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Lamberti ML, Spangler RK, Cerdeira V, Ares M, Rivollet L, Ashley GE, Coronado AR, Tripathi S, Spiousas I, Ward JD, Partch CL, Bénard CY, Goya ME, Golombek DA. Clock gene homologs lin-42 and kin-20 regulate circadian rhythms in C. elegans. Sci Rep 2024; 14:12936. [PMID: 38839826 PMCID: PMC11153552 DOI: 10.1038/s41598-024-62303-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
Circadian rhythms are endogenous oscillations in nearly all organisms, from prokaryotes to humans, allowing them to adapt to cyclical environments for close to 24 h. Circadian rhythms are regulated by a central clock, based on a transcription-translation feedback loop. One important protein in the central loop in metazoan clocks is PERIOD, which is regulated in part by Casein kinase 1ε/δ (CK1ε/δ) phosphorylation. In the nematode Caenorhabditis elegans, period and casein kinase 1ε/δ are conserved as lin-42 and kin-20, respectively. Here, we studied the involvement of lin-42 and kin-20 in the circadian rhythms of the adult nematode using a bioluminescence-based circadian transcriptional reporter. We show that mutations of lin-42 and kin-20 generate a significantly longer endogenous period, suggesting a role for both genes in the nematode circadian clock, as in other organisms. These phenotypes can be partially rescued by overexpression of either gene under their native promoter. Both proteins are expressed in neurons and epidermal seam cells, as well as in other cells. Depletion of LIN-42 and KIN-20, specifically in neuronal cells after development, was sufficient to lengthen the period of oscillating sur-5 expression. Therefore, we conclude that LIN-42 and KIN-20 are critical regulators of the adult nematode circadian clock through neuronal cells.
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Affiliation(s)
- Melisa L Lamberti
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
| | - Victoria Cerdeira
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
| | - Myriam Ares
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
| | - Lise Rivollet
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
| | - Guinevere E Ashley
- Department of Molecular, Cell & Developmental Biology, University of California Santa Cruz, Santa Cruz, USA
| | - Andrea Ramos Coronado
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
| | - Ignacio Spiousas
- Laboratorio Interdisciplinario del Tiempo (LITERA), Universidad de San Andrés/CONICET, Buenos Aires, Argentina
| | - Jordan D Ward
- Department of Molecular, Cell & Developmental Biology, University of California Santa Cruz, Santa Cruz, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
- Center for Circadian Biology, UC San Diego, La Jolla, CA, USA
| | - Claire Y Bénard
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - M Eugenia Goya
- European Institute for the Biology of Aging, University Medical Center Groningen, Groningen, The Netherlands.
| | - Diego A Golombek
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes, Buenos Aires, Argentina.
- Laboratorio Interdisciplinario del Tiempo (LITERA), Universidad de San Andrés/CONICET, Buenos Aires, Argentina.
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2
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Spangler RK, Ashley GE, Braun K, Wruck D, Ramos-Coronado A, Ragle JM, Iesmantavicius V, Hess D, Partch CL, Großhans H, Ward JD. A conserved chronobiological complex times C. elegans development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593322. [PMID: 38766223 PMCID: PMC11100808 DOI: 10.1101/2024.05.09.593322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The mammalian PAS-domain protein PERIOD (PER) and its C. elegans orthologue LIN-42 have been proposed to constitute an evolutionary link between two distinct, circadian and developmental, timing systems. However, while the function of PER in animal circadian rhythms is well understood molecularly and mechanistically, this is not true for the function of LIN-42 in timing rhythmic development. Here, using targeted deletions, we find that the LIN-42 PAS domains are dispensable for the protein's function in timing molts. Instead, we observe arrhythmic molts upon deletion of a distinct sequence element, conserved with PER. We show that this element mediates stable binding to KIN-20, the C. elegans CK1δ/ε orthologue. We demonstrate that CK1δ phosphorylates LIN-42 and define two conserved helical motifs, CK1δ-binding domain A (CK1BD-A) and CK1BD-B, that have distinct roles in controlling CK1δ-binding and kinase activity in vitro. KIN-20 and the LIN-42 CK1BD are required for proper molting timing in vivo. These interactions mirror the central role of a stable circadian PER-CK1 complex in setting a robust ~24-hour period. Hence, our results establish LIN-42/PER - KIN-20/CK1δ/ε as a functionally conserved signaling module of two distinct chronobiological systems.
