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Anna G, Kannan NN. Post-transcriptional modulators and mediators of the circadian clock. Chronobiol Int 2021; 38:1244-1261. [PMID: 34056966 PMCID: PMC7611477 DOI: 10.1080/07420528.2021.1928159] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 01/04/2023]
Abstract
The endogenous circadian timekeeping system drives ~24-h rhythms in gene expression and rhythmically coordinates the physiology, metabolism and behavior in a wide range of organisms. Regulation at various levels is important for the accurate functioning of this circadian timing system. The core circadian oscillator consists of an interlocked transcriptional-translational negative feedback loop (TTFL) that imposes a substantial delay between the accumulation of clock gene mRNA and its protein to generate 24-h oscillations. This TTFL mediated daily oscillation of clock proteins is further fine-tuned by post-translational modifications that regulate the clock protein stability, interaction with other proteins and subcellular localization. Emerging evidence from various studies indicates that besides TTFL and post-translational modifications, post-transcriptional regulation plays a key role in shaping the rhythmicity of mRNAs and to delay the accumulation of clock proteins in relation to their mRNAs. In this review, we summarize the current knowledge on the importance of post-transcriptional regulatory mechanisms such as splicing, polyadenylation, the role of RNA-binding proteins, RNA methylation and microRNAs in the context of shaping the circadian rhythmicity in Drosophila and mammals. In particular, we discuss microRNAs, an important player in post-transcriptional regulation of core-clock machinery, circadian neural circuit, clock input, and output pathways. Furthermore, we provide an overview of the microRNAs that exhibit diurnal rhythm in expression and their role in mediating rhythmic physiological processes.
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Affiliation(s)
- Geo Anna
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala 695551, India
| | - Nisha N Kannan
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala 695551, India
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2
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Yang L, Wang ZA, Zuo H, Geng R, Guo Z, Niu S, Weng S, He J, Xu X. The LARK protein is involved in antiviral and antibacterial responses in shrimp by regulating humoral immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103826. [PMID: 32784011 DOI: 10.1016/j.dci.2020.103826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
The LARK proteins containing a C2HC-type zinc finger motif and two RNA recognition motifs are conserved across vertebrates and invertebrates. Previous studies have suggested that invertebrate LARKs and their mammalian counterparts, the RBM4 proteins, regulate gene expression by affecting RNA stability and post-transcriptional processing, participating in multiple life processes. In the current study, the LARK gene from Pacific white shrimp Litopenaeus vannamei was identified and functionally explored in the context of immunity. The LARK protein was mainly present in the nucleus of its expression vector-transfected S2 cells, and the LARK mRNA was detectable in all the tested shrimp tissues. Expression of LARK in gill was up-regulated by immune stimulation with various pathogens. In vivo experiments demonstrated that LARK played positive roles in both antiviral and antibacterial responses and silencing of LARK could make shrimp more susceptible to infection with Vibrio parahaemolyticus and white spot syndrome virus (WSSV). Although silencing of LARK did not affect the phagocytic activity of hemocytes, it regulated expression of many components of the NF-κB and JAK-STAT pathways and a series of immune function proteins. These suggested that LARK could be mainly involved in regulation of humoral immunity. The current study could help reveal the roles of LARK/RBM4 in immunity and further explore the regulatory mechanisms of shrimp immunity.
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Affiliation(s)
- Linwei Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Zi-Ang Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Hongliang Zuo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Ran Geng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Zhixun Guo
- South China Sea Fisheries Research Institute (CAFS), Guangzhou, PR China
| | - Shengwen Niu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
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3
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Bou Sleiman M, Frochaux MV, Andreani T, Osman D, Guigo R, Deplancke B. Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes. Genome Biol 2020; 21:4. [PMID: 31948480 PMCID: PMC6966827 DOI: 10.1186/s13059-019-1918-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/09/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females from classical Drosophila melanogaster strains as well as 38 inbred lines. RESULTS We find that infection leads to extensive differences in isoform ratios, which results in a more diverse transcriptome with longer 5' untranslated regions (5'UTRs). We establish a role for genetic variation in mediating inter-individual splicing differences, with local splicing quantitative trait loci (local-sQTLs) being preferentially located at the 5' end of transcripts and directly upstream of splice donor sites. Moreover, local-sQTLs are more numerous in the infected state, indicating that acute stress unmasks a substantial number of silent genetic variants. We observe a general increase in intron retention concentrated at the 5' end of transcripts across multiple strains, whose prevalence scales with the degree of pathogen virulence. The length, GC content, and RNA polymerase II occupancy of these introns with increased retention suggest that they have exon-like characteristics. We further uncover that retained intron sequences are enriched for the Lark/RBM4 RNA binding motif. Interestingly, we find that lark is induced by infection in wild-type flies, its overexpression and knockdown alter survival, and tissue-specific overexpression mimics infection-induced intron retention. CONCLUSION Our collective findings point to pervasive and consistent RNA splicing changes, partly mediated by Lark/RBM4, as being an important aspect of the gut response to infection.
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Affiliation(s)
- Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institue of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Vincent Frochaux
- Laboratory of System Biology and Genetics and Swiss Institute of Bioinformatics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Tommaso Andreani
- Computational Biology and Data Mining Group, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Dani Osman
- Faculty of Sciences III and Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300 Lebanon
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Catalonia Spain
| | - Bart Deplancke
- Laboratory of Integrative Systems Physiology, Institue of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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4
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Niu K, Xiang L, Jin Y, Peng Y, Wu F, Tang W, Zhang X, Deng H, Xiang H, Li S, Wang J, Song Q, Feng Q. Identification of LARK as a novel and conserved G-quadruplex binding protein in invertebrates and vertebrates. Nucleic Acids Res 2019; 47:7306-7320. [PMID: 31165881 PMCID: PMC6698653 DOI: 10.1093/nar/gkz484] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 12/30/2022] Open
Abstract
Double-stranded DNAs are usually present in the form of linear B-form double-helix with the base pairs of adenine (A) and thymine (T) or cytosine (C) and guanine (G), but G-rich DNA can form four-stranded G-quadruplex (G4) structures, which plays important roles in transcription, replication, translation and protection of telomeres. In this study, a RNA recognition motif (RRM)-containing protein, BmLARK, was identified and demonstrated to bind G4 structures in the promoters of a transcription factor BmPOUM2 and other three unidentified genes of Bombyx mori, as well as three well-defined G4 structures in the human genes. Homologous LARKs from Bombyx mori, Drosophila melanogaster, Mus musculus and Homo sapiens bound G4 structures in BmPOUM2 and other genes in B. mori and H. sapiens. Upon binding, LARK facilitated the formation and stability of the G4 structure, enhancing the transcription of target genes. The G4 structure was visualized in vivo in cells and testis from invertebrate B. mori and vertebrate Chinese hamster ovary (CHO) cells. The results of this study strongly suggest that LARK is a novel and conserved G4-binding protein and that the G4 structure may have developed into an elaborate epigenetic mechanism of gene transcription regulation during evolution.
