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McKnight BM, Kang S, Le TH, Fang M, Carbonel G, Rodriguez E, Govindarajan S, Albocher-Kedem N, Tran AL, Duncan NR, Amster-Choder O, Golden SS, Cohen SE. Roles for the Synechococcus elongatus RNA-Binding Protein Rbp2 in Regulating the Circadian Clock. J Biol Rhythms 2023; 38:447-460. [PMID: 37515350 PMCID: PMC10528358 DOI: 10.1177/07487304231188761] [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] [Indexed: 07/30/2023]
Abstract
The cyanobacterial circadian oscillator, consisting of KaiA, KaiB, and KaiC proteins, drives global rhythms of gene expression and compaction of the chromosome and regulates the timing of cell division and natural transformation. While the KaiABC posttranslational oscillator can be reconstituted in vitro, the Kai-based oscillator is subject to several layers of regulation in vivo. Specifically, the oscillator proteins undergo changes in their subcellular localization patterns, where KaiA and KaiC are diffuse throughout the cell during the day and localized as a focus at or near the pole of the cell at night. Here, we report that the CI domain of KaiC, when in a hexameric state, is sufficient to target KaiC to the pole. Moreover, increased ATPase activity of KaiC correlates with enhanced polar localization. We identified proteins associated with KaiC in either a localized or diffuse state. We found that loss of Rbp2, found to be associated with localized KaiC, results in decreased incidence of KaiC localization and long-period circadian phenotypes. Rbp2 is an RNA-binding protein, and it appears that RNA-binding activity of Rbp2 is required to execute clock functions. These findings uncover previously unrecognized roles for Rbp2 in regulating the circadian clock and suggest that the proper localization of KaiC is required for a fully functional clock in vivo.
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Affiliation(s)
- Briana M. McKnight
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Shannon Kang
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Tam H. Le
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Genelyn Carbonel
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Esbeydi Rodriguez
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Sutharsan Govindarajan
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
- Department of Biological Sciences, SRM University AP, Amaravati, India
| | - Nitsan Albocher-Kedem
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Amanda L. Tran
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Nicholas R. Duncan
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Susan S. Golden
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Susan E. Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
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2
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Köster T, Haas M, Staiger D. The RIPper case: identification of RNA-binding protein targets by RNA immunoprecipitation. Methods Mol Biol 2014; 1158:107-121. [PMID: 24792047 DOI: 10.1007/978-1-4939-0700-7_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Control at the posttranscriptional level emerges as an important layer of regulation in the circadian timing system. RNA-binding proteins that specifically interact with cis-regulatory motifs within pre-mRNAs are key elements of this regulation. While the ability to interact with RNA in vitro has been demonstrated for numerous Arabidopsis RNA-binding proteins, a full understanding of posttranscriptional networks controlled by an RNA-binding protein requires the identification of its immediate in vivo targets. Here we describe differential RNA immunoprecipitation in transgenic Arabidopsis thaliana plants expressing RNA-binding protein variants epitope-tagged with green fluorescent protein. To control for RNAs that nonspecifically co-purify with the RNA-binding protein, transgenic plants are generated with a mutated version of the RNA-binding protein that is not capable of binding to its target RNAs. The RNA-binding protein variants are expressed under the control of their authentic promoter and cis-regulatory motifs. Incubation of the plants with formaldehyde in vivo cross-links the proteins to their RNA targets. A whole-cell extract is then prepared and subjected to immunoprecipitation with an antibody against the GFP tag and to mock precipitation with an antibody against the unrelated red fluorescent protein. The RNAs coprecipitating with the proteins are eluted from the immunoprecipitate and identified via reverse transcription-PCR.
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Affiliation(s)
- Tino Köster
- Department of Molecular Cell Physiology, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
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Chauton MS, Winge P, Brembu T, Vadstein O, Bones AM. Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles. PLANT PHYSIOLOGY 2013; 161:1034-48. [PMID: 23209127 PMCID: PMC3561001 DOI: 10.1104/pp.112.206177] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time points provide a comprehensive data set on carbon incorporation, fate, and regulation. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidly in the light period. A near-linear decline in both glucans and lipids was observed during the dark period, and transcription profile data indicated that this decline was associated with the onset of mitosis. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light-responding genes in, for example, fatty acid biosynthesis were identified and allocated to biosynthetic processes. Transcripts and cell chemistry data reflect the link between light energy availability and light energy-consuming metabolic processes. Our data confirm the spatial localization of processes in carbon metabolism to either plastids or mitochondria or to glycolysis/gluconeogenesis, which are localized to the cytosol, chloroplast, and mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes and the mining of genes involved in light responses and circadian rhythms.
