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Vipat S, Moiseeva TN. The TIMELESS Roles in Genome Stability and Beyond. J Mol Biol 2024; 436:168206. [PMID: 37481157 DOI: 10.1016/j.jmb.2023.168206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
TIMELESS protein (TIM) protects replication forks from stalling at difficult-to-replicate regions and plays an important role in DNA damage response, including checkpoint signaling, protection of stalled replication forks and DNA repair. Loss of TIM causes severe replication stress, while its overexpression is common in various types of cancer, providing protection from DNA damage and resistance to chemotherapy. Although TIM has mostly been studied for its part in replication stress response, its additional roles in supporting genome stability and a wide variety of other cellular pathways are gradually coming to light. This review discusses the diverse functions of TIM and its orthologs in healthy and cancer cells, open questions, and potential future directions.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia.
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Salbaum JM, Stone KP, Kruger C, Kappen C. Differential responses to maternal diabetes in embryo and visceral yolk sac. Front Cell Dev Biol 2023; 11:1273641. [PMID: 37928898 PMCID: PMC10620973 DOI: 10.3389/fcell.2023.1273641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction: Maternal diabetes during pregnancy is well known to be associated with a higher risk for structural birth defects in the offspring. Recent searches for underlying mechanisms have largely focused on aberrant processes in the embryo itself, although prior research in rodent models implicated dysfunction also of the visceral yolk sac. The objective of our research was to investigate both tissues within the conceptus simultaneously. Methods: We conducted unbiased transcriptome profiling by RNA sequencing on pairs of individual yolk sacs and their cognate embryos, using the non-obese diabetic (NOD) mouse model. The analysis was performed at gestational day 8.5 on morphologically normal specimen to circumvent confounding by defective development. Results: Even with large sample numbers (n = 33 in each group), we observed considerable variability of gene expression, primarily driven by exposure to maternal diabetes, and secondarily by developmental stage of the embryo. Only a moderate number of genes changed expression in the yolk sac, while in the embryo, the exposure distinctly influenced the relationship of gene expression levels to developmental progression, revealing a possible role for altered cell cycle regulation in the response. Also affected in embryos under diabetic conditions were genes involved in cholesterol biosynthesis and NAD metabolism pathways. Discussion: Exposure to maternal diabetes during gastrulation changes transcriptomic profiles in embryos to a substantially greater effect than in the corresponding yolk sacs, indicating that despite yolk sac being of embryonic origin, different mechanisms control transcriptional activity in these tissues. The effects of maternal diabetes on expression of many genes that are correlated with developmental progression (i.e. somite stage) highlight the importance of considering developmental maturity in the interpretation of transcriptomic data. Our analyses identified cholesterol biosynthesis and NAD metabolism as novel pathways not previously implicated in diabetic pregnancies. Both NAD and cholesterol availability affect a wide variety of cellular signaling processes, and can be modulated by diet, implying that prevention of adverse outcomes from diabetic pregnancies may require broad interventions, particularly in the early stages of pregnancy.
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Affiliation(s)
- J. Michael Salbaum
- Department of Regulation of Gene Expression, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
| | - Kirsten P. Stone
- Department of Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
| | - Claudia Kruger
- Department of Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
| | - Claudia Kappen
- Department of Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
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Neilsen BK, Frodyma DE, McCall JL, Fisher KW, Lewis RE. ERK-mediated TIMELESS expression suppresses G2/M arrest in colon cancer cells. PLoS One 2019; 14:e0209224. [PMID: 30629587 PMCID: PMC6328106 DOI: 10.1371/journal.pone.0209224] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/30/2018] [Indexed: 01/04/2023] Open
Abstract
The cell cycle is under circadian regulation. Oncogenes can dysregulate circadian-regulated genes to disrupt the cell cycle, promoting tumor cell proliferation. As a regulator of G2/M arrest in response to DNA damage, the circadian gene Timeless Circadian Clock (TIMELESS) coordinates this connection and is a potential locus for oncogenic manipulation. TIMELESS expression was evaluated using RNASeq data from TCGA and by RT-qPCR and western blot analysis in a panel of colon cancer cell lines. TIMELESS expression following ERK inhibition was examined via western blot. Cell metabolic capacity, propidium iodide, and CFSE staining were used to evaluate the effect of TIMELESS depletion on colon cancer cell survival and proliferation. Cell metabolic capacity following TIMELESS depletion in combination with Wee1 or CHK1 inhibition was assessed. TIMELESS is overexpressed in cancer and required for increased cancer cell proliferation. ERK activation promotes TIMELESS expression. TIMELESS depletion increases γH2AX, a marker of DNA damage, and triggers G2/M arrest via increased CHK1 and CDK1 phosphorylation. TIMELESS depletion in combination with Wee1 or CHK1 inhibition causes an additive decrease in cancer cell metabolic capacity with limited effects in non-transformed human colon epithelial cells. The data show that ERK activation contributes to the overexpression of TIMELESS in cancer. Depletion of TIMELESS increases γH2AX and causes G2/M arrest, limiting cell proliferation. These results demonstrate a role for TIMELESS in cancer and encourage further examination of the link between circadian rhythm dysregulation and cancer cell proliferation.