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Affiliation(s)
- Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lijun Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Ying Jin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Feng Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wenhuan Tang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
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5
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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6
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Xu J, Zhang P, Kusakabe T, Mon H, Li Z, Zhu L, Iiyama K, Banno Y, Morokuma D, Lee JM. Comparative proteomic analysis of hemolymph proteins from Autographa californica multiple nucleopolyhedrovirus (AcMNPV)-sensitive or -resistant silkworm strains during infections. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 16:36-47. [DOI: 10.1016/j.cbd.2015.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 07/21/2015] [Accepted: 07/26/2015] [Indexed: 01/07/2023]
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7
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Huang Y, McNeil GP, Jackson FR. Translational regulation of the DOUBLETIME/CKIδ/ε kinase by LARK contributes to circadian period modulation. PLoS Genet 2014; 10:e1004536. [PMID: 25211129 PMCID: PMC4161311 DOI: 10.1371/journal.pgen.1004536] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 06/12/2014] [Indexed: 12/02/2022] Open
Abstract
The Drosophila homolog of Casein Kinase I δ/ε, DOUBLETIME (DBT), is required for Wnt, Hedgehog, Fat and Hippo signaling as well as circadian clock function. Extensive studies have established a critical role of DBT in circadian period determination. However, how DBT expression is regulated remains largely unexplored. In this study, we show that translation of dbt transcripts are directly regulated by a rhythmic RNA-binding protein (RBP) called LARK (known as RBM4 in mammals). LARK promotes translation of specific alternative dbt transcripts in clock cells, in particular the dbt-RC transcript. Translation of dbt-RC exhibits circadian changes under free-running conditions, indicative of clock regulation. Translation of a newly identified transcript, dbt-RE, is induced by light in a LARK-dependent manner and oscillates under light/dark conditions. Altered LARK abundance affects circadian period length, and this phenotype can be modified by different dbt alleles. Increased LARK delays nuclear degradation of the PERIOD (PER) clock protein at the beginning of subjective day, consistent with the known role of DBT in PER dynamics. Taken together, these data support the idea that LARK influences circadian period and perhaps responses of the clock to light via the regulated translation of DBT. Our study is the first to investigate translational control of the DBT kinase, revealing its regulation by LARK and a novel role of this RBP in Drosophila circadian period modulation. The CKI family of serine/threonine kinase regulates diverse cellular processes, through binding to and phosphorylation of a variety of protein substrates. In mammals, mutations in two members of the family, CKIε and CKIδ were found to affect circadian period length, causing phenotypes such as altered circadian period in rodents and the Familial Advanced Sleep Phase Syndrome (FASPS) in human. The Drosophila CKI δ/ε homolog DOUBLETIME (DBT) is known to have important roles in development and circadian clock function. Despite extensive studies of DBT function, little is known about how its expression is regulated. In a previous genome-wide study, we identified dbt mRNAs as potential targets of the LARK RBP. Here we describe a detailed study of the regulation of DBT expression by LARK. We found that LARK binds to and regulates translation of dbt mRNA, promoting expression of a smaller isoform; we suggest this regulatory mechanism contributes to circadian period determination. In addition, we have identified a dbt mRNA that exhibits light-induced changes in translational status, in a LARK-dependent manner. Our study is the first to analyze the translational regulation of DBT, setting the stage for similar studies in other contexts and model systems.
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Affiliation(s)
- Yanmei Huang
- Department of Neuroscience, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Gerard P McNeil
- Department of Biology, York College, Jamaica, New York, New York, United States of America
| | - F Rob Jackson
- Department of Neuroscience, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
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8
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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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9
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Ribonucleoprotein complexes that control circadian clocks. Int J Mol Sci 2013; 14:9018-36. [PMID: 23698761 PMCID: PMC3676770 DOI: 10.3390/ijms14059018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/07/2013] [Accepted: 04/15/2013] [Indexed: 12/03/2022] Open
Abstract
Circadian clocks are internal molecular time-keeping mechanisms that enable organisms to adjust their physiology and behavior to the daily surroundings. Misalignment of circadian clocks leads to both physiological and health impairment. Post-transcriptional regulation and translational regulation of circadian clocks have been extensively investigated. In addition, accumulating evidence has shed new light on the involvement of ribonucleoprotein complexes (RNPs) in the post-transcriptional regulation of circadian clocks. Numerous RNA-binding proteins (RBPs) and RNPs have been implicated in the post-transcriptional modification of circadian clock proteins in different model organisms. Herein, we summarize the advances in the current knowledge on the role of RNP complexes in circadian clock regulation.
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10
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Protein phosphorylation changes reveal new candidates in the regulation of egg activation and early embryogenesis in D. melanogaster. Dev Biol 2012; 370:125-34. [PMID: 22884528 DOI: 10.1016/j.ydbio.2012.07.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 07/20/2012] [Accepted: 07/21/2012] [Indexed: 11/24/2022]
Abstract
Egg activation is the series of events that must occur for a mature oocyte to become capable of supporting embryogenesis. These events include changes to the egg's outer coverings, the resumption and completion of meiosis, the translation of new proteins, and the degradation of specific maternal mRNAs. While we know some of the molecules that direct the initial events of egg activation, it remains unclear how multiple pathways are coordinated to change the cellular state from mature oocyte to activated egg. Using a proteomic approach we have identified new candidates for the regulation and progression of egg activation. Reasoning that phosphorylation can simultaneously and rapidly modulate the activity of many proteins, we identified proteins that are post-translationally modified during the transition from oocyte to activated egg in Drosophila melanogaster. We find that at least 311 proteins change in phosphorylation state between mature oocytes and activated eggs. These proteins fall into various functional classes related to the events of egg activation including calcium binding, proteolysis, and protein translation. Our set of candidates includes genes already associated with egg activation, as well as many genes not previously studied during this developmental period. RNAi knockdown of a subset of these genes revealed a new gene, mrityu, necessary for embryonic development past the first mitosis. Thus, by identifying phospho-modulated proteins we have produced a focused candidate set for future genetic studies to test their roles in egg activation and the initiation of embryogenesis.
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11
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Molecular and genetic analysis of the Drosophila model of fragile X syndrome. Results Probl Cell Differ 2012; 54:119-56. [PMID: 22009350 DOI: 10.1007/978-3-642-21649-7_7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Drosophila genome contains most genes known to be involved in heritable disease. The extraordinary genetic malleability of Drosophila, coupled to sophisticated imaging, electrophysiology, and behavioral paradigms, has paved the way for insightful mechanistic studies on the causes of developmental and neurological disease as well as many possible interventions. Here, we focus on one of the most advanced examples of Drosophila genetic disease modeling, the Drosophila model of Fragile X Syndrome, which for the past decade has provided key advances into the molecular, cellular, and behavioral defects underlying this devastating disorder. We discuss the multitude of RNAs and proteins that interact with the disease-causing FMR1 gene product, whose function is conserved from Drosophila to human. In turn, we consider FMR1 mechanistic relationships in non-neuronal tissues (germ cells and embryos), peripheral motor and sensory circuits, and central brain circuits involved in circadian clock activity and learning/memory.
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12
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Kojima S, Shingle DL, Green CB. Post-transcriptional control of circadian rhythms. J Cell Sci 2011; 124:311-20. [PMID: 21242310 DOI: 10.1242/jcs.065771] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circadian rhythms exist in most living organisms. The general molecular mechanisms that are used to generate 24-hour rhythms are conserved among organisms, although the details vary. These core clocks consist of multiple regulatory feedback loops, and must be coordinated and orchestrated appropriately for the fine-tuning of the 24-hour period. Many levels of regulation are important for the proper functioning of the circadian clock, including transcriptional, post-transcriptional and post-translational mechanisms. In recent years, new information about post-transcriptional regulation in the circadian system has been discovered. Such regulation has been shown to alter the phase and amplitude of rhythmic mRNA and protein expression in many organisms. Therefore, this Commentary will provide an overview of current knowledge of post-transcriptional regulation of the clock genes and clock-controlled genes in dinoflagellates, plants, fungi and animals. This article will also highlight how circadian gene expression is modulated by post-transcriptional mechanisms and how this is crucial for robust circadian rhythmicity.
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Affiliation(s)
- Shihoko Kojima
- Department of Neuroscience, University of Texas Southwestern Medical Center, NB4.204G, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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13
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Zhang L, Weng W, Guo J. Posttranscriptional mechanisms in controlling eukaryotic circadian rhythms. FEBS Lett 2011; 585:1400-5. [PMID: 21414314 DOI: 10.1016/j.febslet.2011.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
Abstract
The circadian clock is essential in almost all living organisms to synchronise biochemical, metabolic, physiological and behavioural cycles to daily changing environmental factors. In a highly conserved fashion, the circadian clock is primarily controlled by multiple positive and negative molecular circuitries that control gene expression. More recently, research in Neurospora and other eukaryotes has uncovered the involvement of additional regulatory components that operate at the posttranslational level to fine tune the circadian system. Though it remains poorly understood, a growing body of evidence has shown that posttranscriptional regulation controls the expression of both circadian oscillator and output gene transcripts at a number of different steps. This regulation is crucial for driving and maintaining robust circadian rhythms. Here we review recent advances in circadian rhythm research at the RNA level.