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Stirk WA, van Staden J, Novák O, Doležal K, Strnad M, Dobrev PI, Sipos G, Ördög V, Bálint P. CHANGES IN ENDOGENOUS CYTOKININ CONCENTRATIONS IN CHLORELLA (CHLOROPHYCEAE) IN RELATION TO LIGHT AND THE CELL CYCLE(1). JOURNAL OF PHYCOLOGY 2011; 47:291-301. [PMID: 27021861 DOI: 10.1111/j.1529-8817.2010.00952.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Endogenous cytokinins were quantified in synchronized Chlorella minutissima Fott et Novákova (MACC 361) and Chlorella sp. (MACC 458) grown in a 14:10 light:dark (L:D) photoperiod. In 24 h experiments, cell division occurred during the dark period, and cells increased in size during the light period. Cytokinin profiles were similar in both strains, consisting of five cis-zeatin (cZ) and three N(6) -(2-isopentenyl)adenine (iP) derivatives. Cytokinin concentrations were low during the dark period and increased during the light period. In 48 h experiments using synchronized C. minutissima (MACC 361), half the cultures were maintained in continuous dark conditions for the second photoperiod. Cell division occurred during both dark periods, and cells increased in size during the light periods. Cultures kept in continuous dark did not increase in size following cell division. DNA analysis confirmed these results, with cultures grown in light having increased DNA concentrations prior to cell division, while cultures maintained in continuous dark had less DNA. Cytokinins (cZ and iP derivatives) were detected in all samples with concentrations increasing over the first 24 h. This increase was followed by a large increase, especially during the second light period where cytokinin concentrations increased 4-fold. Cytokinin concentrations did not increase in cultures maintained in continuous dark conditions. In vivo deuterium-labeling technology was used to measure cytokinin biosynthetic rates during the dark and light periods in C. minutissima with highest biosynthetic rates measured during the light period. These results show that there is a relationship between light, cell division, and cytokinins.
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Affiliation(s)
- Wendy A Stirk
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - Johannes van Staden
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - Ondřej Novák
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - Karel Doležal
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - Miroslav Strnad
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - Petre I Dobrev
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - György Sipos
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - Vince Ördög
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
| | - Péter Bálint
- Research Centre for Plant Growth and Development, University of KwaZulu-Natal Pietermaritzburg, P/Bag X01, Scottsville 3209, South AfricaLaboratory of Growth Regulators, Palacký University and Institute of Experimental Botany AS CR, Slechtitelů 11, CZ-783 71 Olomouc, Czech RepublicInstitute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, CZ-16502, Praha 6, Czech RepublicInstitute of Plant Biology, Faculty of Agricultural and Food Sciences, University of West Hungary, H-9200 Mosonmagyaróvár, Hungary
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Gau BH, Chen TM, Shih YHJ, Sun HS. FUBP3 interacts with FGF9 3' microsatellite and positively regulates FGF9 translation. Nucleic Acids Res 2011; 39:3582-93. [PMID: 21252297 PMCID: PMC3089454 DOI: 10.1093/nar/gkq1295] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A TG microsatellite in the 3'-untranslated region (UTR) of FGF9 mRNA has previously been shown to modulate FGF9 expression. In the present study, we investigate the possible interacting protein that binds to FGF9 3'-UTR UG-repeat and study the mechanism underlying this protein-RNA interaction. We first applied RNA pull-down assays and LC-MS analysis to identify proteins associated with this repetitive sequence. Among the identified proteins, FUBP3 specifically bound to the synthetic (UG)(15) oligoribonucleotide as shown by supershift in RNA-EMSA experiments. The endogenous FGF9 protein was upregulated in response to transient overexpression and downregulated after knockdown of FUBP3 in HEK293 cells. As the relative levels of FGF9 mRNA were similar in these two conditions, and the depletion of FUBP3 had no effect on the turn-over rate of FGF9 mRNA, these data suggested that FUBP3 regulates FGF9 expression at the post-transcriptional level. Further examination using ribosome complex pull-down assay showed overexpression of FUBP3 promotes FGF9 expression. In contrast, polyribosome-associated FGF9 mRNA decreased significantly in FUBP3-knockdown HEK293 cells. Finally, reporter assay suggested a synergistic effect of the (UG)-motif with FUBP3 to fine-tune the expression of FGF9. Altogether, results from this study showed the novel RNA-binding property of FUBP3 and the interaction between FUBP3 and FGF9 3'-UTR UG-repeat promoting FGF9 mRNA translation.