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Affiliation(s)
- Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guinevere E Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kathrin Braun
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Daniel Wruck
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrea Ramos-Coronado
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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3
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Hiroki S, Yoshitane H. Ror homolog nhr-23 is essential for both developmental clock and circadian clock in C. elegans. Commun Biol 2024; 7:243. [PMID: 38418700 PMCID: PMC10902330 DOI: 10.1038/s42003-024-05894-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Animals have internal clocks that generate biological rhythms. In mammals, clock genes such as Period form the circadian clock to generate approximately 24-h biological rhythms. In C. elegans, the clock gene homologs constitute the "developmental clock", which has an 8-h period during larval development to determine the timing of molting. Thus, the ancestral circadian clock has been believed to evolve into the oscillator with a shorter period in C. elegans. However, circadian rhythms have also been observed in adult C. elegans, albeit relatively weak. This prompts the question: if the clock gene homologs drive the developmental rhythm with 8-h period, which genes generate the circadian rhythms in C. elegans? In this study, we discovered that nhr-23, a homolog of the mammalian circadian clock gene Ror, is essential for circadian transcriptional rhythms in adult C. elegans. Interestingly, nhr-23 was also known to be essential for the molting clock. The bilaterian ancestral circadian clock genes might have evolved to function over multiple periods depending on developmental contexts rather than a single 8-h period in C. elegans.
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Affiliation(s)
- Shingo Hiroki
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
| | - Hikari Yoshitane
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
- Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan.
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4
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Lamberti ML, Spangler RK, Cerdeira V, Ares M, Rivollet L, Ashley GE, Coronado AR, Tripathi S, Spiousas I, Ward JD, Partch CL, Bénard CY, Goya ME, Golombek DA. Regulation of the circadian clock in C. elegans by clock gene homologs kin-20 and lin-42. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536481. [PMID: 38105938 PMCID: PMC10723253 DOI: 10.1101/2023.04.13.536481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Circadian rhythms are endogenous oscillations present in nearly all organisms from prokaryotes to humans, allowing them to adapt to cyclical environments close to 24 hours. Circadian rhythms are regulated by a central clock, which is based on a transcription-translation feedback loop. One important protein in the central loop in metazoan clocks is PERIOD, which is regulated in part by Casein kinase 1 ε/δ (CK1 ε/δ ) phosphorylation. In the nematode Caenorhabditis elegans , period and casein kinase 1ε/δ are conserved as lin-42 and kin-20 , respectively. Here we studied the involvement of lin-42 and kin-20 in circadian rhythms of the adult nematode using a bioluminescence-based circadian transcriptional reporter. We show that mutations of lin-42 and kin-20 generate a significantly longer endogenous period, suggesting a role for both genes in the nematode circadian clock, as in other organisms. These phenotypes can be partially rescued by overexpression of either gene under their native promoter. Both proteins are expressed in neurons and seam cells, a population of epidermal stem cells in C. elegans that undergo multiple divisions during development. Depletion of LIN-42 and KIN-20 specifically in neuronal cells after development was sufficient to lengthen the period of oscillating sur-5 expression. Therefore, we conclude that LIN-42 and KIN-20 are critical regulators of the adult nematode circadian clock through neuronal cells.
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5
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Andreatta G, Montagnese S, Costa R. Natural alleles of the clock gene timeless differentially affect life-history traits in Drosophila. Front Physiol 2023; 13:1092951. [PMID: 36703932 PMCID: PMC9871817 DOI: 10.3389/fphys.2022.1092951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/30/2022] [Indexed: 01/12/2023] Open
Abstract
Circadian clocks orchestrate a variety of physiological and behavioural functions within the 24-h day. These timekeeping systems have also been implicated in developmental and reproductive processes that span more (or less) than 24 h. Whether natural alleles of cardinal clock genes affect entire sets of life-history traits (i.e., reproductive arrest, developmental time, fecundity), thus providing a wider substrate for seasonal adaptation, remains unclear. Here we show that natural alleles of the timeless (tim) gene of Drosophila melanogaster, previously shown to modulate flies' propensity to enter reproductive dormancy, differentially affect correlated traits such as early-life fecundity and developmental time. Homozygous flies expressing the shorter TIM isoform (encoded by the s-tim allele) not only show a lower dormancy incidence compared to those homozygous for ls-tim (which produce both the short and an N-terminal additional 23-residues longer TIM isoform), but also higher fecundity in the first 12 days of adult life. Moreover, s-tim homozygous flies develop faster than ls-tim homozygous flies at both warm (25°C) and cold (15°C) temperatures, with the gap being larger at 15°C. In summary, this phenotypic analysis shows that natural variants of tim affect a set of life-history traits associated with reproductive dormancy in Drosophila. We speculate that this provides further adaptive advantage in temperate regions (with seasonal changes) and propose that the underlying mechanisms might not be exclusively dependent on photoperiod, as previously suggested.