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Affiliation(s)
- Lin Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
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14
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Staiger D, Köster T. Spotlight on post-transcriptional control in the circadian system. Cell Mol Life Sci 2011; 68:71-83. [PMID: 20803230 PMCID: PMC11114774 DOI: 10.1007/s00018-010-0513-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 08/16/2010] [Accepted: 08/16/2010] [Indexed: 10/19/2022]
Abstract
An endogenous timing mechanism, the circadian clock, causes rhythmic expression of a considerable fraction of the genome of most organisms to optimally align physiology and behavior with their environment. Circadian clocks are self-sustained oscillators primarily based on transcriptional feedback loops and post-translational modification of clock proteins. It is increasingly becoming clear that regulation at the RNA level strongly impacts the cellular circadian transcriptome and proteome as well as the oscillator mechanism itself. This review focuses on posttranscriptional events, discussing RNA-binding proteins that, by influencing the timing of pre-mRNA splicing, polyadenylation and RNA decay, shape rhythmic expression profiles. Furthermore, recent findings on the contribution of microRNAs to orchestrating circadian rhythms are summarized.
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Affiliation(s)
- Dorothee Staiger
- Molecular Cell Physiology, Bielefeld University, 33501, Bielefeld, Germany.
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15
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Guo J, Cheng P, Yuan H, Liu Y. The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop. Cell 2009; 138:1236-46. [PMID: 19747717 DOI: 10.1016/j.cell.2009.06.043] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 04/20/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
Abstract
The eukaryotic circadian oscillators consist of autoregulatory negative feedback loops. However, little is known about the role of posttranscriptional regulation of RNA in circadian oscillators. In the Neurospora circadian negative feedback loop, FRQ and FRH form the FFC complex that represses frq transcription. Here, we show that FFC also binds frq RNA and interacts with the exosome to regulate frq RNA decay. Consequently, frq RNA is robustly rhythmic as it is more stable when FRQ levels are low. Silencing of RRP44, the catalytic subunit of the exosome, elevates frq RNA levels and impairs clock function. In addition, rrp44 is a clock-controlled gene and a direct target of the WHITE COLLAR complex, and RRP44 controls the circadian expression of some ccgs. Taken together, these results suggest that FFC and the exosome are part of a posttranscriptional negative feedback loop that regulates frq transcript levels and the circadian output pathway.
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Affiliation(s)
- Jinhu Guo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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16
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Abstract
Eclosion is the stage in development when the adult insect emerges from the shell of its old cuticle. The sequence of behaviors necessary for eclosion is coordinated by an integrated system of hormones and is activated by hormones that relay developmental readiness. The circadian clock, which controls the timing of behaviors such as the rest: activity rhythm of adult insects, also controls eclosion timing. A number of groups are actively investigating the mechanisms by which the circadian clock restricts or gates eclosion to a particular time of day. Data from these studies are beginning to reveal details of the molecular and physiological basis of the eclosion rhythm.
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Affiliation(s)
- Edith M Myers
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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17
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Altered LARK expression perturbs development and physiology of the Drosophila PDF clock neurons. Mol Cell Neurosci 2009; 41:196-205. [PMID: 19303442 DOI: 10.1016/j.mcn.2009.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Accepted: 02/25/2009] [Indexed: 11/22/2022] Open
Abstract
The LARK RNA-binding protein (RBP) has well documented roles in the circadian systems of Drosophila and mammals. Recent studies have demonstrated that the Drosophila LARK RBP is associated with many mRNA targets, in vivo, including those that regulate either neurophysiology or development of the nervous system. In the present study, we have employed conditional expression techniques to distinguish developmental and physiological functions of LARK for a defined class of neurons: the Pigment-Dispersing Factor (PDF)-containing LNv clock neurons. We found that increased LARK expression during development dramatically alters the small LNv class of neurons with no obvious effects on the large LNv cells. Conversely, conditional expression of LARK at the adult stage results in altered clock protein rhythms and circadian locomotor activity, even though neural morphology is normal in such animals. Electrophysiological analyses at the larval neuromuscular junction indicate a role for LARK in regulating neuronal excitability. Altogether, our results demonstrate that LARK activity is critical for neuronal development and physiology.
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The Drosophila FMRP and LARK RNA-binding proteins function together to regulate eye development and circadian behavior. J Neurosci 2008; 28:10200-5. [PMID: 18842880 DOI: 10.1523/jneurosci.2786-08.2008] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common form of hereditary mental retardation. FXS patients have a deficit for the fragile X mental retardation protein (FMRP) that results in abnormal neuronal dendritic spine morphology and behavioral phenotypes, including sleep abnormalities. In a Drosophila model of FXS, flies lacking the dfmr1 protein (dFMRP) have abnormal circadian rhythms apparently as a result of altered clock output. In this study, we present biochemical and genetic evidence that dFMRP interacts with a known clock output component, the LARK RNA-binding protein. Our studies demonstrate physical interactions between dFMRP and LARK, that the two proteins are present in a complex in vivo, and that LARK promotes the stability of dFMRP. Furthermore, we show genetic interactions between the corresponding genes indicating that dFMRP and LARK function together to regulate eye development and circadian behavior.
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Pfuhl T, Mamiani A, Dürr M, Welter S, Stieber J, Ankara J, Liss M, Dobner T, Schmitt A, Falkai P, Kremmer E, Jung V, Barth S, Grässer FA. The LARK/RBM4a protein is highly expressed in cerebellum as compared to cerebrum. Neurosci Lett 2008; 444:11-5. [DOI: 10.1016/j.neulet.2008.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 07/04/2008] [Accepted: 08/05/2008] [Indexed: 10/21/2022]
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20
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Wisor JP, Striz M, DeVoss J, Murphy GM, Edgar DM, O'Hara BF. A novel quantitative trait locus on mouse chromosome 18, "era1," modifies the entrainment of circadian rhythms. Sleep 2008; 30:1255-63. [PMID: 17969459 DOI: 10.1093/sleep/30.10.1255] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
STUDY OBJECTIVE The mammalian circadian clock in the suprachiasmatic nuclei (SCN) of the hypothalamus conveys 24-h rhythmicity to sleep-wake cycles, locomotor activity, and other behavioral and physiological processes. The timing of rhythms relative to the light/dark (LD12:12) cycle is influenced in part by the endogenous circadian period and the time of day specific sensitivity of the clock to light. We now describe a novel circadian rhythm phenotype, and a locus influencing that phenotype, in a segregating population of mice. METHODS By crossbreeding 2 genetically distinct nocturnal strains of mice (Cast/Ei and C57BL/6J) and backcrossing the resulting progeny to Cast/Ei, we have produced a novel circadian phenotype, called early runner mice. RESULTS Early runner mice entrain to a light/dark cycle at an advanced phase, up to 9 hours before dark onset. This phenotype is not significantly correlated with circadian period in constant darkness and is not associated with disruption of molecular circadian rhythms in the SCN, as assessed by analysis of period gene expression. We have identified a genomic region that regulates this phenotype-a major quantitative trait locus on chromosome 18 (near D18Mit184) that we have named era1 for Early Runner Activity locus one. Phase delays caused by light exposure early in the subjective night were of smaller magnitude in backcross offspring that were homozygous Cast/Ei at D18Mit184 than in those that were heterozygous at this locus. CONCLUSION Genetic variability in the circadian response to light may, in part, explain the variance in phase angle of entrainment in this segregating mouse population.
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Affiliation(s)
- Jonathan P Wisor
- Molecular Neurobiology Laboratory, SRI International, Menlo Park, CA 94025, USA.
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21
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Huang Y, Genova G, Roberts M, Jackson FR. The LARK RNA-binding protein selectively regulates the circadian eclosion rhythm by controlling E74 protein expression. PLoS One 2007; 2:e1107. [PMID: 17971870 PMCID: PMC2040218 DOI: 10.1371/journal.pone.0001107] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Accepted: 10/05/2007] [Indexed: 11/19/2022] Open
Abstract
Despite substantial progress in defining central components of the circadian pacemaker, the output pathways coupling the clock to rhythmic physiological events remain elusive. We previously showed that LARK is a Drosophila RNA-binding protein which functions downstream of the clock to mediate behavioral outputs. To better understand the roles of LARK in the circadian system, we sought to identify RNA molecules associated with it, in vivo, using a three-part strategy to (1) capture RNA ligands by immunoprecipitation, (2) visualize the captured RNAs using whole-genome microarrays, and (3) identify functionally relevant targets through genetic screens. We found that LARK is associated with a large number of RNAs, in vivo, consistent with its broad expression pattern. Overexpression of LARK increases protein abundance for certain targets without affecting RNA level, suggesting a translational regulatory role for the RNA-binding protein. Phenotypic screens of target-gene mutants have identified several with rhythm-specific circadian defects, indicative of effects on clock output pathways. In particular, a hypomorphic mutation in the E74 gene, E74(BG01805), was found to confer an early-eclosion phenotype reminiscent of that displayed by a mutant with decreased LARK gene dosage. Molecular analyses demonstrate that E74A protein shows diurnal changes in abundance, similar to LARK. In addition, the E74(BG01805) allele enhances the lethal phenotype associated with a lark null mutation, whereas overexpression of LARK suppresses the early eclosion phenotype of E74(BG01805), consistent with the idea that E74 is a target, in vivo. Our results suggest a model wherein LARK mediates the transfer of temporal information from the molecular oscillator to different output pathways by interacting with distinct RNA targets.