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Affiliation(s)
- Bing-Huang Gau
- Institute of Molecular Medicine, National Cheng Kung University Medical College, Tainan, Taiwan, ROC
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6
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RNA-protein interaction mediating post-transcriptional regulation in the circadian system. Methods Mol Biol 2009; 479:337-51. [PMID: 19083177 DOI: 10.1007/978-1-59745-289-2_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Post-transcriptional control makes an important contribution to shaping transcript profiles of circadianly regulated genes. In Arabidopsis thaliana, the clock-regulated glycine-rich RNA-binding protein ATGRP7 oscillates with a 24-h rhythm and transmits the rhythmicity generated by the central oscillator within the cell. ATGRP7 negatively auto-regulates its own expression at the post-transcriptional level. In response to an elevated protein level, a shift to a cryptic 5' splice site within the intron occurs, leading to an unproductively spliced transcript that rapidly vanishes due to its short half-life. This feedback regulation relies on direct binding of the RNA-binding protein to its own RNA. Here we describe the analysis of RNA-protein interaction in vitro employing recombinant RNA-binding protein and 32P-labelled in vitro transcripts or synthetic RNA oligoribonucleotides comprising the binding site under study.
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7
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Brunner M, Merrow M. The green yeast uses its plant-like clock to regulate its animal-like tail. Genes Dev 2008; 22:825-31. [PMID: 18381887 PMCID: PMC2732389 DOI: 10.1101/gad.1664508] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Michael Brunner
- University of Heidelberg Biochemistry Center, 69120 Heidelberg, Germany
| | - Martha Merrow
- Department of Chronobiology, University of Groningen, 9750AA Haren, The Netherlands
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8
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9
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Vitalini MW, de Paula RM, Park WD, Bell-Pedersen D. The rhythms of life: circadian output pathways in Neurospora. J Biol Rhythms 2007; 21:432-44. [PMID: 17107934 DOI: 10.1177/0748730406294396] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Research in Neurospora crassa pioneered the isolation of clock-controlled genes (ccgs), and more than 180 ccgs have been identified that function in various aspects of the fungal life cycle. Many clock-controlled genes are associated with damage repair, stress responses, intermediary metabolism, protein synthesis, and development. The expression of most of these genes peaks just before dawn and appears to prepare the cells for the desiccation, mutagenesis, and stress caused by sunlight. Progress on characterization of the output signaling pathways from the circadian oscillator mechanism to the ccgs is discussed. The authors also review evidence suggesting that, similar to other clock model organisms, a connection exists between the redox state of the cell and the Neurospora clock. The authors speculate that the clock system may sense not only light but also the redox potential of the cell through one of the PAS domains of the core clock components WC-1 or WC-2.
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Affiliation(s)
- Michael W Vitalini
- Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, TX 77843, USA
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10
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Garbarino-Pico E, Green CB. Posttranscriptional regulation of mammalian circadian clock output. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 72:145-156. [PMID: 18419272 DOI: 10.1101/sqb.2007.72.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Circadian clocks are present in many different cell types/tissues and control many aspects of physiology. This broad control is exerted, at least in part, by the circadian regulation of many genes, resulting in rhythmic expression patterns of 5-10% of the mRNAs in a given tissue. Although transcriptional regulation is certainly involved in this process, it is becoming clear that posttranscriptional mechanisms also have important roles in producing the appropriate rhythmic expression profiles. In this chapter, we review the available data about posttranscriptional regulation of circadian gene expression and highlight the potential role of Nocturnin (Noc) in such processes. NOC is a deadenylase-a ribonuclease that specifically removes poly(A) tails from mRNAs-that is expressed widely in the mouse with high-amplitude rhythmicity. Deadenylation affects the stability and translational properties of mRNAs. Mice lacking the Noc gene have metabolic defects including a resistance to diet-induced obesity, decreased fat storage, changes in lipid-related gene expression profiles in the liver, and altered glucose and insulin sensitivities. These findings suggest that NOC has a pivotal role downstream from the circadian clockwork in the post-transcriptional regulation genes involved in the circadian control of metabolism.