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Affiliation(s)
- Gabriele Andreatta
- Department of Biology, University of Padua, Padua, Italy,Max Perutz Laboratories, University of Vienna, Vienna, Austria,*Correspondence: Gabriele Andreatta, ; Rodolfo Costa,
| | - Sara Montagnese
- Department of Medicine, University of Padua, Padua, Italy,Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Rodolfo Costa
- Department of Biology, University of Padua, Padua, Italy,Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom,Institute of Neuroscience, National Research Council (CNR), Padua, Italy,*Correspondence: Gabriele Andreatta, ; Rodolfo Costa,
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6
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Kamal M, Tokmakjian L, Knox J, Mastrangelo P, Ji J, Cai H, Wojciechowski JW, Hughes MP, Takács K, Chu X, Pei J, Grolmusz V, Kotulska M, Forman-Kay JD, Roy PJ. A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins. eLife 2022; 11:e79396. [PMID: 36259463 PMCID: PMC9629831 DOI: 10.7554/elife.79396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
How the cuticles of the roughly 4.5 million species of ecdysozoan animals are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. Forty-eight percent of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families whose transcripts are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs, which are introduced for the first time here. All four families have sequence properties that drive phase separation and we demonstrate phase separation for one exemplar in vitro. This systematic analysis represents the first blueprint for cuticle construction and highlights the massive contribution that phase-separating materials make to the structure.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Levon Tokmakjian
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
| | - Jessica Knox
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Peter Mastrangelo
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Jingxiu Ji
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Hao Cai
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
| | - Jakub W Wojciechowski
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Xiaoquan Chu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Jianfeng Pei
- Department of Computer Science and Technology, Tsinghua UniversityBeijingChina
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Malgorzata Kotulska
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Julie Deborah Forman-Kay
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Peter J Roy
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
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7
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Patel R, Galagali H, Kim JK, Frand AR. Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. eLife 2022; 11:e80010. [PMID: 35968765 PMCID: PMC9377799 DOI: 10.7554/elife.80010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying timing mechanisms are not well understood. Caenorhabditis elegans undergoes four molts at regular 8 to 10 hour intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns and accelerated in let-7(-) mutants, but timed similarly in let-7(-) nhr-23(-) double mutants and wild-type animals. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7-binding site (LCS) in the nhr-23 3' UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also coregulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network, possibly by functioning as a cycle counter.
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Affiliation(s)
- Ruhi Patel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Himani Galagali
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison R Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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8
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Abstract
An enduring mystery of development is how its timing is controlled, particularly for development after birth, where timing is highly flexible and depends on environmental conditions, such as food availability and diet. We followed timing of cell- and organism-level events in individual Caenorhabditis elegans larvae developing from hatching to adulthood, uncovering widespread variations in event timing, both between isogenic individuals in the same environment and when changing conditions and genotypes. However, in almost all cases, we found that events occurred at the same time, when time was rescaled by the duration of development measured in each individual. This observation of “temporal scaling” poses strong constraints on models to explain timing of larval development. It is essential that correct temporal order of cellular events is maintained during animal development. During postembryonic development, the rate of development depends on external conditions, such as food availability, diet, and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism level is not known. We used a unique time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions, and cuticle shedding in individual Caenorhabditis elegans larvae, as they developed from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed “temporal scaling,” meaning that events occurred at the same time when measured relative to the total duration of development in each individual. We also observed pervasive changes in timing when temperature, diet, or genotype were varied, but with larval development divided in “epochs” that differed in how event timing was impacted. Yet, these variations in timing were still explained by temporal scaling when time was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lacking lin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing. However, shifting conditions middevelopment perturbed temporal scaling and changed event order in a highly condition-specific manner, indicating that a complex machinery is responsible for temporal scaling under constant conditions.