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Affiliation(s)
- Yanmei Huang
- Department of Neuroscience, Center for Neuroscience Research, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Ginka Genova
- Department of Neuroscience, Center for Neuroscience Research, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Mary Roberts
- Department of Neuroscience, Center for Neuroscience Research, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - F. Rob Jackson
- Department of Neuroscience, Center for Neuroscience Research, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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22
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Iwai S, Takeda M. Expression analysis of two types of transcripts from circadian output gene lark in Bombyx mori. Comp Biochem Physiol B Biochem Mol Biol 2007; 146:470-6. [PMID: 17287137 DOI: 10.1016/j.cbpb.2006.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 11/03/2006] [Accepted: 11/04/2006] [Indexed: 11/29/2022]
Abstract
We analyzed expression patterns of lark (Bmlark) in Bombyx mori. Southern blot analysis demonstrated that Bmlark was a single copy gene. Northern blot analyses revealed two types of Bmlark transcripts, one being of 1.38 kb (Bmlark-PA) and the other of 0.85 kb (Bmlark-PB). Both transcripts were detected in the eggs, larval and adult heads, testes, ovaries and flight muscles. Both types of transcripts are constitutively expressed with no clear rhythmicity in the adult heads under light:dark (LD) cycles but the amount of the Bmlark-PA transcript was twice as much as that of the Bmlark-PB transcript in the adult heads throughout a day. Real-Time PCR assays also indicated constant expressions of the two types of Bmlark in the pupal brains under LD12:12 and LD16:8.
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Affiliation(s)
- Sachio Iwai
- Division of Molecular Science, Graduate School of Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8567, Japan
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23
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Kojima S, Matsumoto K, Hirose M, Shimada M, Nagano M, Shigeyoshi Y, Hoshino SI, Ui-Tei K, Saigo K, Green CB, Sakaki Y, Tei H. LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1. Proc Natl Acad Sci U S A 2007; 104:1859-64. [PMID: 17264215 PMCID: PMC1794262 DOI: 10.1073/pnas.0607567104] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mammalian molecular clock is composed of feedback loops to keep circadian 24-h rhythms. Although much focus has been on transcriptional regulation, it is clear that posttranscriptional controls also play important roles in molecular circadian clocks. In this study, we found that mouse LARK (mLARK), an RNA binding protein, activates the posttranscriptional expression of the mouse Period1 (mPer1) mRNA. A strong circadian cycling of the mLARK protein is observed in the suprachiasmatic nuclei with a phase similar to that of mPER1, although the level of the Lark transcripts are not rhythmic. We demonstrate that LARK causes increased mPER1 protein levels, most likely through translational regulation and that the LARK1 protein binds directly to a cis element in the 3' UTR of the mPer1 mRNA. Alterations of mLark expression in cycling cells caused significant changes in circadian period, with mLark knockdown by siRNA resulting in a shorter circadian period, and the overexpression of mLARK1 resulting in a lengthened period. These data indicate that mLARKs are novel posttranscriptional regulators of mammalian circadian clocks.
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Affiliation(s)
- Shihoko Kojima
- *Laboratory of Chronogenomics, Mitsubishi Kagaku Institute of Life Sciences, 11 Minamiooya, Machida, Tokyo 194-8511, Japan
- Department of Biology, University of Virginia, Charlottesville, VA 22904-4328; and
| | - Ken Matsumoto
- *Laboratory of Chronogenomics, Mitsubishi Kagaku Institute of Life Sciences, 11 Minamiooya, Machida, Tokyo 194-8511, Japan
| | - Matsumi Hirose
- *Laboratory of Chronogenomics, Mitsubishi Kagaku Institute of Life Sciences, 11 Minamiooya, Machida, Tokyo 194-8511, Japan
| | - Miyuki Shimada
- *Laboratory of Chronogenomics, Mitsubishi Kagaku Institute of Life Sciences, 11 Minamiooya, Machida, Tokyo 194-8511, Japan
| | - Mamoru Nagano
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Shin-ichi Hoshino
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Kumiko Ui-Tei
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Kaoru Saigo
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Carla B. Green
- Department of Biology, University of Virginia, Charlottesville, VA 22904-4328; and
| | - Yoshiyuki Sakaki
- Genomic Science Center, RIKEN, The Institute of Physical and Chemical Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hajime Tei
- *Laboratory of Chronogenomics, Mitsubishi Kagaku Institute of Life Sciences, 11 Minamiooya, Machida, Tokyo 194-8511, Japan
- **To whom correspondence should be addressed. E-mail:
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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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25
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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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26
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Markus MA, Morris BJ. Lark Is the Splicing Factor RBM4 and Exhibits Unique Subnuclear Localization Properties. DNA Cell Biol 2006; 25:457-64. [PMID: 16907643 DOI: 10.1089/dna.2006.25.457] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lark is an RNA-binding protein of the RNA recognition motif (RRM) class and, in Drosophila, Lark is required for embryonic development. In attempting to determine the function of human Lark we uncovered a frame-shift error in the published sequence to reveal that Lark is, in fact, RBM4, a recently described splicing regulator. We then went on to show that RBM4 localizes in nuclear speckles and nucleoli, supporting its potential role in splicing or RNA processing. Immunofluorescence imaging of full-length and mutated RBM4 revealed that the C-terminus of RBM4 is crucial for targeting to speckles. Unlike many other splicing factors, however, RBM4 does not contain an RS-domain or any other known targeting site. RBM4 redistributed to perinucleolar clusters upon the addition of a transcription inhibitor, whereas other splicing factors display increased localization to speckles in the absence of transcription. This finding is consistent with the potential existence of a novel subnuclear targeting pathway. In conclusion, RBM4 and Lark are the same protein, are localized in speckles and nucleoli, but can redistribute to perinucleolar clusters, consistent with a novel subnuclear pathway.
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Affiliation(s)
- M Andrea Markus
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute for Biomedical Research, The University of Sydney, Sydney, Australia
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27
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Wang ZL, Li J, Xia QY, Zhao P, Duan J, Zha XF, Xiang ZH. Identification and expression pattern of Bmlark, a homolog of the Drosophila gene lark in Bombyx mori. ACTA ACUST UNITED AC 2006; 16:224-9. [PMID: 16147879 DOI: 10.1080/10425170500129652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Two Bombyx mori isoforms of the gene lark, which is shown to play an important role in Drosophila circadian rhythms, were identified and named Bmlark-PA and Bmlark-PB, respectively. Bmlark-PA consists of 5 exons and encodes a protein of 343 amino acid residues which contains 3 functional domains: two RRM (RNA recognization motif) domains and an RTZF (retroviral-type zinc finger) and shares 72% identity with the Drosophila gene lark at the amino acid level. Bmlark-PB lacks the sequence between 118 and 791 nt of Bmlark-PA and codes for a protein of 68 amino acid residues, which contains no distinct functional domains. Alignments of the cDNAs of Bmlark to the genomic draft sequence of B. mori showed that the gene Bmlark had a single copy in the genome, suggesting that an alternative splicing mechanism occurs in the gene Bmlark. RT-PCR analysis indicated that Bmlark-PA was expressed only in late pupae and adult but Bmlark-PB was broadly expressed in many tissues and throughout the developmental stages from embryo to adult.
