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Truong A, Myerscough D, Campbell I, Atkinson J, Silberg JJ. A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase. Protein Sci 2023; 32:e4746. [PMID: 37551563 PMCID: PMC10503412 DOI: 10.1002/pro.4746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Flavodoxins (Flds) mediate the flux of electrons between oxidoreductases in diverse metabolic pathways. To investigate whether Flds can support electron transfer to a sulfite reductase (SIR) that evolved to couple with a ferredoxin, we evaluated the ability of Flds to transfer electrons from a ferredoxin-NADP reductase (FNR) to a ferredoxin-dependent SIR using growth complementation of an Escherichia coli strain with a sulfur metabolism defect. We show that Flds from cyanobacteria complement this growth defect when coexpressed with an FNR and an SIR that evolved to couple with a plant ferredoxin. When we evaluated the effect of peptide insertion on Fld-mediated electron transfer, we observed a sensitivity to insertions within regions predicted to be proximal to the cofactor and partner binding sites, while a high insertion tolerance was detected within loops distal from the cofactor and within regions of helices and sheets that are proximal to those loops. Bioinformatic analysis showed that natural Fld sequence variability predicts a large fraction of the motifs that tolerate insertion of the octapeptide SGRPGSLS. These results represent the first evidence that Flds can support electron transfer to assimilatory SIRs, and they suggest that the pattern of insertion tolerance is influenced by interactions with oxidoreductase partners.
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Affiliation(s)
- Albert Truong
- Biochemistry and Cell Biology Graduate ProgramRice UniversityHoustonTexasUSA
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | | | - Ian Campbell
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | | | - Jonathan J. Silberg
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
- Department of Chemical and Biomolecular EngineeringRice UniversityHoustonTexasUSA
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2
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Noorjahan A, Mahesh S, Aiyamperumal B, Anantharaman P. Exploring Marine Fungal Diversity and Their Applications in Agriculture. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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3
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Kroh GE, Pilon M. Iron deficiency and the loss of chloroplast iron-sulfur cluster assembly trigger distinct transcriptome changes in Arabidopsis rosettes. Metallomics 2020; 12:1748-1764. [PMID: 33047775 DOI: 10.1039/d0mt00175a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Regulation of mRNA abundance revealed a genetic program for plant leaf acclimation to iron (Fe) limitation. The transcript for SUFB, a key component of the plastid iron-sulfur (Fe-S) assembly pathway is down-regulated early after Fe deficiency, and prior to down-regulation of mRNAs encoding abundant chloroplast Fe containing proteins, which should economize the use of Fe. What controls this system is unclear. We utilized RNA-seq. aimed to identify differentially expressed transcripts that are co-regulated with SUFB after Fe deficiency in leaves. To distinguish if lack of Fe or lack of Fe-S cofactors and associated loss of enzymatic and photosynthetic activity trigger transcriptome reprogramming, WT plants on low Fe were compared with an inducible sufb-RNAi knockdown. Fe deficiency targeted a limited set of genes and predominantly affected transcripts for chloroplast localized proteins. A set of glutaredoxin transcripts was concertedly down-regulated early after Fe deficiency, however when these same genes were down-regulated by RNAi the effect on known chloroplast Fe deficiency marker proteins was minimal. In promoters of differentially expressed genes, binding motifs for AP2/ERF transcription factors were most abundant and three AP2/ERF transcription factors were also differentially expressed early after low Fe treatment. Surprisingly, Fe deficiency in a WT on low Fe and a sufb-RNAi knockdown presented very little overlap in differentially expressed genes. sufb-RNAi produced expression patterns expected for Fe excess and up-regulation of a transcript for another Fe-S assembly component not affected by low Fe. These findings indicate that Fe scarcity, not Fe utilization, triggers reprogramming of the transcriptome in leaves.
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Affiliation(s)
- Gretchen Elizabeth Kroh
- Biology Department, Colorado State University, 2515 W. Pitkin Street, Fort Collins, CO 80523-1878, USA.
