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Wang Z, Garcia F, Ehlers RU, Molina C. Dauer juvenile recovery transcriptome of two contrasting EMS mutants of the entomopathogenic nematode Heterorhabditis bacteriophora. World J Microbiol Biotechnol 2024; 40:128. [PMID: 38451353 DOI: 10.1007/s11274-024-03902-6] [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: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 03/08/2024]
Abstract
The entomopathogenic nematode Heterorhabditis bacteriophora, symbiotically associated with enterobacteria of the genus Photorhabdus, is a biological control agent against many insect pests. Dauer Juveniles (DJ) of this nematode are produced in industrial-scale bioreactors up to 100 m3 in liquid culture processes lasting approximately 11 days. A high DJ yield (> 200,000 DJ·mL-1) determines the success of the process. To start the mass production, a DJ inoculum proceeding from a previous monoxenic culture is added to pre-cultured (24 h) Photorhabdus bacteria. Within minutes after contact with the bacteria, DJ are expected to perceive signals that trigger their further development (DJ recovery) to reproductive hermaphrodites. A rapid, synchronized, and high DJ recovery is a key factor for an efficient culture process. In case of low percentage of DJ recovery, the final DJ yield is drastically reduced, and the amount of non-desired stages (males and non-fertilized females) hinders the DJ harvest. In a preliminary work, a huge DJ recovery phenotypic variability in H. bacteriophora ethyl methanesulphonate (EMS) mutants was determined. In the present study, two EMS-mutant lines (M31 and M88) with high and low recovery phenotypes were analyzed concerning their differences in gene expression during the first hours of contact with Photorhabdus supernatant containing food signals triggering recovery. A snapshot (RNA-seq analysis) of their transcriptome was captured at 0.5, 1, 3 and 6 h after exposure. Transcripts (3060) with significant regulation changes were identified in the two lines. To analyze the RNA-seq data over time, we (1) divided the expression profiles into clusters of similar regulation, (2) identified over and under-represented gene ontology categories for each cluster, (3) identified Caenorhabditis elegans homologous genes with recovery-related function, and (4) combined the information with available single nucleotide polymorphism (SNP) data. We observed that the expression dynamics of the contrasting mutants (M31 and M88) differ the most within the first 3 h after Photorhabdus supernatant exposure, and during this time, genes related to changes in the DJ cuticle and molting are more active in the high-recovery line (M31). Comparing the gene expression of DJ exposed to the insect food signal in the haemolymph, genes related to host immunosuppressive factors were not found in DJ upon bacterial supernatant exposure. No link between the position of SNPs associated with high recovery and changes in gene expression was determined for genes with high differential expression. Concerning specific transcripts, nine H. bacteriophora gene models with differential expression are provided as candidate genes for further studies.
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Affiliation(s)
- Zhen Wang
- e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Francisco Garcia
- e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Ralf-Udo Ehlers
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Carlos Molina
- e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany.
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2
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Lemieux GA, Yoo S, Lin L, Vohra M, Ashrafi K. The steroid hormone ADIOL promotes learning by reducing neural kynurenic acid levels. Genes Dev 2023; 37:998-1016. [PMID: 38092521 PMCID: PMC10760639 DOI: 10.1101/gad.350745.123] [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: 04/24/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023]
Abstract
Reductions in brain kynurenic acid levels, a neuroinhibitory metabolite, improve cognitive function in diverse organisms. Thus, modulation of kynurenic acid levels is thought to have therapeutic potential in a range of brain disorders. Here we report that the steroid 5-androstene 3β, 17β-diol (ADIOL) reduces kynurenic acid levels and promotes associative learning in Caenorhabditis elegans We identify the molecular mechanisms through which ADIOL links peripheral metabolic pathways to neural mechanisms of learning capacity. Moreover, we show that in aged animals, which normally experience rapid cognitive decline, ADIOL improves learning capacity. The molecular mechanisms that underlie the biosynthesis of ADIOL as well as those through which it promotes kynurenic acid reduction are conserved in mammals. Thus, rather than a minor intermediate in the production of sex steroids, ADIOL is an endogenous hormone that potently regulates learning capacity by causing reductions in neural kynurenic acid levels.