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Affiliation(s)
- Zi-Long Wang
- The Key Laboratory of Sericulture of Agriculture University of Sericulture and Biotechnology, Southwest Agricultural University, Chongqing, China
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28
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Ewer J. Behavioral actions of neuropeptides in invertebrates: insights from Drosophila. Horm Behav 2005; 48:418-29. [PMID: 15996666 DOI: 10.1016/j.yhbeh.2005.05.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 05/17/2005] [Accepted: 05/18/2005] [Indexed: 10/25/2022]
Abstract
This review discusses recent advances in our understanding of the hormonal control of ecdysis behavior in Drosophila, as well as methods that can more generally be used in this organism to investigate the in vivo function of neuropeptide hormones. Ecdysis is a dedicated, vital, behavior that is used by arthropods at the end of each molt to shed the remains of the old exoskeleton. It is under the control of several interacting neuropeptide hormones, and successful ecdysis requires that the behavior and accompanying peripheral events occur at a precise time and in the correct order. The tightly controlled timing and concatenation of these events are due to the complex hormonal control of ecdysis, with several neuropeptides contributing to a particular event, and, conversely, one neuropeptide effecting both central as well as peripheral actions. It is for the analyses of this type of behavior that Drosophila can provide unique insights, and some of these insights are summarized here. In addition, I discuss more generally approaches that are available in this organism, which make it especially useful for investigating the hormonal control of behavior.
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Affiliation(s)
- John Ewer
- Entomology Department, Cornell University, 5130 Comstock Hall, Ithaca, NY 14853, USA.
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29
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Sutherland LC, Rintala-Maki ND, White RD, Morin CD. RNA binding motif (RBM) proteins: a novel family of apoptosis modulators? J Cell Biochem 2005; 94:5-24. [PMID: 15514923 DOI: 10.1002/jcb.20204] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RBM5 is a known modulator of apoptosis, an RNA binding protein, and a putative tumor suppressor. Originally identified as LUCA-15, and subsequently as H37, it was designated "RBM" (for RNA Binding Motif) due to the presence of two RRM (RNA Recognition Motif) domains within the protein coding sequence. Recently, a number of proteins have been attributed with this same RBM designation, based on the presence of one or more RRM consensus sequences. One such protein, RBM3, was also recently found to have apoptotic modulatory capabilities. The high sequence homology at the amino acid level between RBM5, RBM6, and particularly, RBM10 suggests that they, too, may play an important role in regulating apoptosis. It is the intent of this article to ammalgamate the data on the ten originally identified RBM proteins in order to question the existence of a novel family of RNA binding apoptosis regulators.
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Affiliation(s)
- Leslie C Sutherland
- Tumour Biology Group, Northeastern Ontario Regional Cancer Centre, 41 Ramsey Lake Road, Sudbury, Ontario P3E 5J1, Canada.
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30
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McNeil GP, Smith F, Galioto R. The Drosophila RNA-binding protein Lark is required for the organization of the actin cytoskeleton and Hu-li tai shao localization during oogenesis. Genesis 2005; 40:90-100. [PMID: 15452872 DOI: 10.1002/gene.20069] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Elimination of maternal expression of the Drosophila RNA-binding protein Lark results in female sterility. Here we show that this is due to a requirement during oogenesis. Developing oocytes from lark(1) germline clones (GLCs) are often smaller than normal due to defects in nurse cell cytoplasmic "dumping." Late-stage egg chambers from lark(1) GLCs contain low levels of cortical and ring canal associated actin and completely lack nurse cell cytoplasmic F-actin bundles, suggesting the "dumping" phenotype is due to a defect in the actin cytoskeleton. Localization of Hu-li tai shao (Hts) protein, a component of ring canals, is also disrupted in these mutants. In addition to the dumpless phenotype, we observed a buildup of late-stage egg chambers, a phenotype that correlates with the decrease in egg-laying observed in the mutants. We postulate that this phenotype is due to defects in the cytoskeletal integrity of eggs since retained and oviposited eggs are fragile and often deflated. These mutant phenotypes are likely due to disruption of an RNA-binding function of Lark as similar phenotypes were observed in flies carrying specific RNA-binding domain mutations. We propose that Lark functions during oogenesis as an RNA-binding protein, regulating mRNAs required for nurse cell transport or apoptosis.
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Affiliation(s)
- Gerard P McNeil
- Department of Natural Sciences, York College, City University of New York, Jamaica, NY 11451, USA.
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31
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Guo S, Zhang Z, Tong T. Cloning and characterization of cellular senescence-associated genes in human fibroblasts by suppression subtractive hybridization. Exp Cell Res 2004; 298:465-72. [PMID: 15265694 DOI: 10.1016/j.yexcr.2004.04.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2003] [Revised: 04/26/2004] [Accepted: 04/30/2004] [Indexed: 11/19/2022]
Abstract
Cellular senescence marks the end of the proliferative life span of normal cells in tissue culture and occurs after cells have undergone a certain number of population doublings (PDLs). It is accompanied by alterations in the pattern of gene expression. A specific human embryonic lung diploid fibroblast cell line, 2BS, has been studied as a model of senescence in our laboratory. Here, we report a set of cellular senescence-associated genes identified from suppression subtractive cDNA libraries from senescent and young 2BS cells. They include three novel genes and six previously identified genes of unknown function. The genes whose functions are known belong to various functional pathways that have been reported to change with the onset of senescence. These include three pre-mRNA splicing factors with reduced expression in senescent cells, indicating that the regulation of mRNA splicing is altered during cell senescence. In addition, the expression of the gene TOM1 (target of Myb 1), which has not previously been associated with cellular senescence, is shown to increase in senescent cells, and we demonstrate that the expression of antisense TOM1 gene in 2BS cells can delay the progress of senescence.
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Affiliation(s)
- Shuzhen Guo
- Department of Biochemistry and Molecular Biology, Health Science Center, Peking University, Beijing 100083, PR China
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32
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Affiliation(s)
- Paul H Taghert
- Anatomy and Neurobiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
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33
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Hall JC. Genetics and molecular biology of rhythms in Drosophila and other insects. ADVANCES IN GENETICS 2003; 48:1-280. [PMID: 12593455 DOI: 10.1016/s0065-2660(03)48000-0] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Application of generic variants (Sections II-IV, VI, and IX) and molecular manipulations of rhythm-related genes (Sections V-X) have been used extensively to investigate features of insect chronobiology that might not have been experimentally accessible otherwise. Most such tests of mutants and molecular-genetic xperiments have been performed in Drosophila melanogaster. Results from applying visual-system variants have revealed that environmental inputs to the circadian clock in adult flies are mediated by external photoreceptive structures (Section II) and also by direct light reception chat occurs in certain brain neurons (Section IX). The relevant light-absorbing molecuLes are rhodopsins and "blue-receptive" cryptochrome (Sections II and IX). Variations in temperature are another clock input (Section IV), as has been analyzed in part by use of molecular techniques and transgenes involving factors functioning near the heart of the circadian clock (Section VIII). At that location within the fly's chronobiological system, approximately a half-dozen-perhaps up to as many as 10-clock genes encode functions that act and interact to form the circadian pacemaker (Sections III and V). This entity functions in part by transcriptional control of certain clock genes' expressions, which result in the production of key proteins that feed back negatively to regulate their own mRNA production. This occurs in part by interactions of such proteins with others that function as transcriptional activators (Section V). The implied feedback loop operates such that there are daily variations in the abundances of products put out by about one-half of the core clock genes. Thus, the normal expression of these genes defines circadian rhythms of their own, paralleling the effects of mutations at the corresponding genetic loci (Section III), which are to disrupt or apparently eliminate clock functioning. The fluctuations in the abundance of gene products are controlled transciptionally and posttranscriptionally. These clock mechanisms are being analyzed in ways that are increasingly complex and occasionally obscure; not all panels of this picture are comprehensive or clear, including problems revolving round the biological meaning or a given features of all this molecular cycling (Section V). Among the complexities and puzzles that have recently arisen, phenomena that stand out are posttranslational modifications of certain proteins that are circadianly regulated and regulating; these biochemical events form an ancillary component of the clock mechanism, as revealed in part by genetic identification of Factors (Section III) that turned out to encode protein kinases whose substrates include other pacemaking polypeptides (Section V). Outputs from insect circadian clocks have been long defined on formalistic and in some cases concrete criteria, related to revealed rhythms such as periodic eclosion and daily fluctuations of locomotion (Sections II and III). Based on the reasoning that if clock genes can regulate circadian cyclings of their own products, they can do the same for genes that function along output pathways; thus clock-regulated genes have been identified in part by virtue of their products' oscillations (Section X). Those studied most intensively have their expression influenced by circadian-pacemaker mutations. The clock-regulated genes discovered on molecular criteria have in some instances been analyzed further in their mutant forms and found to affect certain features of overt whole-organismal rhythmicity (Sections IV and X). Insect chronogenetics touches in part on naturally occurring gene variations that affect biological rhythmicity or (in some cases) have otherwise informed investigators about certain features of the organism's rhythm system (Section VII). Such animals include at least a dozen insect species other than D. melanogaster in which rhythm variants have been encountered (although usually not looked for systematically). The chronobiological "system" in the fruit fly might better be graced with a plural appellation because there is a myriad of temporally related phenomena that have come under the sway of one kind of putative rhythm variant or the other (Section IV). These phenotypes, which range well beyond the bedrock eclosion and locomotor circadian rhythms, unfortunately lead to the creation of a laundry list of underanalyzed or occult phenomena that may or may not be inherently real, whether or not they might be meaningfully defective under the influence of a given chronogenetic variant. However, such mutants seem to lend themselves to the interrogation of a wide variety of time-based attributes-those that fall within the experimental confines of conventionally appreciated circadian rhythms (Sections II, III, VI, and X); and others that consist of 24-hr or nondaily cycles defined by many kinds of biological, physiological, or biochemical parameters (Section IV).