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4
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Georg J, Kostova G, Vuorijoki L, Schön V, Kadowaki T, Huokko T, Baumgartner D, Müller M, Klähn S, Allahverdiyeva Y, Hihara Y, Futschik ME, Aro EM, Hess WR. Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1. Curr Biol 2017; 27:1425-1436.e7. [PMID: 28479323 DOI: 10.1016/j.cub.2017.04.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 01/01/2023]
Abstract
Oxygenic photosynthesis crucially depends on proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Here, we show that the small regulatory RNA (sRNA) IsaR1 (Iron-Stress-Activated RNA 1) plays a pivotal role in acclimation to low-iron conditions. The IsaR1 regulon consists of more than 15 direct targets, including Fe2+-containing proteins involved in photosynthetic electron transfer, detoxification of anion radicals, citrate cycle, and tetrapyrrole biogenesis. IsaR1 is essential for maintaining physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (1) directly, via posttranscriptional repression of gene expression; (2) indirectly, via suppression of pigment; and (3) Fe/S cluster biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a critically important riboregulator. These findings provide a new perspective for understanding the regulation of iron homeostasis in photosynthetic organisms.
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Affiliation(s)
- Jens Georg
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Gergana Kostova
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Linda Vuorijoki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Verena Schön
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Tuomas Huokko
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Desirée Baumgartner
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Maximilian Müller
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Stephan Klähn
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Matthias E Futschik
- CCMAR - Center of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, Devon PL4 8AA, UK
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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Kumar S, Bhatia S. A polymorphic (GA/CT)n- SSR influences promoter activity of Tryptophan decarboxylase gene in Catharanthus roseus L. Don. Sci Rep 2016; 6:33280. [PMID: 27623355 PMCID: PMC5020687 DOI: 10.1038/srep33280] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/17/2016] [Indexed: 12/31/2022] Open
Abstract
Simple Sequence Repeats (SSRs) of polypurine-polypyrimidine type motifs occur very frequently in the 5' flanks of genes in plants and have recently been implicated to have a role in regulation of gene expression. In this study, 2 accessions of Catharanthus roseus having (CT)8 and (CT)21 varying motifs in the 5'UTR of Tryptophan decarboxylase (Tdc) gene, were investigated for its role in regulation of gene expression. Extensive Tdc gene expression analysis in the 2 accessions was carried out both at the level of transcription and translation. Transcript abundance was estimated using Northern analysis and qRT-PCR, whereas the rate of Tdc gene transcription was assessed using in-situ nuclear run-on transcription assay. Translation status of Tdc gene was monitored by quantification of polysome associated Tdc mRNA using qRT-PCR. These observations were validated through transient expression analysis using the fusion construct [CaM35S:(CT)8-21:GUS]. Our study demonstrated that not only does the length of (CT)n -SSRs influences the promoter activity, but the presence of SSRs per se in the 5'-UTR significantly enhances the level of gene expression. We termed this phenomenon as "microsatellite mediated enhancement" (MME) of gene expression. Results presented here will provide leads for engineering plants with enhanced amounts of medicinally important alkaloids.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India
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González A, Sevilla E, Bes MT, Peleato ML, Fillat MF. Pivotal Role of Iron in the Regulation of Cyanobacterial Electron Transport. Adv Microb Physiol 2016; 68:169-217. [PMID: 27134024 DOI: 10.1016/bs.ampbs.2016.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-containing metalloproteins are the main cornerstones for efficient electron transport in biological systems. The abundance and diversity of iron-dependent proteins in cyanobacteria makes those organisms highly dependent of this micronutrient. To cope with iron imbalance, cyanobacteria have developed a survey of adaptation strategies that are strongly related to the regulation of photosynthesis, nitrogen metabolism and other central electron transfer pathways. Furthermore, either in its ferrous form or as a component of the haem group, iron plays a crucial role as regulatory signalling molecule that directly or indirectly modulates the composition and efficiency of cyanobacterial redox reactions. We present here the major mechanism used by cyanobacteria to couple iron homeostasis to the regulation of electron transport, making special emphasis in processes specific in those organisms.
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Affiliation(s)
| | - E Sevilla
- University of Zaragoza, Zaragoza, Spain
| | - M T Bes
- University of Zaragoza, Zaragoza, Spain
| | | | - M F Fillat
- University of Zaragoza, Zaragoza, Spain.