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Affiliation(s)
- Beth K. Neilsen
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Danielle E. Frodyma
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jamie L. McCall
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kurt W. Fisher
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Robert E. Lewis
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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Gnocchi D, Bruscalupi G. Circadian Rhythms and Hormonal Homeostasis: Pathophysiological Implications. BIOLOGY 2017; 6:biology6010010. [PMID: 28165421 PMCID: PMC5372003 DOI: 10.3390/biology6010010] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 02/07/2023]
Abstract
Over recent years, a deeper comprehension of the molecular mechanisms that control biological clocks and circadian rhythms has been achieved. In fact, many studies have contributed to unravelling the importance of the molecular clock for the regulation of our physiology, including hormonal and metabolic homeostasis. Here we will review the structure, organisation and molecular machinery that make our circadian clock work, and its relevance for the proper functioning of physiological processes. We will also describe the interconnections between circadian rhythms and endocrine homeostasis, as well as the underlying consequences that circadian dysregulations might have in the development of several pathologic affections. Finally, we will discuss how a better knowledge of such relationships might prove helpful in designing new therapeutic approaches for endocrine and metabolic diseases.
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Affiliation(s)
- Davide Gnocchi
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm 14186, Sweden.
| | - Giovannella Bruscalupi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome 00185, Italy.
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A Timeless Link Between Circadian Patterns and Disease. Trends Mol Med 2016; 22:68-81. [DOI: 10.1016/j.molmed.2015.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
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Mah IK, Soloff R, Hedrick SM, Mariani FV. Atypical PKC-iota Controls Stem Cell Expansion via Regulation of the Notch Pathway. Stem Cell Reports 2015; 5:866-880. [PMID: 26527382 PMCID: PMC4649379 DOI: 10.1016/j.stemcr.2015.09.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/16/2022] Open
Abstract
The number of stem/progenitor cells available can profoundly impact tissue homeostasis and the response to injury or disease. Here, we propose that an atypical PKC, Prkci, is a key player in regulating the switch from an expansion to a differentiation/maintenance phase via regulation of Notch, thus linking the polarity pathway with the control of stem cell self-renewal. Prkci is known to influence symmetric cell division in invertebrates; however a definitive role in mammals has not yet emerged. Using a genetic approach, we find that loss of Prkci results in a marked increase in the number of various stem/progenitor cells. The mechanism used likely involves inactivation and symmetric localization of NUMB, leading to the activation of NOTCH1 and its downstream effectors. Inhibition of atypical PKCs may be useful for boosting the production of pluripotent stem cells, multipotent stem cells, or possibly even primordial germ cells by promoting the stem cell/progenitor fate. PRKCi, a polarity protein, regulates expansion of various stem/progenitor cells PRKCi acts in this capacity via a Notch-dependent pathway Thus, PRKCi acts as a link between polarity and stem cell self-renewal Inhibition of aPKCs may be generally useful for expanding progenitor populations
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Affiliation(s)
- In Kyoung Mah
- Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, 1425 San Pablo St., Los Angeles, CA 90033, USA
| | - Rachel Soloff
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephen M Hedrick
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Francesca V Mariani
- Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, 1425 San Pablo St., Los Angeles, CA 90033, USA.
