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Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data. BMC Genomics 2021; 22:298. [PMID: 33892645 PMCID: PMC8063479 DOI: 10.1186/s12864-021-07598-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, little is known about the transcriptional features of green algal chloroplast-encoded genes. RESULTS Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in the chloroplast genome. With the newly annotated exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries. CONCLUSION Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and provides new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastids.
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Pinard D, Myburg AA, Mizrachi E. The plastid and mitochondrial genomes of Eucalyptus grandis. BMC Genomics 2019; 20:132. [PMID: 30760198 PMCID: PMC6373115 DOI: 10.1186/s12864-019-5444-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/10/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes. RESULTS In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. grandis plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of E. grandis. The 478,813 bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the E. grandis nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in E. grandis. CONCLUSIONS The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between Eucalyptus genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species.
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Affiliation(s)
- Desre Pinard
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
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3
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Smith DR, Sanitá Lima M. Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline. Brief Bioinform 2018; 18:1012-1016. [PMID: 27677960 PMCID: PMC5862312 DOI: 10.1093/bib/bbw088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Indexed: 11/18/2022] Open
Abstract
Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. Consequently, GenBank contains massive amounts of organelle RNA-Seq data that are just waiting to be downloaded and analyzed. Recently, a team of scientists designed an open-source bioinformatics program called ChloroSeq, which systemically analyzes an organelle transcriptome using RNA-Seq. The ChloroSeq pipeline uses RNA-Seq alignment data to deliver detailed analyses of organelle transcriptomes, which can be fed into statistical software for further analysis and for generating graphical representations of the data. In addition to providing data on expression levels via coverage statistics, ChloroSeq can examine splicing efficiency and RNA editing profiles. Ultimately, ChloroSeq provides a well-needed avenue for researchers of all stripes to start exploring organelle transcription and could be a key step toward a more thorough understanding of organelle gene expression.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Corresponding author: David Roy Smith, Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada. Tel.: (519) 661 2111, ext; 86482; E-mail:
| | - Matheus Sanitá Lima
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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Pinard D, Mizrachi E. Unsung and understudied: plastids involved in secondary growth. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:30-36. [PMID: 29459221 DOI: 10.1016/j.pbi.2018.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 05/17/2023]
Abstract
Plastids represent the only subcellular compartment where aromatic amino acid precursors for lignin can be synthesized during secondary growth in vascular plants. Despite this, aside from a general shared understanding that plastid-localized metabolism occurs during secondary growth, virtually no research has been performed on understanding their biology. Of particular importance will be insight into their ontogeny, morphology and ultrastructure, and (given the complex cytonuclear communication required) their nuclear-encoded and organellar-encoded regulation. Updating and integrating this knowledge will contribute to our fundamental understanding of a ubiquitous developmental process in vascular plants, and a major terrestrial carbon sink, as well as carbon-related plant biotechnology. Given available evidence, we propose a new name for a distinct plastid derivative-the 'xyloplast', is required.
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Affiliation(s)
- Desre Pinard
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
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5
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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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Zielinski BL, Allen AE, Carpenter EJ, Coles VJ, Crump BC, Doherty M, Foster RA, Goes JI, Gomes HR, Hood RR, McCrow JP, Montoya JP, Moustafa A, Satinsky BM, Sharma S, Smith CB, Yager PL, Paul JH. Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume. PLoS One 2016; 11:e0160929. [PMID: 27598790 PMCID: PMC5012681 DOI: 10.1371/journal.pone.0160929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 07/27/2016] [Indexed: 11/24/2022] Open
Abstract
The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as silicon became limiting. Expression of these genes, including carbonic anhydrase and transporters for nitrate and phosphate, were found to reflect the physiological status and biogeochemistry of river plume environments. These relatively stable patterns of eukaryotic transcript abundance occurred over modest spatiotemporal scales, with similarity observed in sample duplicates collected up to 2.45 km in space and 120 minutes in time. These results confirm the use of metatranscriptomics as a valuable tool to understand and predict microbial community function.
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Affiliation(s)
- Brian L. Zielinski
- University of South Florida College of Marine Science, St. Petersburg, FL, United States of America
| | - Andrew E. Allen
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, United States of America
| | - Edward J. Carpenter
- Romberg Tiburon Center, San Francisco State University, Tiburon, California, United States of America
| | - Victoria J. Coles
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Byron C. Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Mary Doherty
- Rhodes College, Memphis, TN, United States of America
| | - Rachel A. Foster
- Ocean Sciences, University of California, Santa Cruz, CA, United States of America
- Department of Ecology, Environment, and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Joaquim I. Goes
- Lamont Doherty Earth Observatory, Columbia University, Palisades, NY, United States of America
| | - Helga R. Gomes
- Lamont Doherty Earth Observatory, Columbia University, Palisades, NY, United States of America
| | - Raleigh R. Hood
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - John P. McCrow
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, United States of America
| | - Joseph P. Montoya
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
| | - Brandon M. Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Shalabh Sharma
- Department of Marine Sciences, University of Georgia, Athens, GA, United States of America
| | - Christa B. Smith
- Department of Marine Sciences, University of Georgia, Athens, GA, United States of America
| | - Patricia L. Yager
- Department of Marine Sciences, University of Georgia, Athens, GA, United States of America
| | - John H. Paul
- University of South Florida College of Marine Science, St. Petersburg, FL, United States of America
- * E-mail:
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7
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Lv DW, Zhu GR, Zhu D, Bian YW, Liang XN, Cheng ZW, Deng X, Yan YM. Proteomic and phosphoproteomic analysis reveals the response and defense mechanism in leaves of diploid wheat T. monococcum under salt stress and recovery. J Proteomics 2016; 143:93-105. [PMID: 27095598 DOI: 10.1016/j.jprot.2016.04.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/05/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED Salinity is a major abiotic stress factor affecting crops production and productivity. Triticum monococcum is closely related to Triticum urartu (A(U)A(U)), which is used as a model plant of wheat A genome study. Here, salt stress induced dynamic proteome and phosphoproteome profiling was focused. The T. monococcum seedlings were initially treated with different concentrations of NaCl ranging from 80 to 320mM for 48h followed by a recovery process for 48h prior to proteomic and phosphoproteomic analysis. As a result, a total of 81 spots corresponding to salt stress and recovery were identified by MALDI-TOF/TOF-MS from 2-DE gels. These proteins were mainly involved in regulatory, stress defense, protein folding/assembly/degradation, photosynthesis, carbohydrate metabolism, energy production and transportation, protein metabolism, and cell structure. Pro-Q Diamond staining was used to detect the phosphoproteins. Finally, 20 spots with different phosphorylation levels during salt treatment or recovery compared with controls were identified. A set of potential salt stress response and defense biomarkers was identified, such as cp31BHv, betaine-aldehyde dehydrogenase, leucine aminopeptidase 2, Cu/Zn superoxide dismutase, and 2-Cys peroxiredoxin BAS1, which could lead to a better understanding of the molecular basis of salt response and defense in food crops. BIOLOGICAL SIGNIFICANCE Soil salinity reduces the yield of the major crops, which is one of the severest problems in irrigated agriculture worldwide. However, how crops response and defense during different levels of salt treatment and recovery processes is still unclear, especially at the post-translational modification level. T. monococcum is a useful model for common wheat. Thus, proteomic and phosphoproteomic analyses of T. monococcum leaves were performed in our study, which provided novel insights into the underlying salt response and defense mechanisms in wheat and other crops.
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Affiliation(s)
- Dong-Wen Lv
- College of Life Science, Capital Normal University, 100048 Beijing, China; VCU Philips Institute for Oral Health Research, Virginia Commonwealth University, School of Dentistry, Department of Oral and Craniofacial Molecular Biology, 23298 Richmond, VA, USA
| | - Geng-Rui Zhu
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Dong Zhu
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yan-Wei Bian
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiao-Na Liang
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Zhi-Wei Cheng
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiong Deng
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yue-Ming Yan
- College of Life Science, Capital Normal University, 100048 Beijing, China.