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9
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Tsiairis C, Großhans H. Gene expression oscillations in C. elegans underlie a new developmental clock. Curr Top Dev Biol 2020; 144:19-43. [PMID: 33992153 DOI: 10.1016/bs.ctdb.2020.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
During C. elegans larval development, thousands of genes, accounting for >20% of the transcriptome, exhibit oscillatory expression with large amplitudes. The time of peaking varies for different genes, but expression generally peaks once per larval stage, with both the oscillation period and larval stage duration varying in concert with temperature. This and other evidence support the existence of a gene expression oscillator that functions as a developmental clock. In this article, we review what is known about the biology, architecture and possible mechanisms of this clock. We compare it to other oscillators, and highlight tools and approaches suited to its study. Finally, we point out implications of these wide-spread and dynamic changes of gene expression on any type of gene expression profiling experiment in C. elegans larvae and how such experiments need to be controlled.
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Affiliation(s)
- Charisios Tsiairis
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland; University of Basel, Basel, Switzerland.
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10
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Marsac R, Pinson B, Saint-Marc C, Olmedo M, Artal-Sanz M, Daignan-Fornier B, Gomes JE. Purine Homeostasis Is Necessary for Developmental Timing, Germline Maintenance and Muscle Integrity in Caenorhabditis elegans. Genetics 2019; 211:1297-1313. [PMID: 30700528 PMCID: PMC6456310 DOI: 10.1534/genetics.118.301062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 01/24/2019] [Indexed: 12/12/2022] Open
Abstract
Purine homeostasis is ensured through a metabolic network widely conserved from prokaryotes to humans. Purines can either be synthesized de novo, reused, or produced by interconversion of extant metabolites using the so-called recycling pathway. Although thoroughly characterized in microorganisms, such as yeast or bacteria, little is known about regulation of the purine biosynthesis network in metazoans. In humans, several diseases are linked to purine metabolism through as yet poorly understood etiologies. Particularly, the deficiency in adenylosuccinate lyase (ADSL)-an enzyme involved both in the purine de novo and recycling pathways-causes severe muscular and neuronal symptoms. In order to address the mechanisms underlying this deficiency, we established Caenorhabditis elegans as a metazoan model organism to study purine metabolism, while focusing on ADSL. We show that the purine biosynthesis network is functionally conserved in C. elegans Moreover, adsl-1 (the gene encoding ADSL in C. elegans) is required for developmental timing, germline stem cell maintenance and muscle integrity. Importantly, these traits are not affected when solely the de novo pathway is abolished, and we present evidence that germline maintenance is linked specifically to ADSL activity in the recycling pathway. Hence, our results allow developmental and tissue specific phenotypes to be ascribed to separable steps of the purine metabolic network in an animal model.
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Affiliation(s)
- Roxane Marsac
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - Benoît Pinson
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - Christelle Saint-Marc
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - María Olmedo
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Department of Molecular Biology and Biochemical Engineering, 41013 Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Department of Molecular Biology and Biochemical Engineering, 41013 Seville, Spain
| | - Bertrand Daignan-Fornier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - José-Eduardo Gomes
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
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11
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Berardi S, McFall A, Toledo-Hernandez A, Coote C, Graham H, Stine L, Rhodehouse K, Auernhamer A, Van Wynsberghe PM. The Period protein homolog LIN-42 regulates germline development in C. elegans. Mech Dev 2018; 153:42-53. [PMID: 30144508 DOI: 10.1016/j.mod.2018.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Germline stem cells are maintained in the distal region of the C. elegans gonad. These cells undergo mitotic divisions, and GLP-1/Notch signaling dictates whether they remain in this state. The somatic distal tip cell (DTC) caps the end of the distal gonad and is essential for maintenance of the germline mitotic zone. As germ cells move away from the DTC they exit mitosis and enter early meiotic prophase. Here we identify the Period protein homolog LIN-42 as a new regulator of germline development in C. elegans. LIN-42 is expressed in almost all somatic cells including the DTC, and LIN-42 functions as a transcription factor in the heterochronic pathway and to regulate molting. We found that the mitotic proliferative zone size in the distal gonad was significantly reduced by ~25% in lin-42 mutants compared to WT N2 worms. A lin-42 mutation also reduced the mitotic proliferative zone size caused by glp-1 partial loss-of-function and gain-of-function alleles. LIN-42 mediates this effect, at least in part, by regulating expression of the GLP-1/Notch ligand LAG-2. We further show that lin-42 expression itself is regulated by ATX-2, which promotes germline proliferation and is the homolog of the RNA binding protein ataxin-2 that is implicated in human neurodegenerative diseases. Altogether our results establish a new role for the conserved, important Period protein homolog LIN-42 in regulating early germline development. These results also suggest that in addition to regulating behavioral rhythms, the circadian clock plays an important role in communicating environmental signals to essential reproductive pathways.