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Gnocchi D, Pedrelli M, Hurt-Camejo E, Parini P. Lipids around the Clock: Focus on Circadian Rhythms and Lipid Metabolism. BIOLOGY 2015; 4:104-32. [PMID: 25665169 PMCID: PMC4381220 DOI: 10.3390/biology4010104] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/28/2015] [Indexed: 12/24/2022]
Abstract
Disorders of lipid and lipoprotein metabolism and transport are responsible for the development of a large spectrum of pathologies, ranging from cardiovascular diseases, to metabolic syndrome, even to tumour development. Recently, a deeper knowledge of the molecular mechanisms that control our biological clock and circadian rhythms has been achieved. From these studies it has clearly emerged how the molecular clock tightly regulates every aspect of our lives, including our metabolism. This review analyses the organisation and functioning of the circadian clock and its relevance in the regulation of physiological processes. We also describe metabolism and transport of lipids and lipoproteins as an essential aspect for our health, and we will focus on how the circadian clock and lipid metabolism are greatly interconnected. Finally, we discuss how a deeper knowledge of this relationship might be useful to improve the recent spread of metabolic diseases.
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Affiliation(s)
- Davide Gnocchi
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, 14186, Sweden.
| | - Matteo Pedrelli
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, 14186, Sweden.
- Strategy and Externalization, CVMD iMED, AstraZeneca, R&D, Mölndal, SE-431 83, Sweden.
| | - Eva Hurt-Camejo
- Strategy and Externalization, CVMD iMED, AstraZeneca, R&D, Mölndal, SE-431 83, Sweden.
| | - Paolo Parini
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, 14186, Sweden.
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Xiao L, Kumazawa Y, Okamura H. Cell death, cavitation and spontaneous multi-differentiation of dental pulp stem cells-derived spheroidsin vitro: A journey to survival and organogenesis. Biol Cell 2014; 106:405-19. [DOI: 10.1111/boc.201400024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/25/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Li Xiao
- Department of Pharmacology; School of Life Dentistry at Tokyo, The Nippon Dental University; Chiyoda-ku, Tokyo 102-0071 Japan
| | - Yasuo Kumazawa
- Department of Oral and Maxillofacial Surgery; The Nippon Dental University Hospital; Chiyoda-ku, Tokyo 102-0071 Japan
| | - Hisashi Okamura
- Department of Oral and Maxillofacial Surgery; The Nippon Dental University Hospital; Chiyoda-ku, Tokyo 102-0071 Japan
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Uth K, Sleigh R. Deregulation of the circadian clock constitutes a significant factor in tumorigenesis: a clockwork cancer. Part I: clocks and clocking machinery. BIOTECHNOL BIOTEC EQ 2014; 28:176-183. [PMID: 26019503 PMCID: PMC4434034 DOI: 10.1080/13102818.2014.915155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/11/2014] [Indexed: 12/18/2022] Open
Abstract
Many physiological processes occur in a rhythmic fashion, consistent with a 24-h cycle. The central timing of the day/night rhythm is set by a master clock, located in the suprachiasmatic nucleus (a tiny region in the hypothalamus), but peripheral clocks exist in different tissues, adjustable by cues other than light (temperature, food, hormone stimulation, etc.), functioning autonomously to the master clock. Presence of unrepaired DNA damage may adjust the circadian clock so that the phase in which checking for damage and DNA repair normally occurs is advanced or extended. The expression of many of the genes coding for proteins functioning in DNA damage-associated response pathways and DNA repair is directly or indirectly regulated by the core clock proteins. Setting up the normal rhythm of the circadian cycle also involves oscillating changes in the chromatin structure, allowing differential activation of various chromatin domains within the 24-h cycle.