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Affiliation(s)
- George A Lemieux
- Department of Physiology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Shinja Yoo
- Department of Physiology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Lin Lin
- Department of Physiology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Mihir Vohra
- Department of Physiology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kaveh Ashrafi
- Department of Physiology, University of California, San Francisco, San Francisco, California 94143, USA
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3
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Sarkar GC, Rautela U, Goyala A, Datta S, Anand N, Singh A, Singh P, Chamoli M, Mukhopadhyay A. DNA damage signals from somatic uterine tissue arrest oogenesis through activated DAF-16. Development 2023; 150:dev201472. [PMID: 37577954 DOI: 10.1242/dev.201472] [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: 11/24/2022] [Accepted: 07/21/2023] [Indexed: 08/15/2023]
Abstract
Germ line integrity is crucial for progeny fitness. Organisms deploy the DNA damage response (DDR) signaling to protect the germ line from genotoxic stress, facilitating the cell-cycle arrest of germ cells and DNA repair or their apoptosis. Cell-autonomous regulation of germ line quality in response to DNA damage is well studied; however, how quality is enforced cell non-autonomously on sensing somatic DNA damage is less known. Using Caenorhabditis elegans, we show that DDR disruption, only in the uterus, when insulin/IGF-1 signaling (IIS) is low, arrests oogenesis in the pachytene stage of meiosis I, in a FOXO/DAF-16 transcription factor-dependent manner. Without FOXO/DAF-16, germ cells of the IIS mutant escape the arrest to produce poor-quality oocytes, showing that the transcription factor imposes strict quality control during low IIS. Activated FOXO/DAF-16 senses DDR perturbations during low IIS to lower ERK/MPK-1 signaling below a threshold to promote germ line arrest. Altogether, we elucidate a new surveillance role for activated FOXO/DAF-16 that ensures optimal germ cell quality and progeny fitness in response to somatic DNA damage.
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Affiliation(s)
- Gautam Chandra Sarkar
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Umanshi Rautela
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anita Goyala
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sudeshna Datta
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nikhita Anand
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anupama Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prachi Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manish Chamoli
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Arnab Mukhopadhyay
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Unno T, Takatsuka H, Ohnishi Y, Ito M, Kubota Y. A class I histone deacetylase HDA-2 is essential for embryonic development and size regulation of fertilized eggs in Caenorhabditis elegans. Genes Genomics 2021; 44:343-357. [PMID: 34843089 DOI: 10.1007/s13258-021-01195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/21/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Caenorhabditis elegans encodes three class I histone deacetylases (HDACs), HDA-1, HDA-2, and HDA-3. Although HDA-1 is known to be involved in embryogenesis, the regulatory roles of HDA-2 and HDA-3 in embryonic development remain unexplored. OBJECTIVE To elucidate the functional roles of the three class I HDACs in C. elegans embryonic development. METHODS The roles of Class I HDACs, HDA-1, HDA-2, and HDA-3 in Caenorhabditis elegans during embryogenesis were investigated through the analysis of embryonic lethality via gene knockdown or deletion mutants. Additionally, the size of these knockdown and mutant eggs was observed using a differential interference contrast microscope. Finally, expression pattern and tissue-specific role of hda-2 and transcriptome of the hda-2 mutant were analyzed. RESULTS Here, we report that HDA-1 and HDA-2, but not HDA-3, play essential roles in Caenorhabditis elegans embryonic development. Our observations of the fertilized egg size variance demonstrated that HDA-2 is involved in regulating the size of fertilized eggs. Combined analysis of expression patterns and sheath cell-specific rescue experiments indicated that the transgenerational role of HDA-2 is involved in the viability of embryonic development and fertilized egg size regulation. Furthermore, transcriptome analysis of hda-2 mutant embryos implies that HDA-2 is involved in epigenetic regulation of embryonic biological processes by downregulating and upregulating the gene expression. CONCLUSION Our finding suggests that HDA-2 regulates the embryonic development in Caenorhabditis elegans by controling a specific subset of genes, and this function might be mediated by transgenerational epigenetic effect.