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7
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Nesbit AD, Whippo C, Hangarter RP, Kehoe DM. Translation initiation factor 3 families: what are their roles in regulating cyanobacterial and chloroplast gene expression? PHOTOSYNTHESIS RESEARCH 2015; 126:147-59. [PMID: 25630975 DOI: 10.1007/s11120-015-0074-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 01/02/2015] [Indexed: 05/09/2023]
Abstract
Initiation is a key control point for the regulation of translation in prokaryotes and prokaryotic-like translation systems such as those in plant chloroplasts. Genome sequencing and biochemical studies are increasingly demonstrating differences in many aspects of translation between well-studied microbes such as Escherichia coli and lesser studied groups such as cyanobacteria. Analyses of chloroplast translation have revealed its prokaryotic origin but also uncovered many unique aspects that do not exist in E. coli. Recently, a novel form of posttranscriptional regulation by light color was discovered in the filamentous cyanobacterium Fremyella diplosiphon that requires a putative stem-loop and involves the use of two different prokaryotic translation initiation factor 3s (IF3s). Multiple (up to five) putative IF3s have now been found to be encoded in 22 % of sequenced cyanobacterial genomes and 26 % of plant nuclear genomes. The lack of similar light-color regulation of gene expression in most of these species suggests that IF3s play roles in regulating gene expression in response to other environmental and developmental cues. In the plant Arabidopsis, two nuclear-encoded IF3s have been shown to localize to the chloroplasts, and the mRNA levels encoding these vary significantly in certain organ and tissue types and during several phases of development. Collectively, the accumulated data suggest that in about one quarter of photosynthetic prokaryotes and eukaryotes, IF3 gene families are used to regulate gene expression in addition to their traditional roles in translation initiation. Models for how this might be accomplished in prokaryotes versus eukaryotic plastids are presented.
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Affiliation(s)
- April D Nesbit
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Biology/Chemistry, Purdue University North Central, 1401 S. US 421, Westville, IN, 46391, USA
| | - Craig Whippo
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Natural Science, Dickinson State University, Dickinson, ND, 58601, USA
| | - Roger P Hangarter
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
- Indiana Molecular Biology Institute, Indiana University, Bloomington, IN, 47405, USA.
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Pierella Karlusich JJ, Lodeyro AF, Carrillo N. The long goodbye: the rise and fall of flavodoxin during plant evolution. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5161-78. [PMID: 25009172 PMCID: PMC4400536 DOI: 10.1093/jxb/eru273] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 05/18/2023]
Abstract
Ferredoxins are electron shuttles harbouring iron-sulfur clusters that connect multiple oxido-reductive pathways in organisms displaying different lifestyles. Some prokaryotes and algae express an isofunctional electron carrier, flavodoxin, which contains flavin mononucleotide as cofactor. Both proteins evolved in the anaerobic environment preceding the appearance of oxygenic photosynthesis. The advent of an oxygen-rich atmosphere proved detrimental to ferredoxin owing to iron limitation and oxidative damage to the iron-sulfur cluster, and many microorganisms induced flavodoxin expression to replace ferredoxin under stress conditions. Paradoxically, ferredoxin was maintained throughout the tree of life, whereas flavodoxin is absent from plants and animals. Of note is that flavodoxin expression in transgenic plants results in increased tolerance to multiple stresses and iron deficit, through mechanisms similar to those operating in microorganisms. Then, the question remains open as to why a trait that still confers plants such obvious adaptive benefits was not retained. We compare herein the properties of ferredoxin and flavodoxin, and their contrasting modes of expression in response to different environmental stimuli. Phylogenetic analyses suggest that the flavodoxin gene was already absent in the algal lineages immediately preceding land plants. Geographical distribution of phototrophs shows a bias against flavodoxin-containing organisms in iron-rich coastal/freshwater habitats. Based on these observations, we propose that plants evolved from freshwater macroalgae that already lacked flavodoxin because they thrived in an iron-rich habitat with no need to back up ferredoxin functions and therefore no selective pressure to keep the flavodoxin gene. Conversely, ferredoxin retention in the plant lineage is probably related to its higher efficiency as an electron carrier, compared with flavodoxin. Several lines of evidence supporting these contentions are presented and discussed.