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Affiliation(s)
- Kristin Uth
- Centre for Molecular and Cellular Biosensor Research (CMCBR), Abertay University , Dundee , Scotland , UK
| | - Roger Sleigh
- Centre for Molecular and Cellular Biosensor Research (CMCBR), Abertay University , Dundee , Scotland , UK
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Zhang X, Meyn MA, Smithgall TE. c-Yes tyrosine kinase is a potent suppressor of ES cell differentiation and antagonizes the actions of its closest phylogenetic relative, c-Src. ACS Chem Biol 2014; 9:139-46. [PMID: 23895624 DOI: 10.1021/cb400249b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Embryonic stem (ES) cells are derived from the inner cell mass of the blastocyst stage embryo and are characterized by self-renewal and pluripotency. Previous work has shown that Src-family tyrosine kinases display dynamic expression and activity changes during ES cell differentiation, suggesting distinct functions in the control of developmental fate. Here we used ES cells to test the hypothesis that c-Src and its closest phylogenetic relative, c-Yes, act in biological opposition despite their strong homology. Unlike c-Src, enforced expression of active c-Yes blocked ES cell differentiation to embryoid bodies by maintaining pluripotency gene expression. To explore the interplay of c-Src and c-Yes in ES cell differentiation, we engineered c-Src and c-Yes mutants that are resistant to A-419259, a potent pyrrolopyrimidine inhibitor of the Src kinase family. Previous studies have shown that A-419259 treatment blocks all Src-family kinase activity in ES cells, preventing differentiation while maintaining pluripotency. Expression of inhibitor-resistant c-Src but not c-Yes rescued the A-419259 differentiation block, resulting in a cell population with properties of both primitive ectoderm and endoderm. Remarkably, when inhibitor-resistant c-Src and c-Yes were expressed together in ES cells, c-Yes activity suppressed c-Src-mediated differentiation. These studies show that even closely related kinases such as c-Src and c-Yes have unique and opposing functions in the same cell type. Selective agonists or inhibitors of c-Src versus c-Yes activity may allow more precise pharmacological manipulation of ES cell fate and have broader applications in other biological systems that express multiple Src family members such as tumor cells.
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Affiliation(s)
- Xiong Zhang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania 15219, United States
| | - Malcolm A. Meyn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania 15219, United States
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania 15219, United States
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O’Reilly LP, Zhang X, Smithgall TE. Individual Src-family tyrosine kinases direct the degradation or protection of the clock protein Timeless via differential ubiquitylation. Cell Signal 2013; 25:860-6. [PMID: 23266470 PMCID: PMC3595377 DOI: 10.1016/j.cellsig.2012.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 12/05/2012] [Accepted: 12/17/2012] [Indexed: 01/10/2023]
Abstract
Timeless was originally identified in Drosophila as an essential component of circadian cycle regulation, where its function is tightly controlled at the protein level by tyrosine phosphorylation and subsequent degradation. In mammals, Timeless has also been implicated in circadian rhythms as well as cell cycle control and embryonic development. Here we report that mammalian Timeless is an SH3 domain-binding protein and substrate for several members of the Src protein-tyrosine kinase family, including Fyn, Hck, c-Src and c-Yes. Co-expression of Tim with Fyn or Hck was followed by ubiquitylation and subsequent degradation in human 293T cells. While c-Src and c-Yes also promoted Tim ubiquitylation, in this case ubiquitylation correlated with Tim protein accumulation rather than degradation. Both c-Src and c-Yes selectively promoted modification of Tim through Lys63-linked polyubiquitin, which may explain the differential effects on Tim protein turnover. These data show distinct and opposing roles for individual Src-family members in the regulation of Tim protein levels, suggesting a unique mechanism for the regulation of Tim function in mammals.
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Affiliation(s)
- Linda P. O’Reilly
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Xiong Zhang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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Tobback J, Vuerinckx K, Boerjan B, Huybrechts R. RNA interference mortality points to noncircadian functions for the clock gene in the desert locust Schistocerca gregaria. INSECT MOLECULAR BIOLOGY 2012; 21:369-381. [PMID: 22433062 DOI: 10.1111/j.1365-2583.2012.01143.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
One of the core genes in the circadian regulation network is clock (clk). By forming a heterodimer with CYCLE (CYC) that binds on an E-box in the promoter region, it induces the transcription of other elements in the circadian transcriptional feedback loops and different clock output genes. In contrast to other insects, a clk double-stranded RNA (dsRNA) treatment is lethal in adults and fifth instar nymphs of the desert locust, Schistocerca gregaria, in a dose-dependent manner. Clk knock down fifth instar nymphs are able to undergo their imaginal moult but, depending on the amount of dsRNA, it takes them longer than the controls to reach adulthood. As adults, clk knock down animals do not develop their fat body and ovaries like the control animals. Therefore, we tested the expression of different genes involved in energy metabolism and reproduction to see the effect of the clk RNA interference knock down. Surprisingly, the expression of the vitellogenin gene was up-regulated in the clk knock down females who did not appear to invest their energy in egg development. Taken together, our results point out that the clk gene in the desert locust has an additional function in development besides its established role in maintaining the circadian rhythms in the brain.
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Affiliation(s)
- J Tobback
- Research Group of Insect Physiology and Molecular Ethology, Department of Biology, K.U. Leuven, Leuven, Belgium.
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