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Affiliation(s)
- Takuma Unno
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hisashi Takatsuka
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yuto Ohnishi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.,Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yukihiko Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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5
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Das D, Chen SY, Arur S. ERK phosphorylates chromosomal axis component HORMA domain protein HTP-1 to regulate oocyte numbers. SCIENCE ADVANCES 2020; 6:6/44/eabc5580. [PMID: 33127680 PMCID: PMC7608811 DOI: 10.1126/sciadv.abc5580] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/18/2020] [Indexed: 05/10/2023]
Abstract
Oocyte numbers, a critical determinant of female reproductive fitness, are highly regulated, yet the mechanisms underlying this regulation remain largely undefined. In the Caenorhabditis elegans gonad, RAS/extracellular signal-regulated kinase (ERK) signaling regulates oocyte numbers; mechanisms are unknown. We show that the RAS/ERK pathway phosphorylates meiotic chromosome axis protein HTP-1 at serine-325 to control chromosome dynamics and regulate oocyte number. Phosphorylated HTP-1(S325) accumulates in vivo in an ERK-dependent manner in early-mid pachytene stage germ cells and is necessary for synaptonemal complex extension and/or maintenance. Lack of HTP-1 phosphorylation leads to asynapsis and persistence of meiotic double-strand breaks, causing delayed meiotic progression and reduced oocyte number. In contrast, early onset of ERK activation causes precocious meiotic progression, resulting in increased oocyte number, which is reversed by removal of HTP-1 phosphorylation. The RAS/ERK/HTP-1 signaling cascade thus functions to monitor formation and maintenance of synapsis for timely resolution of double-strand breaks, oocyte production, and reproductive fitness.
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Affiliation(s)
- Debabrata Das
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shin-Yu Chen
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Swathi Arur
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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The Role of pkc-3 and Genetic Suppressors in Caenorhabditis elegans Epithelial Cell Junction Formation. Genetics 2020; 214:941-959. [PMID: 32005655 DOI: 10.1534/genetics.120.303085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022] Open
Abstract
Epithelial cells form intercellular junctions to strengthen cell-cell adhesion and limit diffusion, allowing epithelia to function as dynamic tissues and barriers separating internal and external environments. Junctions form as epithelial cells differentiate; clusters of junction proteins first concentrate apically, then mature into continuous junctional belts that encircle and connect each cell. In mammals and Drosophila, atypical protein kinase C (aPKC) is required for junction maturation, although how it contributes to this process is poorly understood. A role for the Caenorhabditis elegans aPKC homolog PKC-3 in junction formation has not been described previously. Here, we show that PKC-3 is essential for junction maturation as epithelia first differentiate. Using a temperature-sensitive allele of pkc-3 that causes junction breaks in the spermatheca and leads to sterility, we identify intragenic and extragenic suppressors that render pkc-3 mutants fertile. Intragenic suppressors include an unanticipated stop-to-stop mutation in the pkc-3 gene, providing evidence for the importance of stop codon identity in gene activity. One extragenic pkc-3 suppressor is a loss-of-function allele of the lethal(2) giant larvae homolog lgl-1, which antagonizes aPKC within epithelia of Drosophila and mammals, but was not known previously to function in C. elegans epithelia. Finally, two extragenic suppressors are loss-of-function alleles of sups-1-a previously uncharacterized gene. We show that SUPS-1 is an apical extracellular matrix protein expressed in epidermal cells, suggesting that it nonautonomously regulates junction formation in the spermatheca. These findings establish a foundation for dissecting the role of PKC-3 and interacting genes in epithelial junction maturation.
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7
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Cell Non-autonomous Function of daf-18/PTEN in the Somatic Gonad Coordinates Somatic Gonad and Germline Development in C. elegans Dauer Larvae. Curr Biol 2019; 29:1064-1072.e8. [PMID: 30827916 DOI: 10.1016/j.cub.2019.01.076] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 12/21/2022]
Abstract
C. elegans larvae integrate environmental information and developmental decisions [1-3]. In favorable conditions, worms develop rapidly and continuously through four larval stages into reproductive adulthood. However, if conditions are unfavorable through the second larval stage, worms enter dauer diapause, a state of global and reversible developmental arrest in which precursor cells remain quiescent and preserve developmental potential, anticipating developmental progression if conditions improve. Signaling from neurons, hypodermis, and intestine regulate the appearance and behavior of dauer larvae and many aspects of developmental arrest of the non-gonadal soma [1, 4, 5]. Here, we show that the decision of somatic gonad blast cells (SGBs) and germline stem cells (GSCs) to be quiescent or progress developmentally is regulated differently from the non-gonadal soma: daf-18/PTEN acts non-autonomously within the somatic gonad to maintain developmental quiescence of both SGBs and GSCs. Our analysis suggests that daf-18 acts in somatic gonad cells to produce a "pro-quiescence" signal (or signals) that acts inter se and between the somatic gonad and the germline. The inferred signal does not require DAF-2/insulin receptor or maintain quiescence of the nearby sex myoblasts, and developmental progression in daf-18(0) does not require dafachronic acids. Abrogating quiescence in dauer results in post-dauer sterility. Our results implicate the somatic gonad as an endocrine organ to synchronize somatic gonad and germline development during dauer diapause and recovery, and our finding that PTEN acts non-autonomously to control blast cell quiescence may be relevant to its function as a tumor suppressor in mammals and to combating parasitic nematodes.