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Affiliation(s)
- Juan J Pierella Karlusich
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Anabella F Lodeyro
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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Führs H, Behrens C, Gallien S, Heintz D, Van Dorsselaer A, Braun HP, Horst WJ. Physiological and proteomic characterization of manganese sensitivity and tolerance in rice (Oryza sativa) in comparison with barley (Hordeum vulgare). ANNALS OF BOTANY 2010; 105:1129-40. [PMID: 20237113 PMCID: PMC2887067 DOI: 10.1093/aob/mcq046] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/04/2010] [Accepted: 01/18/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Research on manganese (Mn) toxicity and tolerance indicates that Mn toxicity develops apoplastically through increased peroxidase activities mediated by phenolics and Mn, and Mn tolerance could be conferred by sequestration of Mn in inert cell compartments. This comparative study focuses on Mn-sensitive barley (Hordeum vulgare) and Mn-tolerant rice (Oryza sativa) as model organisms to unravel the mechanisms of Mn toxicity and/or tolerance in monocots. METHODS Bulk leaf Mn concentrations as well as peroxidase activities and protein concentrations were analysed in apoplastic washing fluid (AWF) in both species. In rice, Mn distribution between leaf compartments and the leaf proteome using 2D isoelectric focusing IEF/SDS-PAGE and 2D Blue native BN/SDS-PAGE was studied. KEY RESULTS The Mn sensitivity of barley was confirmed since the formation of brown spots on older leaves was induced by low bulk leaf and AWF Mn concentrations and exhibited strongly enhanced H2O2-producing and consuming peroxidase activities. In contrast, by a factor of 50, higher Mn concentrations did not produce Mn toxicity symptoms on older leaves in rice. Peroxidase activities, lower by a factor of about 100 in the rice leaf AWF compared with barley, support the view of a central role for these peroxidases in the apoplastic expression of Mn toxicity. The high Mn tolerance of old rice leaves could be related to a high Mn binding capacity of the cell walls. Proteomic studies suggest that the lower Mn tolerance of young rice leaves could be related to Mn excess-induced displacement of Mg and Fe from essential metabolic functions. CONCLUSIONS The results provide evidence that Mn toxicity in barley involves apoplastic lesions mediated by peroxidases. The high Mn tolerance of old leaves of rice involves a high Mn binding capacity of the cell walls, whereas Mn toxicity in less Mn-tolerant young leaves is related to Mn-induced Mg and Fe deficiencies.
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Affiliation(s)
- Hendrik Führs
- Institute for Plant Nutrition, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Christof Behrens
- Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Sébastien Gallien
- Laboratoire de Spectrométrie de Masse Bio-organique, IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Mooléculaire des Plantes (IBMP), 28 rue Goethe, CNRS-UPR2357, Université de Strasbourg, 67083 Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-organique, IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Hans-Peter Braun
- Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Walter J. Horst
- Institute for Plant Nutrition, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
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Régnier P, Hajnsdorf E. Poly(A)-assisted RNA decay and modulators of RNA stability. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:137-85. [PMID: 19215772 DOI: 10.1016/s0079-6603(08)00804-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In Escherichia coli, RNA degradation is orchestrated by the degradosome with the assistance of complementary pathways and regulatory cofactors described in this chapter. They control the stability of each transcript and regulate the expression of many genes involved in environmental adaptation. The poly(A)-dependent degradation machinery has diverse functions such as the degradation of decay intermediates generated by endoribonucleases, the control of the stability of regulatory non coding RNAs (ncRNAs) and the quality control of stable RNA. The metabolism of poly(A) and mechanism of poly(A)-assisted degradation are beginning to be understood. Regulatory factors, exemplified by RraA and RraB, control the decay rates of subsets of transcripts by binding to RNase E, in contrast to regulatory ncRNAs which, assisted by Hfq, target RNase E to specific transcripts. Destabilization is often consecutive to the translational inactivation of mRNA. However, there are examples where RNA degradation is the primary regulatory step.
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Affiliation(s)
- Philippe Régnier
- CNRS UPR9073, Institut de Biologie Physico-Chimique, Paris, France
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11
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Folta KM, Kaufman LS. Isolation of Arabidopsis nuclei and measurement of gene transcription rates using nuclear run-on assays. Nat Protoc 2007; 1:3094-100. [PMID: 17406505 DOI: 10.1038/nprot.2006.471] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Isolation of transcriptionally active nuclei from plant tissues is a fundamental first step in many plant molecular biology protocols. Enriched nuclear fractions may be used in "run-on" assays to measure the rate of transcription for any given gene, adding additional resolution to assays of steady-state transcript accumulation such as RNA-gel blots, RT-PCR or microarrays. The protocols presented here streamline, adapt and optimize existing methods for use in Arabidopsis thaliana. Plant materials are ground in hexylene glycol-based buffers and highly enriched nuclear fractions are obtained using Percoll density gradients. Standard and small-scale protocols are presented, along with a tested method for nuclear run-on assays. The entire process may be completed within 3 days. This capability complements the immense body of steady-state transcript measurements and indirectly identifies instances where message turnover may have a critical and/or primary role in regulating gene expression levels.
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Affiliation(s)
- Kevin M Folta
- Horticultural Sciences Department and the Plant Molecular and Cellular Biology Program, University of Florida, 1301 Fifield Hall, Gainesville, Florida 32611, USA.
