot analysis of the cell extracts of tobacco plants also supports this notion. These results suggest that the sigma factors encoded by sigA1 and sigA2 play a role in chloroplast development and regulation of gene expression in matured chloroplasts.
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MESH Headings
- Amino Acid Sequence
- Blotting, Northern
- Chloroplasts/metabolism
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Gene Expression Regulation, Plant/radiation effects
- Green Fluorescent Proteins
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Microscopy, Confocal
- Molecular Sequence Data
- Photoperiod
- Phylogeny
- Plants, Toxic
- Plastids/metabolism
- Protein Isoforms/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Messenger/radiation effects
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sigma Factor/genetics
- Tissue Distribution
- Nicotiana/cytology
- Nicotiana/genetics
- Nicotiana/metabolism
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Affiliation(s)
- K Oikawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, 113-0032, Tokyo, Japan
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Fujiwara M, Nagashima A, Kanamaru K, Tanaka K, Takahashi H. Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid RNA polymerase sigma factors in Aarabidopsis thaliana. FEBS Lett 2000; 481:47-52. [PMID: 10984613 DOI: 10.1016/s0014-5793(00)01965-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three new nuclear genes (sigD, sigE and sigF) of Arabidopsis thaliana, encoding putative plastid RNA polymerase sigma factors, were identified and analyzed. Phylogenetic analysis revealed that higher plant sigma factors fell into at least four distinct subgroups within a diverse protein family. In addition, Arabidopsis sig genes contained conserved chromosomal intron sites, indicating that these genes arose by DNA duplication events during plant evolution. Transcript analyses revealed two alternatively spliced transcripts generated from the sigD region, one of which is predicted to encode a sigma protein lacking the carboxy-terminal regions 3 and 4. Finally, the amino-terminal sequence of the sigF gene product was shown to function as a plastid-targeting signal using green fluorescent protein fusions.
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Affiliation(s)
- M Fujiwara
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, 113-0032, Japan
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Lahiri SD, Allison LA. Complementary expression of two plastid-localized sigma-like factors in maize. PLANT PHYSIOLOGY 2000; 123:883-94. [PMID: 10889237 PMCID: PMC59051 DOI: 10.1104/pp.123.3.883] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/1999] [Accepted: 03/15/2000] [Indexed: 05/21/2023]
Abstract
The eubacterial-like RNA polymerase of plastids is composed of organelle-encoded core subunits and nuclear-encoded sigma-factors. Families of sigma-like factors (SLFs) have been identified in several plants, including maize (Zea mays) and Arabidopsis. In vitro import assays determined that at least two of the maize sigma-like proteins have functional chloroplast transit peptides and thus are likely candidates for chloroplast transcriptional regulators. However, the roles of individual SLFs in chloroplast transcription remain to be determined. We have raised antibodies against the unique amino-terminal domains of two maize SLFs, ZmSig1 and ZmSig3, and have used these specific probes to examine the accumulation of each protein in different maize tissues and during chloroplast development. The expression of ZmSig1 is tissue specific and parallels the light-activated chloroplast development program in maize seedling leaves. Its accumulation in mature chloroplasts however, is not affected by subsequent changes in the light regime. It is interesting that the expression profile of ZmSig3 is complementary to that of ZmSig1. It accumulates in non-green tissues, including roots, etiolated seedling leaves, and the basal region of greening seedling leaves. The nonoverlapping expression patterns of these two plastid-localized SLFs suggest that they may direct differential expression of plastid genes during chloroplast development.
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Affiliation(s)
- S D Lahiri
- Department of Biochemistry, University of Nebraska, N258 Beadle Center, Lincoln, Nebraska 68588-0664, USA
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22
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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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