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8
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Yarbakht M, Jalali-Javaran M, Nikkhah M, Mohebodini M. Dicistronic expression of human proinsulin-protein A fusion in tobacco chloroplast. Biotechnol Appl Biochem 2015; 62:55-63. [PMID: 24716841 DOI: 10.1002/bab.1230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/01/2014] [Indexed: 11/10/2022]
Abstract
Different expression systems such as bacteria and mammalian cells have been used to produce pharmaceutical proteins. In recent years, the use of plants as bioreactors offers efficient and economical systems in recombinant protein production. Furthermore, because of the large number of plastid copies in plants, chloroplast engineering functions as an effective method to increase recombinant protein expression. Because the commercially available insulin for treatment does not contain C-peptide, which is of great importance for type 1 diabetic patients, the current study introduces the human proinsulin gene fused with protein A into the tobacco chloroplast genome using the biolistic method. To achieve homoplasmy, three rounds of selection and regeneration of transforming cells were performed on the medium that contained spectinomycin antibiotic and hormones. The PCR analysis indicated the presence of the proinsulin gene in transplastomic plants. The reverse-transcription PCR analysis confirmed the expression of the proinsulin-protein A fusion at the transcription level. Immunoblot assays of leaf-derived protein extracts confirmed that the target gene expression is up to 0.2% of the total soluble protein. Our study showed that protein A fusion is not as efficient as other reported fusions. The transplastomic plants were also confirmed for homoplasmy using Southern blot analysis.
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Affiliation(s)
- Melina Yarbakht
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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9
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Mohanty BK, Kushner SR. Bacterial/archaeal/organellar polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 2:256-76. [PMID: 21344039 DOI: 10.1002/wrna.51] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although the first poly(A) polymerase (PAP) was discovered in Escherichia coli in 1962, the study of polyadenylation in bacteria was largely ignored for the next 30 years. However, with the identification of the structural gene for E. coli PAP I in 1992, it became possible to analyze polyadenylation using both biochemical and genetic approaches. Subsequently, it has been shown that polyadenylation plays a multifunctional role in prokaryotic RNA metabolism. Although the bulk of our current understanding of prokaryotic polyadenylation comes from studies on E. coli, recent limited experiments with Cyanobacteria, organelles, and Archaea have widened our view on the diversity, complexity, and universality of the polyadenylation process. For example, the identification of polynucleotide phosphorylase (PNPase), a reversible phosphorolytic enzyme that is highly conserved in bacteria, as an additional PAP in E. coli caught everyone by surprise. In fact, PNPase has now been shown to be the source of post-transcriptional RNA modifications in a wide range of cells of prokaryotic origin including those that lack a eubacterial PAP homolog. Accordingly, the past few years have witnessed increased interest in the mechanism and role of post-transcriptional modifications in all species of prokaryotic origin. However, the fact that many of the poly(A) tails are very short and unstable as well as the presence of polynucleotide tails has posed significant technical challenges to the scientific community trying to unravel the mystery of polyadenylation in prokaryotes. This review discusses the current state of knowledge regarding polyadenylation and its functions in bacteria, organelles, and Archaea.
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Affiliation(s)
- Bijoy K Mohanty
- Department of Genetics, University of Georgia, Athens, GA 30605, USA
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10
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Cardi T, Giegé P, Kahlau S, Scotti N. Expression Profiling of Organellar Genes. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Johnson JG, Morey JS, Neely MG, Ryan JC, Van Dolah FM. Transcriptome remodeling associated with chronological aging in the dinoflagellate, Karenia brevis. Mar Genomics 2011; 5:15-25. [PMID: 22325718 DOI: 10.1016/j.margen.2011.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/15/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
Abstract
The toxic dinoflagellate, Karenia brevis, forms dense blooms in the Gulf of Mexico that persist for many months in coastal waters, where they can cause extensive marine animal mortalities and human health impacts. The mechanisms that enable cell survival in high density, low growth blooms, and the mechanisms leading to often rapid bloom demise are not well understood. To gain an understanding of processes that underlie chronological aging in this dinoflagellate, a microarray study was carried out to identify changes in the global transcriptome that accompany the entry and maintenance of stationary phase up to the onset of cell death. The transcriptome of K. brevis was assayed using a custom 10,263 feature oligonucleotide microarray from mid-logarithmic growth to the onset of culture demise. A total of 2958 (29%) features were differentially expressed, with the mid-stationary phase timepoint demonstrating peak changes in expression. Gene ontology enrichment analyses identified a significant shift in transcripts involved in energy acquisition, ribosome biogenesis, gene expression, stress adaptation, calcium signaling, and putative brevetoxin biosynthesis. The extensive remodeling of the transcriptome observed in the transition into a quiescent non-dividing phase appears to be indicative of a global shift in the metabolic and signaling requirements and provides the basis from which to understand the process of chronological aging in a dinoflagellate.
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Affiliation(s)
- Jillian G Johnson
- NOAA Center for Coastal Environmental Health and Biomolecular Research, Charleston, SC 29412, USA.
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12
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Gray BN, Yang H, Ahner BA, Hanson MR. An efficient downstream box fusion allows high-level accumulation of active bacterial beta-glucosidase in tobacco chloroplasts. PLANT MOLECULAR BIOLOGY 2011; 76:345-55. [PMID: 21279422 DOI: 10.1007/s11103-011-9743-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 01/17/2011] [Indexed: 05/03/2023]
Abstract
Production of enzymes for lignocellulose hydrolysis in planta has been proposed as a lower-cost alternative to microbial production, with plastid transformation as a preferred method due to high foreign protein yields. An important regulator of chloroplast protein production is the downstream box (DB) region, located immediately downstream of the start codon. Protein accumulation can vary over several orders of magnitude by altering the DB region. Experiments in bacteria have suggested that these differences in protein accumulation may result from changes in translation efficiency, though the precise mechanism of DB function is not known. In this study, three DB regions were fused to the bglC ORF encoding a β-glucosidase from the thermophilic bacterium Thermobifida fusca and inserted into the tobacco (Nicotiana tabacum) plastid genome. More than a two order of magnitude of difference in BglC protein accumulation was observed, dependent on the identity of the DB fusion. Differential transcript accumulation explained some the observed differences in protein accumulation, but in addition, less 3' degradation of bglC transcripts was observed in transgenic plants that accumulated the most BglC enzyme. Chloroplast-produced BglC was active against both pure cellobiose and against tobacco lignocellulose. These experiments demonstrate the potential utility of transplastomic plants as a vehicle for heterologous β-glucosidase production for the cellulosic ethanol industry.
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Affiliation(s)
- Benjamin N Gray
- Department of Biological and Environmental Engineering, Cornell University, 202 Riley Robb, Ithaca, NY 14853, USA
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13
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Walter M, Piepenburg K, Schöttler MA, Petersen K, Kahlau S, Tiller N, Drechsel O, Weingartner M, Kudla J, Bock R. Knockout of the plastid RNase E leads to defective RNA processing and chloroplast ribosome deficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:851-63. [PMID: 21105931 DOI: 10.1111/j.1365-313x.2010.04377.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Ribonuclease E (RNase E) represents a key enzyme in bacterial RNA metabolism. It plays multifarious roles in RNA processing and also initiates degradation of mRNA by endonucleolytic cleavage. Plastids (chloroplasts) are derived from formerly free-living bacteria and have largely retained eubacterial gene expression mechanisms. Here we report the functional characterization of a chloroplast RNase E that is encoded by a single-copy nuclear gene in the model plant Arabidopsis thaliana. Analysis of knockout plants revealed that, unlike in bacteria, RNase E is not essential for survival. Absence of RNase E results in multiple defects in chloroplast RNA metabolism. Most importantly, polycistronic precursor transcripts overaccumulate in the knockout plants, while several mature monocistronic mRNAs are strongly reduced, suggesting an important function of RNase E in intercistronic processing of primary transcripts from chloroplast operons. We further show that disturbed maturation of a transcript encoding essential ribosomal proteins results in plastid ribosome deficiency and, therefore, provides a molecular explanation for the observed mutant phenotype.