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12
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Mazouni K, Domain F, Chauvat F, Cassier-Chauvat C. Expression and regulation of the crucial plant-like ferredoxin of cyanobacteria. Mol Microbiol 2003; 49:1019-29. [PMID: 12890025 DOI: 10.1046/j.1365-2958.2003.03609.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Synechocystis fedI gene (petF, ssl0020) was found to be strongly expressed under the negative control of H2O2 or heavy metals, and the positive control of light fluence (regulation dependent on active photosynthesis) or carbon availability [under the control of NdhR, the regulator of the ndh3 operon encoding NAD(P)H dehydrogenase subunits]. The basic and constitutive promoter (BP) of fedI extending from -62 to +25 (relative to the transcription start point) is weakly active, presumably because it harbours a long (30 bp) spacer between the two crucial motifs: the -10 box (5'-TAgtAT-3', -13 to -8) and the '-35' box (5'-TTGctA-3', -49 to -44). BP strength is strongly enhanced by the two upstream regions, -113 to -82 and -151 to -114, mediating the 30-fold constitutive stimulation and the fourfold light activation respectively. Three well-conserved transcriptional elements were characterized for the first time, namely the -19 box (5'-TTTT-3') that is essential to transcription, and the two twice repeated elements that are both critical to light induction: the TTGyCA-3' box (-35 to -30, and -125 to -120) and the 5'-ATTTyA-3' box (-55 to -50, and -134 to -129). That two of these light induction motifs (5'-TTGtCA-3', -35 to -30; 5'-ATTTcA-3', -55 to -50) occur in the constitutive BP promoter indicate that in the fedI gene light activation and transcription per se are closely interacting. Interestingly, the fedI gene from marine strains was found to lack the three transcriptional elements presently described, as well as the 5'-AGGA-3' Shine-Dalgarno sequence, which are all conserved among the fedI from non-marine strains.
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Affiliation(s)
- Khalil Mazouni
- Service de Biochimie et Génétique Moléculaire, DBJC, CEA Saclay 91191 Gif Sur Yvette, France
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Abstract
Iron is essential to virtually all organisms, but poses problems of toxicity and poor solubility. Bacteria have evolved various mechanisms to counter the problems imposed by their iron dependence, allowing them to achieve effective iron homeostasis under a range of iron regimes. Highly efficient iron acquisition systems are used to scavenge iron from the environment under iron-restricted conditions. In many cases, this involves the secretion and internalisation of extracellular ferric chelators called siderophores. Ferrous iron can also be directly imported by the G protein-like transporter, FeoB. For pathogens, host-iron complexes (transferrin, lactoferrin, haem, haemoglobin) are directly used as iron sources. Bacterial iron storage proteins (ferritin, bacterioferritin) provide intracellular iron reserves for use when external supplies are restricted, and iron detoxification proteins (Dps) are employed to protect the chromosome from iron-induced free radical damage. There is evidence that bacteria control their iron requirements in response to iron availability by down-regulating the expression of iron proteins during iron-restricted growth. And finally, the expression of the iron homeostatic machinery is subject to iron-dependent global control ensuring that iron acquisition, storage and consumption are geared to iron availability and that intracellular levels of free iron do not reach toxic levels.
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Affiliation(s)
- Simon C Andrews
- School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, UK.
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14
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Martı́nez AT. Molecular biology and structure-function of lignin-degrading heme peroxidases. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(01)00521-x] [Citation(s) in RCA: 321] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Ruiz-Dueñas FJ, Guillén F, Camarero S, Pérez-Boada M, Martínez MJ, Martínez AT. Regulation of peroxidase transcript levels in liquid cultures of the ligninolytic fungus Pleurotus eryngii. Appl Environ Microbiol 1999; 65:4458-63. [PMID: 10508075 PMCID: PMC91593 DOI: 10.1128/aem.65.10.4458-4463.1999] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A versatile peroxidase able to oxidize Mn(2+) as well as phenolic and nonphenolic aromatic compounds is produced in peptone-containing liquid cultures of Pleurotus eryngii encoded by the gene mnpl. The regulation of its transcript levels was investigated by Northern blotting of total RNA. High-peroxidase transcripts and activity were found in cultures grown in glucose-peptone medium, whereas only basal levels were detected in glucose-ammonium medium. The addition of more than 25 microM Mn(2+) to the former medium did not result in detectable peroxidase transcripts or activity. Potential regulators were also added to isolated mycelium. In this way, it was shown that high transcript levels (in peroxidase-expressing mycelium) were maintained on peptone, whereas expression was not induced in short-term incubation experiments. Similar results were obtained with Mn(2+) ions. Strong induction of mnpl expression was caused by exogenous H(2)O(2) or by continuous H(2)O(2) generation during redox cycling of menadione. By the use of the latter system in the presence of Fe(3+), which catalyzes the reduction of H(2)O(2) to hydroxyl radical, it was shown for the first time that the presence of this strong oxidant causes a rapid increase of the transcripts of a ligninolytic peroxidase. In conclusion, peptone and Mn(2+) affect the levels of transcripts of this versatile peroxidase in culture, and reduced oxygen species induce short-term expression in isolated mycelium, probably via a stress response mechanism.