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Affiliation(s)
- E Garbarino-Pico
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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11
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Zhao B, Schneid C, Iliev D, Schmidt EM, Wagner V, Wollnik F, Mittag M. The circadian RNA-binding protein CHLAMY 1 represents a novel type heteromer of RNA recognition motif and lysine homology domain-containing subunits. EUKARYOTIC CELL 2005; 3:815-25. [PMID: 15190002 PMCID: PMC420122 DOI: 10.1128/ec.3.3.815-825.2004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The RNA-binding protein CHLAMY 1 from Chlamydomonas reinhardtii binds specifically to UG> or =7 repeat sequences situated in the 3' untranslated regions of several mRNAs. Its binding activity is controlled by the circadian clock. The biochemical purification and characterization of CHLAMY 1 revealed a novel type of RNA-binding protein. It includes two different subunits (named C1 and C3), whose interaction appears necessary for RNA binding. One of them (C3) belongs to the proteins of the CELF (CUG-BP-ETR-3-like factors) family and thus bears three RNA recognition motif domains. The other is composed of three lysine homology domains and a protein-protein interaction domain (WW). The subunits C1 and C3 have theoretical molecular masses of 45 and 52 kDa, respectively, and are present in nearly equal amounts during the circadian cycle. At the beginning of the subjective night, both can be found in protein complexes of 100 to 160 kDa. However, during subjective day when binding activity of CHLAMY 1 is low, the C1 subunit in addition is present in a high-molecular-mass protein complex of more than 680 kDa. These data indicate posttranslational control of the circadian binding activity of CHLAMY 1. Notably, the C3 subunit shows significant homology to the rat CUG-binding protein 2. Anti-C3 antibodies can recognize the rat homologue, which can also be found in a protein complex in this vertebrate.
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Affiliation(s)
- Bin Zhao
- Institut für Allgemeine Botanik, Friedrich-Schiller-Universität Jena, Am Planetarium 1, 07743 Jena, Germany
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12
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Lidder P, Gutiérrez RA, Salomé PA, McClung CR, Green PJ. Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway. PLANT PHYSIOLOGY 2005; 138:2374-85. [PMID: 16055688 PMCID: PMC1183423 DOI: 10.1104/pp.105.060368] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcriptional and posttranscriptional regulation are well-established mechanisms for circadian gene expression. Among the latter, differential messenger RNA (mRNA) stability has been hypothesized to control gene expression in response to the clock. However, direct proof that the rate of mRNA turnover can be regulated by the clock is lacking. Previous microarray expression data for unstable mRNAs in Arabidopsis (Arabidopsis thaliana) revealed that mRNA instability is associated with a group of genes controlled by the circadian clock. Here, we show that CCR-LIKE (CCL) and SENESCENCE ASSOCIATED GENE 1 transcripts are differentially regulated at the level of mRNA stability at different times of day. In addition, the changes in CCL mRNA stability continue under free-running conditions, indicating that it is controlled by the Arabidopsis circadian clock. Furthermore, we show that these mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant. Disruption of the DST-mediated decay pathway in the dst1 mutant leads to aberrant circadian mRNA oscillations that correlate with alterations of the half-life of CCL mRNA relative to parental plants in the morning and afternoon. That this is due to an effect on the circadian control is evidenced by mRNA decay experiments carried out in continuous light. Finally, we show that the defects exhibited by dst mutants are reflected by an impact on circadian regulation at the whole plant level. Together, these results demonstrate that regulation of mRNA stability is important for clock-controlled expression of specific genes in Arabidopsis. Moreover, these data uncover a connection between circadian rhythms and a sequence-specific mRNA decay pathway.
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Affiliation(s)
- Preetmoninder Lidder
- Michigan State University-Department of Energy Plant Research Laboratory, Cell and Molecular Biology , Michigan State University, East Lansing, Michigan 48824, USA
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Mittag M, Kiaulehn S, Johnson CH. The circadian clock in Chlamydomonas reinhardtii. What is it for? What is it similar to? PLANT PHYSIOLOGY 2005; 137:399-409. [PMID: 15710681 PMCID: PMC1065344 DOI: 10.1104/pp.104.052415] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 10/04/2004] [Accepted: 10/07/2004] [Indexed: 05/17/2023]
Affiliation(s)
- Maria Mittag
- Institut für Allgemeine Botanik, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
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Abstract
Recent advances in understanding circadian (daily) rhythms in the genera Neurospora, Gonyaulax, and Synechococcus are reviewed and new complexities in their circadian systems are described. The previous model, consisting of a unidirectional flow of information from input to oscillator to output, has now expanded to include multiple input pathways, multiple oscillators, multiple outputs; and feedback from oscillator to input and output to oscillator. New posttranscriptional features of the frq/white-collar oscillator (FWC) of Neurospora are described, including protein phosphorylation and degradation, dimerization, and complex formation. Experimental evidence is presented for frq-less oscillator(s) (FLO) downstream of the FWC. Mathematical models of the Neurospora system are also discussed.
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