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Affiliation(s)
- Michael Walter
- Institut für Botanik, Universität Münster, Schlossplatz 4, 48149 Münster, Germany
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14
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del Campo EM. Post-transcriptional control of chloroplast gene expression. GENE REGULATION AND SYSTEMS BIOLOGY 2009; 3:31-47. [PMID: 19838333 PMCID: PMC2758277 DOI: 10.4137/grsb.s2080] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chloroplasts contain their own genome, organized as operons, which are generally transcribed as polycistronic transcriptional units. These primary transcripts are processed into smaller RNAs, which are further modified to produce functional RNAs. The RNA processing mechanisms remain largely unknown and represent an important step in the control of chloroplast gene expression. Such mechanisms include RNA cleavage of pre-existing RNAs, RNA stabilization, intron splicing, and RNA editing. Recently, several nuclear-encoded proteins that participate in diverse plastid RNA processing events have been characterised. Many of them seem to belong to the pentatricopeptide repeat (PPR) protein family that is implicated in many crucial functions including organelle biogenesis and plant development. This review will provide an overview of current knowledge of the post-transcriptional processing in chloroplasts.
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Affiliation(s)
- Eva M del Campo
- Department of Plant Biology, University of Alcalá, Alcalá de Henares, 28871 Madrid, Spain.
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15
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Abstract
Despite recent elucidation of the three-dimensional structure of major photosynthetic complexes, our understanding of light energy conversion in plant chloroplasts and microalgae under physiological conditions requires exploring the dynamics of photosynthesis. The photosynthetic apparatus is a flexible molecular machine that can acclimate to metabolic and light fluctuations in a matter of seconds and minutes. On a longer time scale, changes in environmental cues trigger acclimation responses that elicit intracellular signaling between the nucleo-cytosol and chloroplast resulting in modification of the biogenesis of the photosynthetic machinery. Here we attempt to integrate well-established knowledge on the functional flexibility of light-harvesting and electron transfer processes, which has greatly benefited from genetic approaches, with data derived from the wealth of recent transcriptomic and proteomic studies of acclimation responses in photosynthetic eukaroytes.
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Affiliation(s)
- Stephan Eberhard
- Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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16
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Piwowarski J, Dziembowski A, Dmochowska A, Minczuk M, Tomecki R, Gewartowski K, Stepien PP. RNA Degradation in Yeast and Human Mitochondria. Toxicol Mech Methods 2008; 14:53-7. [DOI: 10.1080/15376520490257473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Redox Regulation of Chloroplast Gene Expression. PHOTOPROTECTION, PHOTOINHIBITION, GENE REGULATION, AND ENVIRONMENT 2008. [DOI: 10.1007/1-4020-3579-9_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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18
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Zhou F, Karcher D, Bock R. Identification of a plastid intercistronic expression element (IEE) facilitating the expression of stable translatable monocistronic mRNAs from operons. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:961-72. [PMID: 17825052 PMCID: PMC2230500 DOI: 10.1111/j.1365-313x.2007.03261.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 07/12/2007] [Indexed: 05/17/2023]
Abstract
Most plastid genes are part of operons and expressed as polycistronic mRNAs. Many primary polycistronic transcripts undergo post-transcriptional processing in monocistronic or oligocistronic units. At least some polycistronic transcripts are not translatable, and endonucleolytic processing may therefore be a prerequisite for translation to occur. As the requirements for intercistronic mRNA processing into stable monocistronic transcript are not well understood, we have sought to define minimum sequence elements that trigger processing and thus are capable of generating stable translatable monocistronic mRNAs. We describe here the in vivo identification of a small intercistronic expression element that mediates intercistronic cleavage into stable monocistronic transcripts. Separation of foreign genes by this element facilitates transgene stacking in operons, and thus will help to expand the range of applications of transplastomic technology.
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Affiliation(s)
- Fei Zhou
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP)Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP)Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP)Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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19
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Chen HW, Koehler CM, Teitell MA. Human polynucleotide phosphorylase: location matters. Trends Cell Biol 2007; 17:600-8. [DOI: 10.1016/j.tcb.2007.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 09/01/2007] [Accepted: 09/03/2007] [Indexed: 01/21/2023]
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20
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Horie Y, Ito Y, Ono M, Moriwaki N, Kato H, Hamakubo Y, Amano T, Wachi M, Shirai M, Asayama M. Dark-induced mRNA instability involves RNase E/G-type endoribonuclease cleavage at the AU-box and SD sequences in cyanobacteria. Mol Genet Genomics 2007; 278:331-46. [PMID: 17661085 DOI: 10.1007/s00438-007-0254-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 05/21/2007] [Indexed: 11/29/2022]
Abstract
Light-responsive gene expression is crucial to photosynthesizing organisms. Here, we studied functions of cis-elements (AU-box and SD sequences) and a trans-acting factor (ribonuclease, RNase) in light-responsive expression in cyanobacteria. The results indicated that AU-rich nucleotides with an AU-box, UAAAUAAA, just upstream from an SD confer instability on the mRNA under darkness. An RNase E/G homologue, Slr1129, of the cyanobacterium Synechocystis sp. strain PCC 6803 was purified and confirmed capable of endoribonucleolytic cleavage at the AU- (or AG)-rich sequences in vitro. The cleavage depends on the primary target sequence and secondary structure of the mRNA. Complementation tests using Escherichia coli rne/rng mutants showed that Slr1129 fulfilled the functions of both the RNase E and RNase G. An analysis of systematic mutations in the AU-box and SD sequences showed that the cis-elements also affect significantly mRNA stability in light-responsive genes. These results strongly suggested that dark-induced mRNA instability involves RNase E/G-type cleavage at the AU-box and SD sequences in cyanobacteria. The mechanical impact and a possible common mechanism with RNases for light-responsive gene expression are discussed.
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Affiliation(s)
- Yoshinao Horie
- Laboratory of Molecular Genetics, School of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki 300-0393, Japan
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21
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Forner J, Weber B, Thuss S, Wildum S, Binder S. Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: t-elements contribute to 5' and 3' end formation. Nucleic Acids Res 2007; 35:3676-92. [PMID: 17488843 PMCID: PMC1920247 DOI: 10.1093/nar/gkm270] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
With CR–RT–PCR as primary approach we mapped the 5′ and 3′ transcript ends of all mitochondrial protein-coding genes in Arabidopsis thaliana. Almost all transcripts analyzed have single major 3′ termini, while multiple 5′ ends were found for several genes. Some of the identified 5′ ends map within promoter motifs suggesting these ends to be derived from transcription initiation while the majority of the 5' termini seems to be generated post-transcriptionally. Assignment of the extremities of 5′ leader RNAs revealed clear evidence for an endonucleolytic generation of the major cox1 and atp9 5′ mRNA ends. tRNA-like structures, so-called t-elements, are associated either with 5′ or with 3′ termini of several mRNAs. These secondary structures most likely act as cis-signals for endonucleolytic cleavages by RNase Z and/or RNase P. Since no conserved sequence motif is evident at post-transcriptionally derived ends, we suggest t-elements, stem–loops and probably complex higher order structures as cis-elements for processing. This analysis provides novel insights into 5′ and 3′ end formation of mRNAs. In addition, the complete transcript map is a substantial and important basis for future studies of gene expression in mitochondria of higher plants.