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Affiliation(s)
- F J Ruiz-Dueñas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain
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16
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Abstract
Iron is an essential nutrient for nearly all organisms but presents problems of toxicity, poor solubility and low availability. These problems are alleviated through the use of iron-storage proteins. Bacteria possess two types of iron-storage protein, the haem-containing bacterioferritins and the haem-free ferritins. These proteins are widespread in bacteria, with at least 39 examples known so far in eubacteria and archaebacteria. The bacterioferritins and ferritins are distantly related but retain similar structural and functional properties. Both are composed of 24 identical or similar subunits (approximately 19 kDa) that form a roughly spherical protein (approximately 450 kDa, approximately 120 A diameter) containing a large hollow centre (approximately 80 A diameter). The hollow centre acts as an iron-storage cavity with the capacity to accommodate at least 2000 iron atoms in the form of a ferric-hydroxyphosphate core. Each subunit contains a four-helix bundle which carries the active site or ferroxidase centre of the protein. The ferroxidase centres endow ferrous-iron-oxidizing activity and are able to form a di-iron species that is an intermediate in the iron uptake, oxidation and core formation process. Bacterioferritins contain up to 12 protoporphyrin IX haem groups located at the two-fold interfaces between pairs of two-fold related subunits. The role of the haem is unknown, although it may be involved in mediating iron-core reduction and iron release. Some bacterioferritins are composed of two subunit types, one conferring haem-binding ability (alpha) and the other (beta) bestowing ferroxidase activity. Bacterioferritin genes are often adjacent to genes encoding a small [2Fe-2S]-ferredoxin (bacterioferritin-associated ferredoxin or Bfd). Bfd may directly interact with bacterioferritin and could be involved in releasing iron from (or delivering iron to) bacterioferritin or other iron complexes. Some bacteria contain two bacterioferritin subunits, or two ferritin subunits, that in most cases co-assemble. Others possess both a bacterioferritin and a ferritin, while some appear to lack any type of iron-storage protein. The reason for these differences is not understood. Studies on ferritin mutants have shown that ferritin enhances growth during iron starvation and is also involved in iron accumulation in the stationary phase of growth. The ferritin of Campylobacter jejuni is involved in redox stress resistance, although this does not appear to be the case for Escherichia coli ferritin (FtnA). No phenotype has been determined for E. coli bacterioferritin mutants and the precise role of bacterioferritin in E. coli remains uncertain.
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Affiliation(s)
- S C Andrews
- School of Animal and Microbial Sciences, University of Reading, UK
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17
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Westenberg DJ, Guerinot ML. Regulation of bacterial gene expression by metals. ADVANCES IN GENETICS 1998; 36:187-238. [PMID: 9348656 DOI: 10.1016/s0065-2660(08)60310-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- D J Westenberg
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
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18
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Soltes-Rak E, Kushner DJ, Williams DD, Coleman JR. Factors regulating cryIVB expression in the cyanobacterium--Synechococcus PCC 7942. MOLECULAR & GENERAL GENETICS : MGG 1995; 246:301-8. [PMID: 7531814 DOI: 10.1007/bf00288602] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The expression of the larvicidal Bacillus thuringiensis subsp. israelensis cryIVB gene in cyanobacteria has been suggested to be an effective means of controlling mosquito populations. Using a variety of cryIVB constructs, in this study we have examined the effect of Synechococcus PCC 7942 culture age on intracellular toxin levels and have attempted to determine the mechanisms by which cryIVB gene expression is regulated. The data suggest that specific degradation of the cryIVB mRNA limits toxin production; however, the addition of cyanobacterial 3' untranslated DNA sequences to the cryIVB gene did not improve mRNA stability or toxin levels. An analysis of the cryIVB sequence and comparison of codon usage patterns with highly expressed cyanobacterial genes suggest that inefficient translation and intragenic ribosomal binding sites impede protein synthesis and result in rapid turnover of the toxin mRNA.