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8
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McGovern M, Castaneda PG, Pekar O, Vallier LG, Cram EJ, Hubbard EJA. The DSL ligand APX-1 is required for normal ovulation in C. elegans. Dev Biol 2018; 435:162-169. [PMID: 29371032 DOI: 10.1016/j.ydbio.2018.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/14/2017] [Accepted: 01/11/2018] [Indexed: 01/13/2023]
Abstract
DSL ligands activate the Notch receptor in many cellular contexts across metazoa to specify cell fate. In addition, Notch receptor activity is implicated in post-mitotic morphogenesis and neuronal function. In C. elegans, the DSL family ligand APX-1 is expressed in a subset of cells of the proximal gonad lineage, where it can act as a latent proliferation-promoting signal to maintain proximal germline tumors. Here we examine apx-1 in the proximal gonad and uncover a role in the maintenance of normal ovulation. Depletion of apx-1 causes an endomitotic oocyte (Emo) phenotype and ovulation defects. We find that lag-2 can substitute for apx-1 in this role, that the ovulation defect is partially suppressed by loss of ipp-5, and that lin-12 depletion causes a similar phenotype. In addition, we find that the ovulation defects are often accompanied by a delay of spermathecal distal neck closure after oocyte entry. Although calcium oscillations occur in the spermatheca, calcium signals are abnormal when the distal neck does not close completely. Moreover, oocytes sometimes cannot properly transit through the spermatheca, leading to fragmentation of oocytes once the neck closes. Finally, abnormal oocytes and neck closure defects are seen occasionally when apx-1 or lin-12 activity is reduced in adult animals, suggesting a possible post-developmental role for APX-1 and LIN-12 signaling in ovulation.
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Affiliation(s)
- Marie McGovern
- Department of Biological Sciences, Kingsborough Community College, City University of New York, 2001 Oriental Blvd, Brooklyn, NY 11235, United States; Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016, United States
| | | | - Olga Pekar
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016, United States
| | - Laura G Vallier
- Department of Biology, Hofstra University, Hempstead, NY 11549, United States
| | - Erin J Cram
- Department of Biology, Northeastern University, Boston, MA 02115, United States
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016, United States.
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Bhati M, Llamosas E, Jacques DA, Jeffries CM, Dastmalchi S, Ripin N, Nicholas HR, Matthews JM. Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans. Sci Rep 2017; 7:4579. [PMID: 28676648 PMCID: PMC5496915 DOI: 10.1038/s41598-017-04587-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
LIM-Homeodomain (LIM-HD) transcription factors are highly conserved in animals where they are thought to act in a transcriptional ‘LIM code’ that specifies cell types, particularly in the central nervous system. In chick and mammals the interaction between two LIM-HD proteins, LHX3 and Islet1 (ISL1), is essential for the development of motor neurons. Using yeast two-hybrid analysis we showed that the Caenorhabditis elegans orthologs of LHX3 and ISL1, CEH-14 and LIM-7 can physically interact. Structural characterisation of a complex comprising the LIM domains from CEH-14 and a LIM-interaction domain from LIM-7 showed that these nematode proteins assemble to form a structure that closely resembles that of their vertebrate counterparts. However, mutagenic analysis across the interface indicates some differences in the mechanisms of binding. We also demonstrate, using fluorescent reporter constructs, that the two C. elegans proteins are co-expressed in a small subset of neurons. These data show that the propensity for LHX3 and Islet proteins to interact is conserved from C. elegans to mammals, raising the possibility that orthologous cell specific LIM-HD-containing transcription factor complexes play similar roles in the development of neuronal cells across diverse species.