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Affiliation(s)
| | | | | | | | - Stefan Binder
- *To whom correspondence should be addressed. +49 731 5022625+49 731 5022626
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22
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Baginsky S, Grossmann J, Gruissem W. Proteome analysis of chloroplast mRNA processing and degradation. J Proteome Res 2007; 6:809-20. [PMID: 17269737 DOI: 10.1021/pr060473q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chloroplasts have a complex enzymatic machinery to adjust the relative half-life of their mRNAs to environmental signals. Soluble protein extracts from spinach (Spinacia oleracea L.) chloroplasts that correctly reproduce in vitro the differential mRNA stability observed in vivo were analyzed using shotgun proteomics to identify the proteins that are potentially involved in this process. The combination of a novel strategy for the database-independent detection of proteins from MS/MS data with standard database searches allowed us to identify 243 proteins with high confidence, which include several nucleases and RNA binding proteins but also proteins that have no reported function in chloroplast mRNA metabolism. Characterization of enzyme activities that adjust mRNA stability in response to illumination revealed that the dark-induced RNA degradation pathway involves enzymatic activities that differ from those that direct RNA processing and stabilization in the light. Dark-induced mRNA degradation comprises a MgCl2-independent and a MgCl2-dependent step, which releases nucleoside di- and monophosphates from the petD 3'-UTR precursor substrate. RNA degradation can be blocked with RNasin, a potent inhibitor of eukaryotic ribonucleases, suggesting that chloroplast mRNA degradation involves enzymes that are distinct from those found in prokaryotic-type RNA degradation. On the basis of the identified proteins and the in vitro characterization of the RNA degradation activities, we discuss scenarios and components that potentially determine plastid mRNA stability.
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Affiliation(s)
- Sacha Baginsky
- Institute of Plant Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland.
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23
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Calsa T, Figueira A. Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts. PLANT MOLECULAR BIOLOGY 2007; 63:745-62. [PMID: 17211512 DOI: 10.1007/s11103-006-9121-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 11/25/2006] [Indexed: 05/07/2023]
Abstract
Sugarcane (Saccharum spp.) is a highly efficient biomass and sugar producing crop. Leaf reactions have been considered as potential rate-limiting step for sucrose accumulation in sugarcane stalks. To characterize the sugarcane leaf transcriptome, field-grown mature leaves from cultivar "SP80-3280" were analyzed using Serial Analysis of Gene Expression (SAGE). From 480 sequenced clones, 9,482 valid tags were extracted, with 5,227 unique sequences, from which 3,659 (70%) matched at least a sugarcane assembled sequence (SAS) with putative function; while 872 tags (16.7%) matched SAS with unknown function; 523 (10%) matched SAS without a putative annotation; and only 173 (3.3%) did not match any sugarcane ESTs. Based on gene ontology (GO), photosystem (PS) I reaction center was identified as the most frequent gene product location, followed by the remaining sites of PS I, PS II and thylakoid complexes. For metabolic processes, photosynthesis light harvesting complexes; carbon fixation; and chlorophyll biosynthesis were the most enriched GO-terms. Considering the alternative photosynthetic C(4) cycles, tag frequencies related to phosphoenolpyruvate carboxykinase (PEPCK) and aspartate aminotransferase compared to those for NADP(+)-malic enzyme (NADP-ME) and NADP-malate dehydrogenase, suggested that PEPCK-type decarboxylation appeared to predominate over NADP-ME in mature leaves, although both may occur, opposite to currently assumed in sugarcane. From the unique tag set, 894 tags (17.1%) were assigned as potentially derived from antisense transcripts, while 73 tags (1.4%) were assigned to more than one SAS, suggesting the occurrence of alternative processing. The occurrence of antisense was validated by quantitative reverse transcription amplification. Sugarcane leaf transcriptome provided new insights for functional studies associated with sucrose synthesis and accumulation.
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Affiliation(s)
- Tercilio Calsa
- Laboratório de Melhoramento de Plantas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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24
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Kleffmann T, von Zychlinski A, Russenberger D, Hirsch-Hoffmann M, Gehrig P, Gruissem W, Baginsky S. Proteome dynamics during plastid differentiation in rice. PLANT PHYSIOLOGY 2007; 143:912-23. [PMID: 17189339 PMCID: PMC1803725 DOI: 10.1104/pp.106.090738] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We have analyzed proteome dynamics during light-induced development of rice (Oryza sativa) chloroplasts from etioplasts using quantitative two-dimensional gel electrophoresis and tandem mass spectrometry protein identification. In the dark, the etioplast allocates the main proportion of total protein mass to carbohydrate and amino acid metabolism and a surprisingly high number of proteins to the regulation and expression of plastid genes. Chaperones, proteins for photosynthetic energy metabolism, and enzymes of the tetrapyrrole pathway were identified among the most abundant etioplast proteins. The detection of 13 N-terminal acetylated peptides allowed us to map the exact localization of the transit peptide cleavage site, demonstrating good agreement with the prediction for most proteins. Based on the quantitative etioplast proteome map, we examined early light-induced changes during chloroplast development. The transition from heterotrophic metabolism to photosynthesis-supported autotrophic metabolism was already detectable 2 h after illumination and affected most essential metabolic modules. Enzymes in carbohydrate metabolism, photosynthesis, and gene expression were up-regulated, whereas enzymes in amino acid and fatty acid metabolism were significantly decreased in relative abundance. Enzymes involved in nucleotide metabolism, tetrapyrrole biosynthesis, and redox regulation remained unchanged. Phosphoprotein-specific staining at different time points during chloroplast development revealed light-induced phosphorylation of a nuclear-encoded plastid RNA-binding protein, consistent with changes in plastid RNA metabolism. Quantitative information about all identified proteins and their regulation by light is available in plprot, the plastid proteome database (http://www.plprot.ethz.ch).
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Affiliation(s)
- Torsten Kleffmann
- Institute of Plant Sciences, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
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25
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Calsa Jr. T, Figueira A. Citrus plastid-related gene profiling based on expressed sequence tag analyses. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000500013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Processing, degradation, and polyadenylation of chloroplast transcripts. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0235] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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27
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Portnoy V, Schuster G. RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Res 2006; 34:5923-31. [PMID: 17065466 PMCID: PMC1635327 DOI: 10.1093/nar/gkl763] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Polyadenylation is a process common to almost all organisms. In eukaryotes, stable poly(A)-tails, important for mRNA stability and translation initiation, are added to the 3′ ends of most mRNAs. Contrarily, polyadenylation can stimulate RNA degradation, a phenomenon witnessed in prokaryotes, organelles and recently, for nucleus-encoded RNA as well. Polyadenylation takes place in hyperthermophilic archaea and is mediated by the archaeal exosome, but no RNA polyadenylation was detected in halophiles. Here, we analyzed polyadenylation in the third archaea group, the methanogens, in which some members contain genes encoding the exosome but others lack these genes. Polyadenylation was found in the methanogen, Methanopyrus kandleri, containing the exosome genes, but not in members which lack these genes. To explore how RNA is degraded in the absence of the exosome and without polyadenylation, we searched for the exoribonuclease that is involved in this process. No homologous proteins for any other known exoribonuclease were detected in this group. However, the halophilic archaea contain a gene homologous to the exoribonuclease RNase R. This ribonuclease is not able to degrade structured RNA better than PNPase. RNase R, which appears to be the only exoribonucleases in Haloferax volcanii, was found to be essential for viability.