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Affiliation(s)
- Skyler Berardi
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Alanna McFall
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | | | - Carolyn Coote
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Hillary Graham
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Laurel Stine
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Kyle Rhodehouse
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Anna Auernhamer
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
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The Doubletime Homolog KIN-20 Mainly Regulates let-7 Independently of Its Effects on the Period Homolog LIN-42 in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2018; 8:2617-2629. [PMID: 29880558 PMCID: PMC6071595 DOI: 10.1534/g3.118.200392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Caenorhabditis elegans (C. elegans) heterochronic pathway, which regulates developmental timing, is thought to be an ancestral form of the circadian clock in other organisms. An essential member of this clock is the Period protein whose homolog, lin-42, in C. elegans is an important heterochronic gene. LIN-42 functions as a transcriptional repressor of multiple genes including the conserved lin-4 and let-7 microRNAs. Like other Period proteins, levels of LIN-42 oscillate throughout development. In other organisms this cycling is controlled in part by phosphorylation. KIN-20 is the C. elegans homolog of the Drosophila Period protein kinase Doubletime. Worms containing a large deletion in kin-20 have a significantly smaller brood size and develop slower than wild type C. elegans Here we analyze the effect of kin-20 on lin-42 phenotypes and microRNA expression. We find that kin-20 RNAi enhances loss-of-function lin-42 mutant phenotypes and that kin-20 mutant worms express lower levels of LIN-42 We also show that kin-20 is important for post-transcriptional regulation of mature let-7 and lin-4 microRNA expression. In addition, the increased level of let-7 found in lin-42(n1089) mutant worms is not maintained after kin-20 RNAi treatment. Instead, let-7 is further repressed when levels of kin-20 and lin-42 are both decreased. Altogether these results suggest that though kin-20 regulates lin-42 and let-7 microRNA, it mainly affects let-7 microRNA expression independently of lin-42 These findings further our understanding of the mechanisms by which these conserved circadian rhythmic genes interact to ultimately regulate rhythmic processes, developmental timing and microRNA biogenesis in C. elegans.
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Sleeping Beauty? Developmental Timing, Sleep, and the Circadian Clock in Caenorhabditis elegans. ADVANCES IN GENETICS 2017; 97:43-80. [PMID: 28838356 DOI: 10.1016/bs.adgen.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genetics toolkit is pretty successful in drilling down into minutiae. The big challenge is to integrate the information from this specialty as well as those of biochemistry, physiology, behavior, and anatomy to explain how fundamental biological processes really work. Sleep, the circadian clock and development all qualify as overarching processes that encompass levels from molecule to behavior as part of their known mechanisms. They overlap each other, such that understanding the mechanisms of one can lead to insights into one of the others. In this essay, we consider how the experimental approaches and findings relating to Caenorhabditis elegans development and lethargus on one hand, and to the circadian clock and sleep in higher organisms on the other, could complement and enhance one another.
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Lažetić V, Fay DS. Molting in C. elegans. WORM 2017; 6:e1330246. [PMID: 28702275 DOI: 10.1080/21624054.2017.1330246] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 12/21/2022]
Abstract
Molting is an essential developmental process for the majority of animal species on Earth. During the molting process, which is a specialized form of extracellular matrix (ECM) remodeling, the old apical ECM, or cuticle, is replaced with a new one. Many of the genes and pathways identified as important for molting in nematodes are highly conserved in vertebrates and include regulators and components of vesicular trafficking, steroid-hormone signaling, developmental timers, and hedgehog-like signaling. In this review, we discuss what is known about molting, with a focus on studies in Caenorhabditis elegans. We also describe the key structural elements of the cuticle that must be released, newly synthesized, or remodeled for proper molting to occur.
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Affiliation(s)
- Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, USA
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, USA
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