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Affiliation(s)
- Mugdha Bhati
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Teva Pharmaceuticals Australia Pty Ltd, Macquarie Park, NSW, 2113, Australia
| | - Estelle Llamosas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,School of Women's and Children's Health, University of New South Wales, NSW, Australia
| | - David A Jacques
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,iThree Institute, University of Technology, NSW, 2007, Australia
| | - Cy M Jeffries
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Siavoush Dastmalchi
- Biotechnology Research Center and School of Pharmacy, Tabritz Univeristy of Medical Science, Tabritz, Iran
| | - Nina Ripin
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Department of Biology, ETH, Zurich, 8093, Switzerland
| | - Hannah R Nicholas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
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10
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Chi C, Ronai D, Than MT, Walker CJ, Sewell AK, Han M. Nucleotide levels regulate germline proliferation through modulating GLP-1/Notch signaling in C. elegans. Genes Dev 2016; 30:307-20. [PMID: 26833730 PMCID: PMC4743060 DOI: 10.1101/gad.275107.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, Chi et al. researched the link between known nutrient-sensing systems and reproductive programs. Using a model system in C. elegans, they show that a Notch signaling pathway senses the level of uridine/thymidine and controls germline proliferation, delineating a previously unknown nucleotide-sensing mechanism for controlling reproductivity. Animals alter their reproductive programs to accommodate changes in nutrient availability, yet the connections between known nutrient-sensing systems and reproductive programs are underexplored, and whether there is a mechanism that senses nucleotide levels to coordinate germline proliferation is unknown. We established a model system in which nucleotide metabolism is perturbed in both the nematode Caenorhabditis elegans (cytidine deaminases) and its food (Escherichia coli); when fed food with a low uridine/thymidine (U/T) level, germline proliferation is arrested. We provide evidence that this impact of U/T level on the germline is critically mediated by GLP-1/Notch and MPK-1/MAPK, known to regulate germline mitotic proliferation. This germline defect is suppressed by hyperactivation of glp-1 or disruption of genes downstream from glp-1 to promote meiosis but not by activation of the IIS or TORC1 pathways. Moreover, GLP-1 expression is post-transcriptionally modulated by U/T levels. Our results reveal a previously unknown nucleotide-sensing mechanism for controlling reproductivity.
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Affiliation(s)
- Congwu Chi
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Diana Ronai
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Minh T Than
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Cierra J Walker
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Aileen K Sewell
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Min Han
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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11
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Cecchetelli AD, Hugunin J, Tannoury H, Cram EJ. CACN-1 is required in the Caenorhabditis elegans somatic gonad for proper oocyte development. Dev Biol 2016; 414:58-71. [PMID: 27046631 PMCID: PMC4875861 DOI: 10.1016/j.ydbio.2016.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 12/16/2022]
Abstract
CACN-1/Cactin is a conserved protein identified in a genome-wide screen for genes that regulate distal tip cell migration in the nematode Caenorhabditis elegans. In addition to possessing distal tip cells that migrate past their correct stopping point, animals depleted of cacn-1 are sterile. In this study, we show that CACN-1 is needed in the soma for proper germ line development and maturation. When CACN-1 is depleted, sheath cells are absent and/or abnormal. When sheath cells are absent, hermaphrodites produce sperm, but do not switch appropriately to oocyte production. When sheath cells are abnormal, some oocytes develop but are not successfully ovulated and undergo endomitotic reduplication (Emo). Our previous proteomic studies show that CACN-1 interacts with a network of splicing factors. Here, these interactors were screened using RNAi. Depletion of many of these factors led to missing or abnormal sheath cells and germ line defects, particularly absent and/or Emo oocytes. These results suggest CACN-1 is part of a protein network that influences somatic gonad development and function through alternative splicing or post-transcriptional gene regulation.
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Affiliation(s)
| | - Julie Hugunin
- Department of Biology, Northeastern University, Boston, MA 02115, United States
| | - Hiba Tannoury
- Department of Biology, Northeastern University, Boston, MA 02115, United States
| | - Erin J Cram
- Department of Biology, Northeastern University, Boston, MA 02115, United States.