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Affiliation(s)
| | - Gadi Schuster
- To whom correspondence should be addressed. Tel: +972 4 8293171; Fax: +972 4 8295587;
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28
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Lee MYT, Zhou Y, Lung RWM, Chye ML, Yip WK, Zee SY, Lam E. Expression of viral capsid protein antigen against Epstein-Barr virus in plastids of Nicotiana tabacum cv. SR1. Biotechnol Bioeng 2006; 94:1129-37. [PMID: 16586511 DOI: 10.1002/bit.20948] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epstein-Barr virus (EBV) infects nearly 90% of adults worldwide and is the pathogenic source of a broad spectrum of malignancies originating from lymphoid and epithelial cells. Currently, no vaccine has been developed to immunologically inactivate this virus. In infected patients, anti-EBV viral capsid antigen (VCA) immunoglobins represent some of the useful diagnostic markers for carcinoma development. To demonstrate that the EBV VCA antigen can be produced in plants, the plastid genome of tobacco (Nicotiana tabacum cv. SR1) was transformed with a VCA-expressing cassette. The EBV VCA mRNA was actively transcribed in the transplastomic plants and antigen production was detected. This study indicates that plastid transformation could be a promising strategy in EBV VCA antigen production.
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Affiliation(s)
- Maggie Y T Lee
- Department of Botany, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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29
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Tungsuchat T, Kuroda H, Narangajavana J, Maliga P. Gene activation in plastids by the CRE site-specific recombinase. PLANT MOLECULAR BIOLOGY 2006; 61:711-8. [PMID: 16897486 DOI: 10.1007/s11103-006-0044-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2006] [Accepted: 03/09/2006] [Indexed: 05/11/2023]
Abstract
We developed a novel system for gene activation in plastids that uses the CRE/loxP site-specific recombination system to create a translatable reading frame by excision of a blocking sequence. To test the system, we introduced an inactive gfp* gene into the tobacco plastid genome downstream of the selectable spectinomcyin resistance (aadA) marker gene. The aadA gene is the blocking sequence, and is flanked by directly oriented loxP sites for excision by the CRE. In the non-activated state, gfp* is transcribed from the aadA promoter, but the mRNA is not translated due to the lack of an AUG translation initiation codon. Green Fluorescent Protein (GFP) expression is activated by excision of the aadA coding segment to link up the gfp* coding region with the translation initiation codon of aadA. Tobacco plants that carry the inactive gfp* gene do not contain detectable levels of GFP. However, activation of gfp* resulted in GFP accumulation, proving the utility of CRE-induced protein expression in tobacco chloroplasts. The gene activation system described here will be useful to probe plastid gene function and for the production of recombinant proteins in chloroplasts.
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Affiliation(s)
- Tarinee Tungsuchat
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854-8020, USA
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30
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Abstract
The addition of poly(A)-tails to RNA is a process common to almost all organisms. In eukaryotes, stable poly(A)-tails, important for mRNA stability and translation initiation, are added to the 3′ ends of most nuclear-encoded mRNAs, but not to rRNAs. Contrarily, in prokaryotes and organelles, polyadenylation stimulates RNA degradation. Recently, polyadenylation of nuclear-encoded transcripts in yeast was reported to promote RNA degradation, demonstrating that polyadenylation can play a double-edged role for RNA of nuclear origin. Here we asked whether in human cells ribosomal RNA can undergo polyadenylation. Using both molecular and bioinformatic approaches, we detected non-abundant polyadenylated transcripts of the 18S and 28S rRNAs. Interestingly, many of the post-transcriptionally added tails were composed of heteropolymeric poly(A)-rich sequences containing the other nucleotides in addition to adenosine. These polyadenylated RNA fragments are most likely degradation intermediates, as primer extension (PE) analysis revealed the presence of distal fragmented molecules, some of which matched the polyadenylation sites of the proximal cleavage products revealed by oligo(dT) and circled RT–PCR. These results suggest the presence of a mechanism to degrade ribosomal RNAs in human cells, that possibly initiates with endonucleolytic cleavages and involves the addition of poly(A) or poly(A)-rich tails to truncated transcripts, similar to that which operates in prokaryotes and organelles.
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MESH Headings
- Cell Line, Tumor
- Expressed Sequence Tags
- Humans
- Oligonucleotide Probes
- Poly A/analysis
- Polyadenylation
- RNA Stability
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/analysis
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 28S/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
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Affiliation(s)
| | - David Laufer
- Department of Computer Science, Technion—Israel Institute of TechnologyHaifa 32000, Israel
| | - Dan Geiger
- Department of Computer Science, Technion—Israel Institute of TechnologyHaifa 32000, Israel
| | - Gadi Schuster
- To whom correspondence should be addressed. Tel: 972 4 8293171; Fax: 972 4 8295587;
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31
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Revill MJW, Stanley S, Hibberd JM. Plastid genome structure and loss of photosynthetic ability in the parasitic genus Cuscuta. JOURNAL OF EXPERIMENTAL BOTANY 2005; 56:2477-86. [PMID: 16061507 DOI: 10.1093/jxb/eri240] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The genus Cuscuta (dodder) is composed of parasitic plants, some species of which appear to be losing the ability to photosynthesize. A molecular phylogeny was constructed using 15 species of Cuscuta in order to assess whether changes in photosynthetic ability and alterations in structure of the plastid genome relate to phylogenetic position within the genus. The molecular phylogeny provides evidence for four major clades within Cuscuta. Although DNA blot analysis showed that Cuscuta species have smaller plastid genomes than tobacco, and that plastome size varied significantly even within one Cuscuta clade, dot blot analysis indicated that the dodders possess homologous sequence to 101 genes from the tobacco plastome. Evidence is provided for significant rates of DNA transfer from plastid to nucleus in Cuscuta. Size and structure of Cuscuta plastid genomes, as well as photosynthetic ability, appear to vary independently of position within the phylogeny, thus supporting the hypothesis that within Cuscuta photosynthetic ability and organization of the plastid genome are changing in an unco-ordinated manner.
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Affiliation(s)
- Meredith J W Revill
- Department of Plant Sciences, University of Cambridge, Downing St, Cambridge CB2 3EA, UK
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32
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Taanman JW, Llewelyn Williams S. The Human Mitochondrial Genome. OXIDATIVE STRESS AND DISEASE 2005. [DOI: 10.1201/9781420028843.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Pfannschmidt T, Liere K. Redox regulation and modification of proteins controlling chloroplast gene expression. Antioxid Redox Signal 2005; 7:607-18. [PMID: 15890004 DOI: 10.1089/ars.2005.7.607] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Chloroplasts are typical organelles of plant cells and represent the site of photosynthesis. As one very remarkable feature, they possess their own genome and a complete machinery to express the genetic information in it. The plastid gene expression machinery is a unique assembly of prokaryotic-, eukaryotic-, and phage-like components because chloroplasts acquired a great number of regulatory proteins during evolution. Such proteins can be found at all levels of gene expression. They significantly expand the functional and especially the regulatory properties of the "old" gene expression system that chloroplasts inherited from their prokaryotic ancestors. Recent results show that photosynthesis has a strong regulatory effect on plastid gene expression. The redox states of electron transport components, redox-active molecules coupled to photosynthesis, and pools of reactive oxygen species act as redox signals. They provide a functional feedback control, which couples the expression of chloroplast genes to the actual function of photosynthesis and, by this means, helps to acclimate the photosynthetic process to environmental cues. The redox signals are mediated by various specific signaling pathways that involve many of the "new" regulatory proteins. Chloroplasts therefore are an ideal model to study redox-regulated mechanisms in gene expression control. Because of the multiple origins of the expression machinery, these observations are of great relevance for many other biological systems.
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Affiliation(s)
- Thomas Pfannschmidt
- Department for General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany.