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Affiliation(s)
- Jeffrey C Hall
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
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Myers EM, Yu J, Sehgal A. Circadian control of eclosion: interaction between a central and peripheral clock in Drosophila melanogaster. Curr Biol 2003; 13:526-33. [PMID: 12646138 DOI: 10.1016/s0960-9822(03)00167-2] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drosophila melanogaster display overt circadian rhythms in rest:activity behavior and eclosion. These rhythms have an endogenous period of approximately 24 hr and can adjust or "entrain" to environmental inputs such as light. Circadian rhythms depend upon a functioning molecular clock that includes the core clock genes period and timeless (reviewed in and ). Although we know that a clock in the lateral neurons (LNs) of the brain controls rest:activity rhythms, the cellular basis of eclosion rhythms is less well understood. We show that the LN clock is insufficient to drive eclosion rhythms. We establish that the prothoracic gland (PG), a tissue required for fly development, contains a functional clock at the time of eclosion. This clock is required for normal eclosion rhythms. However, both the PG clock function and eclosion rhythms require the presence of LNs. In addition, we demonstrate that pigment-dispersing factor (PDF), a neuropeptide secreted from LNs, is necessary for the PG clock and eclosion rhythms. Unlike other clocks in the fly periphery, the PG is similar to mammalian peripheral oscillators because it depends upon input, including PDF, from central pacemaker cells. This is the first report of a peripheral clock necessary for a circadian event.
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Affiliation(s)
- Edith M Myers
- The Department of Neuroscience, 232 Stemmler Hall, University of Pennsylvania, Philadelphia, PA 19104, USA
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Lai MC, Kuo HW, Chang WC, Tarn WY. A novel splicing regulator shares a nuclear import pathway with SR proteins. EMBO J 2003; 22:1359-69. [PMID: 12628928 PMCID: PMC151058 DOI: 10.1093/emboj/cdg126] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing of precursor mRNA is often regulated by serine/arginine-rich proteins (SR proteins) and hnRNPs, and varying their concentration in the nucleus can be a mechanism for controlling splice site selection. To understand the nucleocytoplasmic transport mechanism of splicing regulators is of key importance. SR proteins are delivered to the nucleus by transportin-SRs (TRN-SRs), importin beta-like nuclear transporters. Here we identify and characterize a non-SR protein, RNA-binding motif protein 4 (RBM4), as a novel substrate of TRN-SR2. TRN-SR2 interacts specifically with RBM4 in a Ran-sensitive manner. TRN-SR2 indeed mediates the nuclear import of a recombinant protein containing the RBM4 C-terminal domain. This domain serves as a signal for both nuclear import and export, and for nuclear speckle targeting. Finally, both in vivo and in vitro splicing analyses demonstrate that RBM4 not only modulates alternative pre-mRNA splicing but also acts antagonistically to authentic SR proteins in splice site and exon selection. Thus, a novel splicing regulator with opposite activities to SR proteins shares an identical import pathway with SR proteins to the nucleus.
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Affiliation(s)
- Ming-Chih Lai
- Institute of Biomedical Sciences, Academia Sinica, Taipei and Institute of Anatomy and Cell Biology, National Yang-Ming University, Shih-Pai, Taipei, Taiwan Corresponding author e-mail:
| | - Hao-Wei Kuo
- Institute of Biomedical Sciences, Academia Sinica, Taipei and Institute of Anatomy and Cell Biology, National Yang-Ming University, Shih-Pai, Taipei, Taiwan Corresponding author e-mail:
| | - Wen-Cheng Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei and Institute of Anatomy and Cell Biology, National Yang-Ming University, Shih-Pai, Taipei, Taiwan Corresponding author e-mail:
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei and Institute of Anatomy and Cell Biology, National Yang-Ming University, Shih-Pai, Taipei, Taiwan Corresponding author e-mail:
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Stanewsky R. Genetic analysis of the circadian system in Drosophila melanogaster and mammals. JOURNAL OF NEUROBIOLOGY 2003; 54:111-47. [PMID: 12486701 DOI: 10.1002/neu.10164] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The fruit fly, Drosophila melanogaster, has been a grateful object for circadian rhythm researchers over several decades. Behavioral, genetic, and molecular studies helped to reveal the genetic bases of circadian time keeping and rhythmic behaviors. Contrary, mammalian rhythm research until recently was mainly restricted to descriptive and physiologic approaches. As in many other areas of research, the surprising similarity of basic biologic principles between the little fly and our own species, boosted the progress of unraveling the genetic foundation of mammalian clock mechanisms. Once more, not only the basic mechanisms, but also the molecules involved in establishing our circadian system are taken or adapted from the fly. This review will try to give a comparative overview about the two systems, highlighting similarities as well as specifics of both insect and murine clocks.
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Affiliation(s)
- Ralf Stanewsky
- Universität Regensburg, Institut für Zoologie, Lehrstuhl für Entwicklungsbiologie, Universitätsstrasse 31, 93040 Regensburg, Germany.
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Staiger D, Zecca L, Wieczorek Kirk DA, Apel K, Eckstein L. The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 33:361-71. [PMID: 12535349 DOI: 10.1046/j.1365-313x.2003.01629.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The clock-regulated RNA-binding protein AtGRP7 is part of a negative feedback circuit through which the protein influences circadian oscillations of its own transcript. Constitutive overexpression of AtGRP7 in transgenic plants leads to the appearance of a low amount of an alternatively spliced Atgrp7 transcript with a premature stop codon. It is generated by the use of a 5' cryptic splice site in the middle of the intron at the expense of the fully spliced mRNA, indicating a role for AtGRP7 in splice site selection. Accelerated decay of this transcript accounts for its low steady state abundance. This implicates a mechanism for the AtGRP7 feedback loop: Atgrp7 expression is downregulated, as AtGRP7 protein accumulates over the circadian cycle, partly by the generation of an alternate transcript that due to its instability does not accumulate to high levels and does not produce a functional protein. Recombinant AtGRP7 protein specifically interacts with the 3' untranslated region and the intron of its transcript, suggesting that the shift in splice site selection and downregulation involves binding of AtGRP7 to its pre-mRNA. AtGRP7 also influences the choice of splice sites in the Atgrp8 transcript encoding a related RNA-binding protein, favoring the production of an alternatively spliced, unstable Atgrp8 transcript. This conservation points to the importance of this regulatory mechanism to control the level of the clock-regulated glycine-rich RNA-binding proteins and shows how AtGRP7 can control abundance of target transcripts.
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Affiliation(s)
- Dorothee Staiger
- Institut für Pflanzenwissenschaften, ETH, CH-8092 Zürich, Switzerland.