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12
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Ni P, Ma X, Lin Y, Lao G, Hao X, Guan L, Li X, Jiang Z, Liu Y, Ye B, Liu X, Wang Y, Zhao L, Cao L, Li T. Methionine sulfoxide reductase A (MsrA) associated with bipolar I disorder and executive functions in A Han Chinese population. J Affect Disord 2015; 184:235-8. [PMID: 26117066 DOI: 10.1016/j.jad.2015.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 06/05/2015] [Accepted: 06/05/2015] [Indexed: 02/05/2023]
Abstract
BACKGROUND The oxidative stress hypothesis proposed to explain bipolar I disorder (BD I) pathogenesis has gained growing attention based on its association with cognitive impairment. The aim of the present study was to explore the association of the methionine sulfoxide reductase A (MsrA) gene with BD I as well as executive functions of BD I patients. METHODS A total of 44 tagging single-nucleotide polymorphisms within the MsrA gene were selected to analyze gene association with BD I in 375 BD I patients and 475 controls in a Han Chinese population. The association of MsrA haplotypes with executive functions was analyzed in 157 clinically stable BD I patients and 210 controls. RESULTS Allele frequencies of the rs4840463 polymorphism were significantly different between BD I patients and controls, and between patients with psychotic symptoms and controls. BD I patients performed more poorly in 11 of the 13 neurocognitive measurements compared with controls. Three MsrA haplotypes showed significant associations with different executive functions. LIMITATIONS The limited sample size requires a cautious conclusion, and further comprehensive approaches are needed to explore the mechanism of MsrA's effect on BD I. CONCLUSIONS The rs4840463 polymorphism in the MsrA gene may be associated with the increased risk of BD I in a Chinese population. The association of MsrA haplotypes with executive functions indicated that MsrA is associated with executive function defects in BD I patients.
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Affiliation(s)
- Peiyan Ni
- Psychiatric Laboratory and Department of Psychiatry, West China Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xiaohong Ma
- Psychiatric Laboratory and Department of Psychiatry, West China Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China.
| | - Yin Lin
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Guohui Lao
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Xiaoyu Hao
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Lijie Guan
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Xuan Li
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Zeyu Jiang
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Yuping Liu
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Biyu Ye
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China
| | - Xiang Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Yingcheng Wang
- Psychiatric Laboratory and Department of Psychiatry, West China Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Liansheng Zhao
- Psychiatric Laboratory and Department of Psychiatry, West China Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Liping Cao
- Guangzhou Brain Hospital (Guangzhou Huiai Hospital, The Affiliated Brain Hospital of Guangzhou Medical University), Guangzhou, Guangdong, PR China.
| | - Tao Li
- Psychiatric Laboratory and Department of Psychiatry, West China Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
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Uehara T, Kage-Nakadai E, Yoshina S, Imae R, Mitani S. The Tumor Suppressor BCL7B Functions in the Wnt Signaling Pathway. PLoS Genet 2015; 11:e1004921. [PMID: 25569233 PMCID: PMC4287490 DOI: 10.1371/journal.pgen.1004921] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/24/2014] [Indexed: 01/05/2023] Open
Abstract
Human BCL7 gene family consists of BCL7A, BCL7B, and BCL7C. A number of clinical studies have reported that BCL7 family is involved in cancer incidence, progression, and development. Among them, BCL7B, located on chromosome 7q11.23, is one of the deleted genes in patients with Williams-Beuren syndrome. Although several studies have suggested that malignant diseases occurring in patients with Williams-Beuren syndrome are associated with aberrations in BCL7B, little is known regarding the function of this gene at the cellular level. In this study, we focused on bcl-7, which is the only homolog of BCL7 gene family in Caenorhabditis elegans, and analyzed bcl-7 deletion mutants. As a result, we found that bcl-7 is required for the asymmetric differentiation of epithelial seam cells, which have self-renewal properties as stem cells and divide asymmetrically through the WNT pathway. Distal tip cell development, which is regulated by the WNT pathway in Caenorhabditis elegans, was also affected in bcl-7-knockout mutants. Interestingly, bcl-7 mutants exhibited nuclear enlargement, reminiscent of the anaplastic features of malignant cells. Furthermore, in KATOIII human gastric cancer cells, BCL7B knockdown induced nuclear enlargement, promoted the multinuclei phenotype and suppressed cell death. In addition, this study showed that BCL7B negatively regulates the Wnt-signaling pathway and positively regulates the apoptotic pathway. Taken together, our data indicate that BCL7B/BCL-7 has some roles in maintaining the structure of nuclei and is involved in the modulation of multiple pathways, including Wnt and apoptosis. This study may implicate a risk of malignancies with BCL7B-deficiency, such as Williams-Beuren syndrome. BCL7B, a member of the human BCL7 gene family, is deleted in patients with Williams-Beuren syndrome. Although several clinical studies have suggested that malignant diseases occurring in patients with Williams-Beuren syndrome are associated with aberrations in BCL7B, little is known regarding the physiological function of this gene. Here, we show that bcl-7, the only homolog of BCL7 gene family in Caenorhabditis elegans, regulates asymmetric cell differentiation in somatic “stem-like” seam cells through at least the Wnt pathway and promotes the apoptotic pathway. In addition, bcl-7 deletion mutants show enlarged nuclei in epidermis and germ cells. Furthermore, in KATOIII human gastric cancer cells, BCL7B knockdown induces nuclear enlargement, as observed in Caenorhabditis elegans, and promotes the multinucleated phenotype, both of which are reminiscent of malignant diseases. BCL7B also negatively regulates the Wnt-signaling pathway and positively regulates the apoptotic pathway, similar to Caenorhabditis elegans. Altogether, this study may open the door for understanding the function of BCL7 family in cell differentiation and malignancies.