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34
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Tomecki R, Dmochowska A, Gewartowski K, Dziembowski A, Stepien PP. Identification of a novel human nuclear-encoded mitochondrial poly(A) polymerase. Nucleic Acids Res 2004; 32:6001-14. [PMID: 15547249 PMCID: PMC534615 DOI: 10.1093/nar/gkh923] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We report here on the identification of a novel human nuclear-encoded mitochondrial poly(A) polymerase. Immunocytochemical experiments confirm that the enzyme indeed localizes to mitochondrial compartment. Inhibition of expression of the enzyme by RNA interference results in significant shortening of the poly(A) tails of the mitochondrial ND3, COX III and ATP 6/8 transcripts, suggesting that the investigated protein represents a bona fide mitochondrial poly(A) polymerase. This is in agreement with our sequencing data which show that poly(A) tails of several mitochondrial messengers are composed almost exclusively of adenosine residues. Moreover, the data presented here indicate that all analyzed mitochondrial transcripts with profoundly shortened poly(A) tails are relatively stable, which in turn argues against the direct role of long poly(A) extensions in the stabilization of human mitochondrial messengers.
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Affiliation(s)
- Rafal Tomecki
- Department of Genetics, Warsaw University, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Robinson SJ, Cram DJ, Lewis CT, Parkin IAP. Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis. PLANT PHYSIOLOGY 2004; 136:3223-33. [PMID: 15489285 PMCID: PMC523381 DOI: 10.1104/pp.104.043406] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Revised: 07/14/2004] [Accepted: 07/16/2004] [Indexed: 05/19/2023]
Abstract
The efficacy of using Serial Analysis of Gene Expression (SAGE) to analyze the transcriptome of the model dicotyledonous plant Arabidopsis was assessed. We describe an iterative tag-to-gene matching process that exploits the availability of the whole genome sequence of Arabidopsis. The expression patterns of 98% of the annotated Arabidopsis genes could theoretically be evaluated through SAGE and using an iterative matching process 79% could be identified by a tag found at a unique site in the genome. A total of 145,170 reliable experimental tags from two Arabidopsis leaf tissue SAGE libraries were analyzed, of which 29,632 were distinct. The majority (93%) of the 12,988 experimental tags observed greater than once could be matched within the Arabidopsis genome. However, only 78% were matched to a single locus within the genome, reflecting the complexities associated with working in a highly duplicated genome. In addition to a comprehensive assessment of gene expression in Arabidopsis leaf tissue, we describe evidence of transcription from pseudo-genes as well as evidence of alternative mRNA processing and anti-sense transcription. This collection of experimental SAGE tags could be exploited to assist in the on-going annotation of the Arabidopsis genome.
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Affiliation(s)
- Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
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36
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Shu Y, Hong-Hui L. Transcription, translation, degradation, and circadian clock. Biochem Biophys Res Commun 2004; 321:1-6. [PMID: 15358206 DOI: 10.1016/j.bbrc.2004.06.093] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Indexed: 01/15/2023]
Abstract
Synthesis and degradation of mRNA together with synthesis and degradation of corresponding protein, this four-step-expression confers great fitness to all organisms. Transcription rate and mRNA stability both are essential for circadian expression of clock genes. In many cases, transcription rates and half-lives of mRNAs and corresponding proteins are not necessarily tightly linked with each other. The methods for measuring four-step-expression should be carefully selected and the experimental conditions should be strictly controlled.
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Affiliation(s)
- Yuan Shu
- College of Life Science, Sichuan University, 29 Wang-Jiang Road, Chengdu 610064, PR China
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37
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Lezhneva L, Meurer J. The nuclear factor HCF145 affects chloroplast psaA-psaB-rps14 transcript abundance in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 38:740-753. [PMID: 15144376 DOI: 10.1111/j.1365-313x.2004.02081.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The high chlorophyll fluorescence (hcf)145 mutant of Arabidopsis thaliana is specifically affected in photosystem (PS)I function as judged from spectroscopic analysis of PSII and PSI activity. The defect is because of a severe deficiency of PSI core subunits, whereas levels of the four outer antenna subunits of PSI were less reduced in hcf145. Pulse labelling of chloroplast proteins indicated that synthesis of the two largest PSI reaction-centre polypeptides, Psa (photosystem I subunit) A and PsaB, is significantly affected by the mutation. A comparison of stationary transcript levels with rates of transcription demonstrates that hcf145 induces a decreased stability and, probably, transcription of the tricistronic psaA-psaB-rps (small-subunit ribosomal protein)14 mRNA, which is generated by the plastid-encoded RNA polymerase. Translation inhibition experiments excluded translational defects as primary cause of impaired mRNA stability. Larger primary transcripts, which also contain sequences of the ycf3 (hypothetical chloroplast reading frame) gene located upstream of the psaA-psaB-rps14 operon and generated by the action of the nuclear-encoded RNA polymerase, are not targeted by the mutation. Real-time reverse transcription (RT)-PCR analysis has successfully been applied to quantify defined intervals of the tricistronic transcript and it was established that the psaA region is less stable than the rps14 region in hcf145. The hcf145 gene has been mapped on the upper part of chromosome 5.
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Affiliation(s)
- Lina Lezhneva
- Department Biologie I, Ludwig-Maximilians-Universität, Botanik, Menzingerstr. 67, 80638 München, Germany
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38
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Redman JC, Haas BJ, Tanimoto G, Town CD. Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 38:545-61. [PMID: 15086809 DOI: 10.1111/j.1365-313x.2004.02061.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We describe the development of a high-density Arabidopsis'whole genome' oligonucleotide probe array for expression analysis (the Affymetrix ATH1 GeneChip probe array) that contains approximately 22 750 probe sets. Precedence on the array was given to genes for which either expression evidence or a credible database match existed. The remaining space was filled with 'hypothetical' genes. The new ATH1 array represents approximately 23 750 genes of which 60% were detected in RNA from cultured seedlings. Sensitivity of the array, determined using spiking controls, was approximately one transcript per cell. The array demonstrated high technical reproducibility and concordance with real-time PCR results. Indole-3 acetic acid (IAA)-induced changes in gene expression were used for biological validation of the array. A total of 222 genes were significantly upregulated and 103 significantly downregulated by exposure to IAA. Of the genes whose products could be functionally classified, the largest specific classes of upregulated genes were transcriptional regulators and protein kinases, many fewer of which were represented among the downregulated genes. Over one-third of the auxin-regulated genes have no known function, although many belong to gene families with members that have previously been shown to be auxin regulated. For the 6714 genes represented both on this and the earlier Arabidopsis Genome (AG) array, both signal intensities and gene expression ratios were very similar. Mapping of the oligonucleotides on the ATH1 array to the latest (version 4.0) annotation showed that over 95% of the probe sets (based on version 2.0 annotation) still fully represented their original target genes.
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Affiliation(s)
- Julia C Redman
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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39
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Zandueta-Criado A, Bock R. Surprising features of plastid ndhD transcripts: addition of non-encoded nucleotides and polysome association of mRNAs with an unedited start codon. Nucleic Acids Res 2004; 32:542-50. [PMID: 14744979 PMCID: PMC373341 DOI: 10.1093/nar/gkh217] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2003] [Revised: 12/04/2003] [Accepted: 12/17/2003] [Indexed: 11/13/2022] Open
Abstract
RNA editing in higher plant plastids is a post- transcriptional RNA maturation process changing single cytidine nucleotides into uridine. In the ndhD transcript of tobacco and several other plant species, editing of an ACG codon to a standard AUG initiator codon is believed to be a prerequisite for translation. In order to test this assumption experimentally, we have analyzed the editing status of ndhD mRNA species in the process of translation. We show that unedited ndhD transcripts are also associated with polysomes in vivo, suggesting that they are translated. This surprising finding challenges the view that ACG to AUG editing is strictly required to make the ndhD message translatable and raises the possibility that ACG can be utilized as an initiator codon in chloroplasts. In addition, we have mapped the termini of the ndhD transcript and discovered a novel form of RNA processing. Unexpectedly, we find that highly specific sequences are added to the 3' end of the ndhD mRNA at high frequency. We propose a model in which these sequences are added by the successive action of a CCA-adding enzyme (tRNA nucleotidyltransferase) and an RNA-dependent RNA polymerase (RdRp) activity. The presence of an RdRp activity may have general implications also for other steps in plastid gene expression.