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MESH Headings
- Bacillus thuringiensis/chemistry
- Bacillus thuringiensis/genetics
- Bacillus thuringiensis Toxins
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Bacterial Toxins
- Base Sequence
- Codon/genetics
- Cyanobacteria/genetics
- Cyanobacteria/growth & development
- Cyanobacteria/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Endotoxins/biosynthesis
- Endotoxins/genetics
- Gene Expression Regulation, Bacterial
- Genes, Bacterial/genetics
- Hemolysin Proteins
- Molecular Sequence Data
- Nucleic Acid Conformation
- Promoter Regions, Genetic/genetics
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/biosynthesis
- Ribosomes/metabolism
- Transcription, Genetic
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Affiliation(s)
- E Soltes-Rak
- Dept. of Botany, University of Toronto, Ontario, Canada
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19
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Bovy A, Van den Berg C, De Vrieze G, Thompson WF, Weisbeek P, Smeekens S. Light-regulated expression of the Arabidopsis thaliana ferredoxin gene requires sequences upstream and downstream of the transcription initiation site. PLANT MOLECULAR BIOLOGY 1995; 27:27-39. [PMID: 7865794 DOI: 10.1007/bf00019176] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The effect of light on the expression of the Arabidopsis thaliana ferredoxin gene (fedA) was studied in mature tobacco plants. In light-treated leaves of tobacco plants transformed with a full-length ferredoxin gene, fedA-specific mRNA levels were more than twenty fold higher than in dark-treated controls. This indicates that all components for regulation of the Arabidopsis ferredoxin gene are present in tobacco. To identify light-regulatory elements in the fedA gene, we have tested a set of chimeric genes containing various parts of the fedA gene for light-dependent expression in mature tobacco plants. A fedA promoter-GUS fusion gene was not light-responsive, indicating that the 5'-upstream promoter region is not sufficient for light regulation. Fusion genes in which different transcribed regions of the fedA gene were expressed from the CaMV 35S promoter showed only limited light regulation, if any at all. This indicates that, like the fedA upstream region, the region downstream of the transcription start site is also not sufficient for full light regulation. The combined results suggest that for full light-regulated expression of the fedA gene, both the promoter region and sequences downstream of the transcription start site are required.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/radiation effects
- Base Sequence
- DNA, Plant/genetics
- DNA, Recombinant/genetics
- Ferredoxins/genetics
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- Light
- Molecular Sequence Data
- Pisum sativum/genetics
- Plants, Genetically Modified
- Plants, Toxic
- Promoter Regions, Genetic/genetics
- RNA, Messenger/analysis
- Regulatory Sequences, Nucleic Acid/genetics
- Nicotiana/genetics
- Transcription, Genetic/genetics
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Affiliation(s)
- A Bovy
- Department of Molecular Cell Biology, University of Utrecht, Netherlands
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Page KM, Connolly EL, Guerinot ML. Effect of iron availability on expression of the Bradyrhizobium japonicum hemA gene. J Bacteriol 1994; 176:1535-8. [PMID: 8113199 PMCID: PMC205226 DOI: 10.1128/jb.176.5.1535-1538.1994] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bradyrhizobium japonicum produces delta-aminolevulinic acid, the universal precursor of tetrapyrroles, in a reaction catalyzed by the product of the hemA gene. Expression of the B. japonicum hemA gene is affected by iron availability. Activity of a hemA-lacZ fusion is increased approximately threefold by iron, and RNA analysis indicates that iron regulation is at the level of mRNA accumulation. To our knowledge, this is the first example of an iron-regulated heme biosynthetic gene in prokaryotes.
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Affiliation(s)
- K M Page
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
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Bauer CC, Scappino L, Haselkorn R. Growth of the cyanobacterium Anabaena on molecular nitrogen: NifJ is required when iron is limited. Proc Natl Acad Sci U S A 1993; 90:8812-6. [PMID: 8415612 PMCID: PMC47450 DOI: 10.1073/pnas.90.19.8812] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The nifJ gene of Klebsiella pneumoniae encodes an oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin, which reduces nitrogenase. The nifJ gene of Anabaena 7120, isolated from a cosmid bank, was found to contain an open reading frame encoding a 1197-aa protein. The deduced amino acid sequence shows 50% identity to the Klebsiella homolog. The nifJ gene in Anabaena 7120 was inactivated by chromosomal interruption. The resulting mutant was unable to grow on medium depleted of both iron and combined nitrogen but grew normally, fixing nitrogen, when iron was present. NifJ transcripts of 2.7 and 4.3 kb are induced by iron depletion irrespective of nitrogen status. One particular stretch of the Anabaena 7120 nifJ gene encodes 12 aa with no complementary matches in the Klebsiella protein. This insert contains five tandem repeats of the heptamer CCCCAGT. These heptamers, as well as heptamers and octamers of other related sequences, have been located in a number of cyanobacterial genomes but are usually not found within the coding region of a gene. The site of the Anabaena 7120 heptamers in the nifJ genes of other filamentous cyanobacteria contains a surprising diversity of repeated sequences, both octamers and heptamers. The corresponding protein inserts range in length from 1 to 21 aa, relative to Klebsiella NifJ.