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38
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Schroeder AJ, Jackson FR. Phenotypic and molecular characterization of GAL4/UAS-mediated LARK expression. Genesis 2002; 34:91-4. [PMID: 12324957 DOI: 10.1002/gene.10105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Andrew J Schroeder
- Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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39
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Inoue S, Shimoda M, Nishinokubi I, Siomi MC, Okamura M, Nakamura A, Kobayashi S, Ishida N, Siomi H. A role for the Drosophila fragile X-related gene in circadian output. Curr Biol 2002; 12:1331-5. [PMID: 12176363 DOI: 10.1016/s0960-9822(02)01036-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mutations that abolish expression of an X-linked gene, FMR1, result in the pathogenesis of fragile X syndrome, the most common form of inherited mental retardation. To understand the normal function of the FMR1 protein, we have produced fly strains bearing deletions in a Drosophila homolog of FMR1 (dfmr1). Since fragile X patients show a number of abnormal behaviors including sleep problems, we investigated whether a loss-of-function mutation of dfmr1 affect circadian behavior. Here we show that under constant darkness (DD), a lack of dfmr1 expression causes arrhythmic locomotor activity, but in light:dark cycles, their behavioral rhythms appear normal. In addition, the clock-controlled eclosion rhythm is normal in DFMR1-deficient flies. These results suggest that DFMR1 plays a critical role in the circadian output pathway regulating locomotor activity in Drosophila.
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Affiliation(s)
- Shunsuke Inoue
- Institute for Genome Research, University of Tokushima, Kuramoto 3-18-15, 770-8503, Tokushima, Japan
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40
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Scully AL, Zelhof AC, Kay SA. A P element with a novel fusion of reporters identifies regular, a C2H2 zinc-finger gene downstream of the circadian clock. Mol Cell Neurosci 2002; 19:501-14. [PMID: 11988018 DOI: 10.1006/mcne.2001.1091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Elucidating the mechanisms that link the circadian pacemaker to the timing of behaviors it controls is one of the greatest challenges in circadian biology. We report the generation of a P element, Pluc+, containing a novel reporter fusion. Our fusion reporter capitalizes on the use of luciferase bioluminescence to easily analyze temporal expression as well as the strength of myc epitopes and GFP to identify spatial expression. Using Pluc+ we have identified and characterized a novel C2H2 zinc-finger gene, regular (rgr), that cycles circadianly in phase with period (per) gene expression, but shifts to light-dark regulation in Clk(Jrk) mutant flies. By following myc expression of the Pluc+ reporter, we demonstrate that Rgr is expressed in a discrete number of neurons in the brain which overlap with axons expressing pigment-dispersing factor.
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Affiliation(s)
- Audra L Scully
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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41
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Stempfl T, Vogel M, Szabo G, Wülbeck C, Liu J, Hall JC, Stanewsky R. Identification of circadian-clock-regulated enhancers and genes of Drosophila melanogaster by transposon mobilization and luciferase reporting of cyclical gene expression. Genetics 2002; 160:571-93. [PMID: 11861563 PMCID: PMC1461973 DOI: 10.1093/genetics/160.2.571] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A new way was developed to isolate rhythmically expressed genes in Drosophila by modifying the classic enhancer-trap method. We constructed a P element containing sequences that encode firefly luciferase as a reporter for oscillating gene expression in live flies. After generation of 1176 autosomal insertion lines, bioluminescence screening revealed rhythmic reporter-gene activity in 6% of these strains. Rhythmically fluctuating reporter levels were shown to be altered by clock mutations in genes that specify various circadian transcription factors or repressors. Intriguingly, rhythmic luminescence in certain lines was affected by only a subset of the pacemaker mutations. By isolating genes near 13 of the transposon insertions and determining their temporal mRNA expression pattern, we found that four of the loci adjacent to the trapped enhancers are rhythmically expressed. Therefore, this approach is suitable for identifying genetic loci regulated by the circadian clock. One transposon insert caused a mutation in the rhythmically expressed gene numb. This novel numb allele, as well as previously described ones, was shown to affect the fly's rhythm of locomotor activity. In addition to its known role in cell fate determination, this gene and the phosphotyrosine-binding protein it encodes are likely to function in the circadian system.
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Affiliation(s)
- Thomas Stempfl
- Institut für Zoologie, Universität Regensburg, Lehrstuhl für Entwicklungsbiologie, 93040 Regensburg, Germany
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42
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Staiger D. RNA-binding proteins and circadian rhythms in Arabidopsis thaliana. Philos Trans R Soc Lond B Biol Sci 2001; 356:1755-9. [PMID: 11710982 PMCID: PMC1088551 DOI: 10.1098/rstb.2001.0964] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An Arabidopsis transcript preferentially expressed at the end of the daily light period codes for the RNA-binding protein AtGRP7. A reverse genetic approach in Arabidopsis thaliana has revealed its role in the generation of circadian rhythmicity: AtGRP7 is part of a negative feedback loop through which it influences the oscillations of its own transcript. Biochemical and genetic experiments indicate a mechanism for this autoregulatory circuit: Atgrp7 gene transcription is rhythmically activated by the circadian clock during the day. The AtGPR7 protein accumulates with a certain delay and represses further accumulation of its transcript, presumably at the post-transcriptional level. In this respect, the AtGRP7 feedback loop differs from known circadian oscillators in the fruitfly Drosophila and mammals based on oscillating clock proteins that repress transcription of their own genes with a 24 h rhythm. It is proposed that the AtGRP7 feedback loop may act within an output pathway from the Arabidopsis clock.
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Affiliation(s)
- D Staiger
- Institute for Plant Sciences, ETH Zurich, CH-8092 Zurich, Switzerland.
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43
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McNeil GP, Schroeder AJ, Roberts MA, Jackson FR. Genetic analysis of functional domains within the Drosophila LARK RNA-binding protein. Genetics 2001; 159:229-40. [PMID: 11560900 PMCID: PMC1461808 DOI: 10.1093/genetics/159.1.229] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
LARK is an essential Drosophila RNA-binding protein of the RNA recognition motif (RRM) class that functions during embryonic development and for the circadian regulation of adult eclosion. LARK protein contains three consensus RNA-binding domains: two RRM domains and a retroviral-type zinc finger (RTZF). To show that these three structural domains are required for function, we performed a site-directed mutagenesis of the protein. The analysis of various mutations, in vivo, indicates that the RRM domains and the RTZF are required for wild-type LARK functions. RRM1 and RRM2 are essential for viability, although interestingly either domain can suffice for this function. Remarkably, mutation of either RRM2 or the RTZF results in the same spectrum of phenotypes: mutants exhibit reduced viability, abnormal wing and mechanosensory bristle morphology, female sterility, and flightlessness. The severity of these phenotypes is similar in single mutants and double RRM2; RTZF mutants, indicating a lack of additivity for the mutations and suggesting that RRM2 and the RTZF act together, in vivo, to determine LARK function. Finally, we show that mutations in RRM1, RRM2, or the RTZF do not affect the circadian regulation of eclosion, and we discuss possible interpretations of these results. This genetic analysis demonstrates that each of the LARK structural domains functions in vivo and indicates a pleiotropic requirement for both the LARK RRM2 and RTZF domains.
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Affiliation(s)
- G P McNeil
- Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111
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44
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Abstract
Photoperiodic clocks allow organisms to predict the coming season. In insects, the seasonal adaptive response mainly takes the form of diapause. The extensively studied photoperiodic clock in insects was primarily characterized by a "black-box" approach, resulting in numerous cybernetic models. This is in contrast with the circadian clock, which has been dissected pragmatically at the molecular level, particularly in Drosophila. Unfortunately, Drosophila melanogaster, the favorite model organism for circadian studies, does not demonstrate a pronounced seasonal response, and consequently molecular analysis has not progressed in this area. In the current article, the authors explore different ways in which identified molecular components of the circadian pacemaker may play a role in photoperiodism. Future progress in understanding the Drosophila circadian pacemaker, particularly as further output components are identified, may provide a direct link between the clock and photoperiodism. In addition, with improved molecular tools, it is now possible to turn to other insects that have a more dramatic photoperiodic response.