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Affiliation(s)
- Aitor Zandueta-Criado
- Westfälische Wilhelms-Universität Münster, Institut für Biochemie und Biotechnologie der Pflanzen, Hindenburgplatz 55, D-48143 Münster, Germany
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40
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Bollenbach TJ, Schuster G, Stern DB. Cooperation of Endo- and Exoribonucleases in Chloroplast mRNA Turnover. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 78:305-37. [PMID: 15210334 DOI: 10.1016/s0079-6603(04)78008-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chloroplasts were acquired by eukaryotic cells through endosymbiosis and have retained their own gene expression machinery. One hallmark of chloroplast gene regulation is the predominance of posttranscriptional control, which is exerted both at the gene-specific and global levels. This review focuses on how chloroplast mRNA stability is regulated, through an examination of poly(A)-dependent and independent pathways. The poly(A)-dependent pathway is catalyzed by polynucleotide phosphorylase (PNPase), which both adds and degrades destabilizing poly(A) tails, whereas RNase II and PNPase may both participate in the poly(A)-independent pathway. Each system is initiated through endonucleolytic cleavages that remove 3' stem-loop structures, which are catalyzed by the related proteins CSP41a and CSP41b and possibly an RNase E-like enzyme. Overall, chloroplasts have retained the prokaryotic endonuclease-exonuclease RNA degradation system despite evolution in the number and character of the enzymes involved. This reflects the presence of the chloroplast within a eukaryotic host and the complex responses that occur to environmental and developmental cues.
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MESH Headings
- Chloroplasts/genetics
- Chloroplasts/metabolism
- Cyanobacteria/genetics
- Cyanobacteria/metabolism
- Endoribonucleases/chemistry
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Evolution, Molecular
- Exoribonucleases/chemistry
- Exoribonucleases/genetics
- Exoribonucleases/metabolism
- Models, Biological
- Models, Molecular
- Plants/genetics
- Plants/metabolism
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Chloroplast/genetics
- RNA, Chloroplast/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
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Affiliation(s)
- Thomas J Bollenbach
- Boyce Thompson Institute for Plant Research, Tower Rd, Ithaca, New York 14853, USA
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41
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42
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Herrin DL, Nickelsen J. Chloroplast RNA processing and stability. PHOTOSYNTHESIS RESEARCH 2004; 82:301-14. [PMID: 16143842 DOI: 10.1007/s11120-004-2741-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Accepted: 03/18/2004] [Indexed: 05/04/2023]
Abstract
Primary chloroplast transcripts are processed in a number of ways, including intron splicing, internal cleavage of polycistronic RNAs, and endonucleolytic or exonucleolytic cleavages at the transcript termini. All chloroplast RNAs are also subject to degradation, although a curious feature of many chloroplast mRNAs is their relative longevity. Some of these processes, e.g., psbA splicing and stability of a number of chloroplast mRNAs, are regulated in response to light-dark cycles or nutrient availability. This review highlights recent advances in our understanding of these processes in the model organism Chlamydomonas reinhardtii, focusing on results since the extensive reviews published in 1998 [Herrin DL et al. 1998 (pp. 183-195), Nickelsen Y 1998 (pp. 151-163), Stern DB and Drager RG 1998 (pp. 164-182), in Rochaix JD et al. (eds) The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas. Kluwer Academic Publishers, Dordrecht, The Netherlands]. We also allude to studies with other organisms, and to the potential impact of the Chlamydomonas genome project where appropriate.
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Affiliation(s)
- David L Herrin
- Section of Molecular Cell and Developmental Biology, University of Texas at Austin, 1 University Station A6700, Austin, TX, 78712, USA,
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43
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Eads BD, Hand SC. Mitochondrial mRNA stability and polyadenylation during anoxia-induced quiescence in the brine shrimp Artemia franciscana. J Exp Biol 2003; 206:3681-92. [PMID: 12966060 DOI: 10.1242/jeb.00595] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polyadenylation of messenger RNA is known to be an important mechanism for regulating mRNA stability in a variety of systems, including bacteria, chloroplasts and plant mitochondria. By comparison, little is known about the role played by polyadenylation in animal mitochondrial gene expression. We have used embryos of the brine shrimp Artemia franciscana to test hypotheses regarding message stability and polyadenylation under conditions simulating anoxia-induced quiescence. In response to anoxia, these embryos undergo a profound and acute metabolic downregulation, characterized by a steep drop in intracellular pH (pH(i)) and ATP levels. Using dot blots of total mitochondrial RNA, we show that during in organello incubations both O(2) deprivation and acidic pH (pH 6.4) elicit increases in half-lives of selected mitochondrial transcripts on the order of five- to tenfold or more, relative to normoxic controls at pH 7.8. Polyadenylation of these transcripts was measured under the same incubation conditions using a reverse transcriptase-polymerase chain reaction (RT-PCR)-based assay. The results demonstrate that low pH and anoxia promote significant deadenylation of the stabilized transcripts in several cases, measured either as change over time in the amount of polyadenylation within a given size class of poly(A)(+) tail, or as the total amount of polyadenylation at the endpoint of the incubation. This study is the first direct demonstration that for a metazoan mitochondrion, polyadenylation is associated with destabilized mRNA. This pattern has also been demonstrated in bacteria, chloroplasts and plant mitochondria and may indicate a conserved mechanism for regulating message half-life that differs from the paradigm for eukaryotic cytoplasm, where increased mRNA stability is associated with polyadenylation.
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Affiliation(s)
- Brian D Eads
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA.
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44
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Nickelsen J. Chloroplast RNA-binding proteins. Curr Genet 2003; 43:392-9. [PMID: 12955455 DOI: 10.1007/s00294-003-0425-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2003] [Revised: 06/20/2003] [Accepted: 06/23/2003] [Indexed: 10/26/2022]
Abstract
Chloroplast gene expression is regulated by nucleus-encoded factors, which mainly act at the post-transcriptional level. Plastid RNA-binding proteins (RBPs) represent good candidates for mediating these functions. The picture emerging from recent analyses is that of a great number of differentially regulated RBPs, which are organized in distinct, spatially separated supramolecular complexes. This reflects the complexity of the regulatory network that underlies the intracellular communication system between the nucleus and the chloroplast.
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Affiliation(s)
- Jörg Nickelsen
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Bochum, Germany.
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45
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Ryan CM, Militello KT, Read LK. Polyadenylation regulates the stability of Trypanosoma brucei mitochondrial RNAs. J Biol Chem 2003; 278:32753-62. [PMID: 12801929 DOI: 10.1074/jbc.m303552200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polyadenylation of RNAs plays a critical role in modulating rates of RNA turnover and ultimately in controlling gene expression in all systems examined to date. In mitochondria, the precise mechanisms by which RNAs are degraded, including the role of polyadenylation, are not well understood. Our previous in organello pulse-chase experiments suggest that poly(A) tails stimulate degradation of mRNAs in the mitochondria of the protozoan parasite Trypanosoma brucei (Militello, K. T., and Read, L. K. (2000) Mol. Cell. Biol. 21, 731-742). In this report, we developed an in vitro assay to directly examine the effects of specific 3'-sequences on RNA degradation. We found that a salt-extracted mitochondrial membrane fraction preferentially degraded polyadenylated mitochondrially and non-mitochondrially encoded RNAs over their non-adenylated counterparts. A poly(A) tail as short as 5 nucleotides was sufficient to stimulate rapid degradation, although an in vivo tail length of 20 adenosines supported the most rapid decay. A poly(U) extension did not promote rapid RNA degradation, and RNA turnover was slowed by the addition of uridine residues to the poly(A) tail. To stimulate degradation, the poly(A) element must be located at the 3' terminus of the RNA. Finally, we demonstrate that degradation of polyadenylated RNAs occurs in the 3' to 5' direction through the action of a hydrolytic exonuclease. These experiments demonstrate that the poly(A) tail can act as a cis-acting element to facilitate degradation of T. brucei mitochondrial mRNAs.