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Affiliation(s)
- C C Bauer
- Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637
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22
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Bovy A, de Kruif J, de Vrieze G, Borrias M, Weisbeek P. Iron-dependent protection of the Synechococcus ferredoxin I transcript against nucleolytic degradation requires cis-regulatory sequences in the 5' part of the messenger RNA. PLANT MOLECULAR BIOLOGY 1993; 22:1047-1065. [PMID: 8400125 DOI: 10.1007/bf00028977] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have previously reported that the ferredoxin I gene from Synechococcus sp. PCC 7942 is regulated by iron at the level of differential mRNA stability. To identify iron-responsive elements in the Synechococcus ferredoxin transcript, we have tested chimaeric constructs containing translational fusions between the Synechococcus and the Anabaena sp. PCC 7937 ferredoxin genes for iron-dependent expression in transgenic Synechococcus strains. This strategy was based on the observation that the level of the Anabaena ferredoxin mRNA did not increase upon iron addition in Synechococcus. Our results show that the presence of the first 207 nucleotides of the Synechococcus ferredoxin transcript is sufficient to confer iron responsiveness to the chimaeric transcripts. This iron responsiveness was accomplished by an increased stability of the chimaeric transcript in the presence of iron, as was found for the intact Synechococcus ferredoxin gene. Addition of the translation inhibitor chloramphenicol to the cultures led to a rapid stabilization, in low- and high-iron conditions, of the wild-type Synechococcus ferredoxin transcript as well as all chimaeric ferredoxin transcripts tested. These results suggest the existence of a constitutively expressed nuclease capable of degrading the ferredoxin transcripts. They further support the suggestion that the first 207 nucleotides of the Synechococcus transcript contain a specific sequence that is recognized by an iron-responsive factor and that this interaction leads to protection against degradation.
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Affiliation(s)
- A Bovy
- Department of Molecular Cell Biology, University of Utrecht, Netherlands
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23
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Vorst O, van Dam F, Weisbeek P, Smeekens S. Light-regulated expression of the Arabidopsis thaliana ferredoxin A gene involves both transcriptional and post-transcriptional processes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1993; 3:793-803. [PMID: 8401612 DOI: 10.1111/j.1365-313x.1993.00793.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ferredoxin is part of the photosynthetic apparatus of the chloroplast and is encoded in the nucleus. In Arabidopsis thaliana expression of the ferredoxin A gene is influenced by both the presence of chloroplasts and light. Tobacco plants transformed with a ferredoxin promoter-GUS fusion gene showed a tissue-specific and light-dependent expression pattern. The effect of light on the expression of the fusion gene in transgenic seedlings was only two- to fourfold, which is less pronounced than the 20-fold effect in Arabidopsis itself. Run-on transcription assays with nuclei isolated from Arabidopsis revealed a twofold modulation of transcriptional activity of the ferredoxin A gene under the influence of light. These results suggest the involvement of post-transcriptional processes in light-regulated gene expression. A ferredoxin promoter deletion series ranging from -1205 to -143 was studied. All but the smallest deletion construct (at position -143 relative to the translation start site) showed comparable expression levels in mature leaves, suggesting the presence of a positive regulating element between -269 and -143. The same pattern of tissue specificity was found in all promoter deletions studied. Expression of the fusion genes is high in all chloroplast-containing cells: mesophyll, chlorenchyma, paravascular tissue, epidermal and stomatal guard cells and trichomes. Transgenic seedlings treated with norflurazon, which blocks the development of green chloroplasts, showed a two- to fourfold reduction in GUS expression for all constructs. In Arabidopsis seedlings the effect of norflurazon on the expression of the ferredoxin A was eightfold. This again can be explained by the need for post-transcriptional processes of the regulated gene expression of Arabidopsis ferredoxin A.
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Affiliation(s)
- O Vorst
- Department of Molecular Cell Biology, University of Utrecht, The Netherlands
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