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Affiliation(s)
- Tomoko Uehara
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Eriko Kage-Nakadai
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Rieko Imae
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan; Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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14
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Yang H, Chen YZ, Zhang Y, Wang X, Zhao X, Godfroy JI, Liang Q, Zhang M, Zhang T, Yuan Q, Ann Royal M, Driscoll M, Xia NS, Yin H, Xue D. A lysine-rich motif in the phosphatidylserine receptor PSR-1 mediates recognition and removal of apoptotic cells. Nat Commun 2015; 6:5717. [PMID: 25564762 PMCID: PMC4306451 DOI: 10.1038/ncomms6717] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 10/31/2014] [Indexed: 02/02/2023] Open
Abstract
The conserved phosphatidylserine receptor (PSR) was first identified as a receptor for phosphatidylserine, an 'eat-me' signal exposed by apoptotic cells. However, several studies suggest that PSR may also act as an arginine demethylase, a lysyl hydroxylase, or an RNA-binding protein through its N-terminal JmjC domain. How PSR might execute drastically different biochemical activities, and whether they are physiologically significant, remain unclear. Here we report that a lysine-rich motif in the extracellular domain of PSR-1, the Caenorhabditis elegans PSR, mediates specific phosphatidylserine binding in vitro and clearance of apoptotic cells in vivo. This motif also mediates phosphatidylserine-induced oligomerization of PSR-1, suggesting a mechanism by which PSR-1 activates phagocytosis. Mutations in the phosphatidylserine-binding motif, but not in its Fe(II) binding site critical for the JmjC activity, abolish PSR-1 phagocytic function. Moreover, PSR-1 enriches and clusters around apoptotic cells during apoptosis. These results establish that PSR-1 is a conserved, phosphatidylserine-recognizing phagocyte receptor.
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Affiliation(s)
- Hengwen Yang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Yu-Zen Chen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Yi Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohui Wang
- Department of Chemistry &Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Xiang Zhao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - James I Godfroy
- Department of Chemistry &Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Qian Liang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Man Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tianying Zhang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Mary Ann Royal
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Ning-Shao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hang Yin
- 1] Department of Chemistry &Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA [2] Center of Basic Molecular Science and Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Ding Xue
- 1] Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA [2] School of Life Sciences, Tsinghua University, Beijing 100084, China
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Two classes of gap junction channels mediate soma-germline interactions essential for germline proliferation and gametogenesis in Caenorhabditis elegans. Genetics 2014; 198:1127-53. [PMID: 25195067 PMCID: PMC4224157 DOI: 10.1534/genetics.114.168815] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In all animals examined, somatic cells of the gonad control multiple biological processes essential for germline development. Gap junction channels, composed of connexins in vertebrates and innexins in invertebrates, permit direct intercellular communication between cells and frequently form between somatic gonadal cells and germ cells. Gap junctions comprise hexameric hemichannels in apposing cells that dock to form channels for the exchange of small molecules. Here we report essential roles for two classes of gap junction channels, composed of five innexin proteins, in supporting the proliferation of germline stem cells and gametogenesis in the nematode Caenorhabditis elegans. Transmission electron microscopy of freeze-fracture replicas and fluorescence microscopy show that gap junctions between somatic cells and germ cells are more extensive than previously appreciated and are found throughout the gonad. One class of gap junctions, composed of INX-8 and INX-9 in the soma and INX-14 and INX-21 in the germ line, is required for the proliferation and differentiation of germline stem cells. Genetic epistasis experiments establish a role for these gap junction channels in germline proliferation independent of the glp-1/Notch pathway. A second class of gap junctions, composed of somatic INX-8 and INX-9 and germline INX-14 and INX-22, is required for the negative regulation of oocyte meiotic maturation. Rescue of gap junction channel formation in the stem cell niche rescues germline proliferation and uncovers a later channel requirement for embryonic viability. This analysis reveals gap junctions as a central organizing feature of many soma–germline interactions in C. elegans.