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Affiliation(s)
- E Tauber
- Department of Genetics, University of Leicester, UK
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45
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Abstract
This paper discusses circadian output in terms of the signaling mechanisms used by circadian pacemaker neurons. In mammals, the suprachiasmatic nucleus houses a clock controlling several rhythmic events. This nucleus contains one or more pacemaker circuits, and exhibits diversity in transmitter content and in axonal projections. In Drosophila, a comparable circadian clock is located among period -expressing neurons, a sub-set of which (called LN-vs) express the neuropeptide PDF. Genetic experiments indicate LN-vs are the primary pacemakers neurons controlling daily locomotion and that PDF is the principal circadian transmitter. Further definition of pacemaker properties in several model systems will provide a useful basis with which to describe circadian output mechanisms.
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Affiliation(s)
- P H Taghert
- Department of Anatomy & Neurobiology, Box 8108, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA.
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46
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Abstract
Much of our current understanding of how circadian rhythms are generated is based on work done with Drosophila melanogaster. Molecular mechanisms used to assemble an endogenous clock in this organism are now known to underlie circadian rhythms in many other species, including mammals. The genetic amenability of Drosophila has led to the identification of some genes that encode components of the clock (so-called clock genes) and others that either link the clock to the environment or act downstream of it. The clock provides time-of-day cues by regulating levels of specific gene products such that they oscillate with a circadian rhythm. The mechanisms that synchronize these oscillations to light are understood to some extent. However, there are still large gaps in our knowledge, in particular with respect to the mechanisms used by the clock to control overt rhythms. It has, however, become clear that in addition to the brain clock, autonomous or semi-autonomous clocks occur in peripheral tissues where they confer circadian regulation on specific functions.
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Affiliation(s)
- J A Williams
- Howard Hughes Medical Institute, Department of Neuroscience, University of Pennsylvania Medical School, Philadelphia, Pennsylvania 19104, USA.
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47
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Heintzen C, Loros JJ, Dunlap JC. The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting. Cell 2001; 104:453-64. [PMID: 11239402 DOI: 10.1016/s0092-8674(01)00232-x] [Citation(s) in RCA: 241] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
vvd, a gene regulating light responses in Neurospora, encodes a novel member of the PAS/LOV protein superfamily. VVD defines a circadian clock-associated autoregulatory feedback loop that influences light resetting, modulates circadian gating of input by connecting output and input, and regulates light adaptation. Rapidly light induced, vvd is an early repressor of light-regulated processes. Further, vvd is clock controlled; the clock gates light induction of vvd and the clock gene frq so identical signals yield greater induction in the morning. Mutation of vvd severely dampens gating, especially of frq, consistent with VVD modulating gating and phasing light-resetting responses. vvd null strains display distinct alterations in the phase-response curve to light. Thus VVD, although not part of the clock, contributes significantly to regulation within the Neurospora circadian system.
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Affiliation(s)
- C Heintzen
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
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48
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Zhang X, McNeil GP, Hilderbrand-Chae MJ, Franklin TM, Schroeder AJ, Jackson FR. Circadian regulation of the lark RNA-binding protein within identifiable neurosecretory cells. JOURNAL OF NEUROBIOLOGY 2000; 45:14-29. [PMID: 10992253 DOI: 10.1002/1097-4695(200010)45:1<14::aid-neu2>3.0.co;2-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular genetic analysis indicates that rhythmic changes in the abundance of the Drosophila lark RNA-binding protein are important for circadian regulation of adult eclosion (the emergence or ecdysis of the adult from the pupal case). To define the tissues and cell types that might be important for lark function, we have characterized the spatial and developmental patterns of lark protein expression. Using immunocytochemical or protein blotting methods, lark can be detected in late embryos and throughout postembryonic development, from the third instar larval stage to adulthood. At the late pupal (pharate adult) stage, lark protein has a broad pattern of tissue expression, which includes two groups of crustacean cardioactive peptide (CCAP)-containing neurons within the ventral nervous system. In other insects, the homologous neurons have been implicated in the physiological regulation of ecdysis. Whereas lark has a nuclear distribution in most cell types, it is present in the cytoplasm of the CCAP neurons and certain other cells, which suggests that the protein might execute two different RNA-binding functions. Lark protein exhibits significant circadian changes in abundance in at least one group of CCAP neurons, with abundance being lowest during the night, several hours prior to the time of adult ecdysis. Such a temporal profile is consistent with genetic evidence indicating that the protein serves a repressor function in mediating the clock regulation of adult ecdysis. In contrast, we did not observe circadian changes in CCAP neuropeptide abundance in late pupae, although CCAP amounts were decreased in newly-emerged adults, presumably because the peptide is released at the time of ecdysis. Given the cytoplasmic localization of the lark RNA-binding protein within CCAP neurons, and the known role of CCAP in the control of ecdysis, we suggest that changes in lark abundance may regulate the translation of a factor important for CCAP release or CCAP cell excitability.
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Affiliation(s)
- X Zhang
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
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49
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Wiellette EL, Harding KW, Mace KA, Ronshaugen MR, Wang FY, McGinnis W. spen encodes an RNP motif protein that interacts with Hox pathways to repress the development of head-like sclerites in the Drosophila trunk. Development 1999; 126:5373-85. [PMID: 10556062 DOI: 10.1242/dev.126.23.5373] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Drosophila has eight Hox proteins, and they require factors acting in parallel to regulate different segmental morphologies. Here we find that the Drosophila gene split ends (spen), has a homeotic mutant phenotype, and appears to encode such a parallel factor. Our results indicate that spen plays two important segment identity roles. One is to promote sclerite development in the head region, in parallel with Hox genes; the other is to cooperate with Antennapedia and teashirt to suppress head-like sclerite development in the thorax. Our results also indicate that without spen and teashirt functions, Antennapedia loses its ability to specify thoracic identity in the epidermis. spen transcripts encode extraordinarily large protein isoforms (approx. 5,500 amino acids), which are concentrated in embryonic nuclei. Both Spen protein isoforms and Spen-like proteins in other animals possess a clustered repeat of three RNP (or RRM) domains, as well as a conserved motif of 165 amino acids (SPOC domain) at their C-termini. Spen is the only known homeotic protein with RNP binding motifs, which indicates that splicing, transport, or other RNA regulatory steps are involved in the diversification of segmental morphology. Previous studies by Dickson and others (Dickson, B. J., Van Der Straten, A., Dominguez, M. and Hafen, E. (1996). Genetics 142, 163–171) identified spen as a gene that acts downstream of Raf to suppress Raf signaling in a manner similar to the ETS transcription factor Aop/Yan. This raises the intriguing possibility that the Spen RNP protein might integrate signals from both the Raf and Hox pathways.
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Affiliation(s)
- E L Wiellette
- Department of Biology, University of California at San Diego, La Jolla, CA, 92093
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McNeil GP, Zhang X, Roberts M, Jackson FR. Maternal function of a retroviral-type zinc-finger protein is essential for Drosophila development. DEVELOPMENTAL GENETICS 1999; 25:387-96. [PMID: 10570470 DOI: 10.1002/(sici)1520-6408(1999)25:4<387::aid-dvg12>3.0.co;2-p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Previous studies have shown that zygotic expression of the Drosophila lark gene, which encodes an RNA-binding protein, is essential for embryogenesis. We now show that lark mRNA is abundant in preblastoderm (0-2 h) embryos, prior to zygotic transcription, indicative of maternal inheritance. Lark can also be detected within the nurse cells of developing egg chambers, suggesting a function for the protein during oogenesis. To test the hypothesis that the maternal inheritance of lark is required for oogenesis or early development, we employed the "FLP-DFS" technique to eliminate the lark maternal component within the germ line. Unfertilized and fertilized eggs lacking the lark maternal component exhibit a "fragile" phenotype, indicating that the protein functions during oogenesis. Furthermore, differentiation of the fertilized eggs is abnormal-most embryos arrest prior to blastoderm formation and exhibit morphological phenotypes that might reflect underlying defects in syncytial nuclear cycling or cellularization. Mutational analysis of a retroviral-type zinc finger within the lark protein indicates that it is required for the maternal function of the protein: females are completely sterile when their only source of lark protein contains a zinc-finger mutation. The aggregate of our studies shows that the germ-line expression of lark is essential for development, and suggests that the retroviral-type zinc finger mediates important RNA-binding functions during oogenesis and/or early development.
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Affiliation(s)
- G P McNeil
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA
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