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Affiliation(s)
- Christopher M Ryan
- Department of Microbiology and the Witebsky Center for Microbial Pathogenesis and Immunology, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York 14214, USA
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46
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Rott R, Zipor G, Portnoy V, Liveanu V, Schuster G. RNA polyadenylation and degradation in cyanobacteria are similar to the chloroplast but different from Escherichia coli. J Biol Chem 2003; 278:15771-7. [PMID: 12601000 DOI: 10.1074/jbc.m211571200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism of RNA degradation in Escherichia coli involves endonucleolytic cleavage, polyadenylation of the cleavage product by poly(A) polymerase, and exonucleolytic degradation by the exoribonucleases, polynucleotide phosphorylase (PNPase) and RNase II. The poly(A) tails are homogenous, containing only adenosines in most of the growth conditions. In the chloroplast, however, the same enzyme, PNPase, polyadenylates and degrades the RNA molecule; there is no equivalent for the E. coli poly(A) polymerase enzyme. Because cyanobacteria is a prokaryote believed to be related to the evolutionary ancestor of the chloroplast, we asked whether the molecular mechanism of RNA polyadenylation in the Synechocystis PCC6803 cyanobacteria is similar to that in E. coli or the chloroplast. We found that RNA polyadenylation in Synechocystis is similar to that in the chloroplast but different from E. coli. No poly(A) polymerase enzyme exists, and polyadenylation is performed by PNPase, resulting in heterogeneous poly(A)-rich tails. These heterogeneous tails were found in the amino acid coding region, the 5' and 3' untranslated regions of mRNAs, as well as in rRNA and the single intron located at the tRNA(fmet). Furthermore, unlike E. coli, the inactivation of PNPase or RNase II genes caused lethality. Together, our results show that the RNA polyadenylation and degradation mechanisms in cyanobacteria and chloroplast are very similar to each other but different from E. coli.
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Affiliation(s)
- Ruth Rott
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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47
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Tregoning JS, Nixon P, Kuroda H, Svab Z, Clare S, Bowe F, Fairweather N, Ytterberg J, van Wijk KJ, Dougan G, Maliga P. Expression of tetanus toxin Fragment C in tobacco chloroplasts. Nucleic Acids Res 2003; 31:1174-9. [PMID: 12582236 PMCID: PMC150239 DOI: 10.1093/nar/gkg221] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Revised: 12/05/2002] [Accepted: 12/13/2002] [Indexed: 11/14/2022] Open
Abstract
Fragment C (TetC) is a non-toxic 47 kDa polypeptide fragment of tetanus toxin that can be used as a subunit vaccine against tetanus. Expression of TetC in Escherichia coli and yeast was dependent on the availability of synthetic genes that were required to improve translation efficiency and stabilize the mRNA. To explore the feasibility of producing TetC in tobacco leaves, we attempted expression of both the bacterial high-AT (72.3% AT) and the synthetic higher-GC genes (52.5% AT) in tobacco chloroplasts. We report here that the bacterial high-AT mRNA is stable in tobacco chloroplasts. Significant TetC accumulation was obtained from both genes, 25 and 10% of total soluble cellular protein, respectively, proving the versatility of plastids for expression of unmodified high-AT and high-GC genes. Mucosal immunization of mice with the plastid- produced TetC induced protective levels of TetC antibodies. Thus, expression of TetC in chloroplasts provides a potential route towards the development of a safe, plant-based tetanus vaccine for nasal and oral applications.
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Affiliation(s)
- John S Tregoning
- Waksman Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
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48
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Abstract
Tobacco chloroplasts are ready to be tested as a platform for the expression of recombinant proteins on a commercial scale. They hold the promise of reproducible yields of 5-25% of total soluble cellular protein in leaves and reliability has been achieved through refinement of an expression toolkit that includes vectors, recently developed expression cassettes and systems for marker gene removal. Implementation of plastid transformation technology in other crops, however, has met with difficulty and has delayed agronomic applications.
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Affiliation(s)
- Pal Maliga
- Waksman Institute, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA.
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49
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Walter M, Kilian J, Kudla J. PNPase activity determines the efficiency of mRNA 3'-end processing, the degradation of tRNA and the extent of polyadenylation in chloroplasts. EMBO J 2002; 21:6905-14. [PMID: 12486011 PMCID: PMC139106 DOI: 10.1093/emboj/cdf686] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The exoribonuclease polynucleotide phosphorylase (PNPase) has been implicated in mRNA processing and degradation in bacteria as well as in chloroplasts of higher plants. Here, we report the first comprehensive in vivo study of chloroplast PNPase function. Modulation of PNPase activity in Arabidopsis chloroplasts by a reverse genetic approach revealed that, although this enzyme is essential for efficient 3'-end processing of mRNAs, it is insufficient to mediate transcript degradation. Surprisingly, we identified PNPase as also being indispensable for 3'-end maturation of 23S rRNA transcripts. Analysis of tRNA amounts in transgenic Arabidopsis plants suggests a direct correlation of PNPase activity and tRNA levels, indicating an additional function of this exoribo nuclease in tRNA decay. Moreover, the extent of polyadenylated mRNAs in chloroplasts is negatively correlated with PNPase activity. Together, our results attribute novel functions to PNPase in the metabolism of all major classes of plastid RNAs and suggest an unexpectedly complex role for PNPase in RNA processing and decay.
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MESH Headings
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Blotting, Northern
- Chloroplasts/metabolism
- Cloning, Molecular
- DNA, Complementary/metabolism
- Operon
- Plants, Genetically Modified
- Plasmids/metabolism
- Plastids/metabolism
- Polyadenylation
- Polyribonucleotide Nucleotidyltransferase/metabolism
- Polyribosomes/metabolism
- Protein Biosynthesis
- Protein Structure, Tertiary
- RNA/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer/metabolism
- Thylakoids/metabolism
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Affiliation(s)
| | | | - Jörg Kudla
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069 Ulm, Germany
Corresponding author e-mail:
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50
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Baginsky S, Gruissem W. Endonucleolytic activation directs dark-induced chloroplast mRNA degradation. Nucleic Acids Res 2002; 30:4527-33. [PMID: 12384600 PMCID: PMC137125 DOI: 10.1093/nar/gkf561] [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] [Received: 05/24/2002] [Revised: 08/20/2002] [Accepted: 08/20/2002] [Indexed: 11/12/2022] Open
Abstract
Plastid mRNA stability is tightly regulated by external signals such as light. We have investigated the biochemical mechanism responsible for the dark-induced decrease of relative half-lives for mRNAs encoding photosynthetic proteins. Protein fractions isolated from plastids of light-grown and dark-adapted plants correctly reproduced an RNA degradation pathway in the dark that is downregulated in the light. This dark-dependent pathway is initiated by endonucleolytic cleavages in the petD mRNA precursor substrate proximal to a region that can fold into a stem-loop structure. Polynucleotide phosphorylase (PNPase) polyadenylation activity was strongly increased in the protein fraction isolated from plastids in dark-adapted plants, but interestingly PNPase activity was not required for the initiation of dark-induced mRNA degradation. A protein factor present in the protein fraction from plastids of light-grown plants could inactivate the endonuclease activity and thereby stabilize the RNA substrate in the protein fraction from plastids of dark-adapted plants. The results show that plastid mRNA stability is effectively controlled by the regulation of a specific dark-induced RNA degradation pathway.
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Affiliation(s)
- Sacha Baginsky
- Institute of Plant Sciences, Swiss Federal Institute of Technology, ETH Zentrum, LFW E51.1, Universitätstrasse 2, CH-8092 Zürich, Switzerland.
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