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16
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Wagner E, Stolfi A, Gi Choi Y, Levine M. Islet is a key determinant of ascidian palp morphogenesis. Development 2014; 141:3084-92. [PMID: 24993943 DOI: 10.1242/dev.110684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The anterior-most ectoderm of ascidian larvae contains the adhesive papillae, or palps, which play an important role in triggering the metamorphosis of swimming tadpoles. In Ciona intestinalis, the palps consist of three conical protrusions within a field of thickened epithelium that form late in embryogenesis, as tailbuds mature into larvae. The palp protrusions express the LIM-homeodomain transcription factor Islet. Protrusion occurs through differential cell elongation, probably mediated by Islet, as we find that ectopic expression of Islet is sufficient to promote cell lengthening. FGF signaling is required for both Islet expression and palp morphogenesis. Importantly, we show that Islet expression can rescue the palp-deficient phenotype that results from inhibition of FGF signaling. We conclude that Islet is a key regulatory factor governing morphogenesis of the palps. It is conceivable that Islet is also essential for the cellular morphogenesis of placode-derived sensory neurons in vertebrates.
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Affiliation(s)
- Eileen Wagner
- Center for Integrative Genomics, Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Alberto Stolfi
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York, NY 10003-6688, USA
| | - Yoon Gi Choi
- Functional Genomics Laboratory, Department of Molecular and Cell Biology, University of California-Berkeley, 255 Life Sciences Addition #3200, Berkeley, CA 94720-3200, USA
| | - Mike Levine
- Center for Integrative Genomics, Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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17
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Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJM. Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res 2013; 42:153-62. [PMID: 24068555 PMCID: PMC3874175 DOI: 10.1093/nar/gkt858] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Gene expression is controlled through the binding of transcription factors (TFs) to regulatory genomic regions. First introns are longer than other introns in multiple eukaryotic species and are under selective constraint. Here we explore the importance of first introns in TF binding in the nematode Caenorhabditis elegans by combining computational predictions and experimentally derived TF–DNA interaction data. We found that first introns of C. elegans genes, particularly those for families enriched in long first introns, are more conserved in length, have more conserved predicted TF interactions and are bound by more TFs than other introns. We detected a significant positive correlation between first intron size and the number of TF interactions obtained from chromatin immunoprecipitation assays or determined by yeast one-hybrid assays. TFs that bind first introns are largely different from those binding promoters, suggesting that the different interactions are complementary rather than redundant. By combining first intron and promoter interactions, we found that genes that share a large fraction of TF interactions are more likely to be co-expressed than when only TF interactions with promoters are considered. Altogether, our data suggest that C. elegans gene regulation may be additive through the combined effects of multiple regulatory regions.
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Affiliation(s)
- Juan I Fuxman Bass
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA and Divisions of Rheumatology and Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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18
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Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, Reis K, Janosch S, Schloissnig S, Ejsmont RK, Slightam C, Xu X, Kim SK, Reinke V, Stewart AF, Snyder M, Waterston RH, Hyman AA. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell 2012; 150:855-66. [PMID: 22901814 DOI: 10.1016/j.cell.2012.08.001] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 03/22/2012] [Accepted: 08/01/2012] [Indexed: 12/21/2022]
Abstract
Understanding the in vivo dynamics of protein localization and their physical interactions is important for many problems in biology. To enable systematic protein function interrogation in a multicellular context, we built a genome-scale transgenic platform for in vivo expression of fluorescent- and affinity-tagged proteins in Caenorhabditis elegans under endogenous cis regulatory control. The platform combines computer-assisted transgene design, massively parallel DNA engineering, and next-generation sequencing to generate a resource of 14,637 genomic DNA transgenes, which covers 73% of the proteome. The multipurpose tag used allows any protein of interest to be localized in vivo or affinity purified using standard tag-based assays. We illustrate the utility of the resource by systematic chromatin immunopurification and automated 4D imaging, which produced detailed DNA binding and cell/tissue distribution maps for key transcription factor proteins.
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Affiliation(s)
- Mihail Sarov
- TransgeneOmics Unit, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
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19
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Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res 2012; 22:2356-67. [PMID: 22722344 PMCID: PMC3514665 DOI: 10.1101/gr.139725.112] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful of exceptional examples are known, typically involving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we report the first systematic survey of microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of unrelated genes that have remained tightly physically linked in diverse lineages across over 600 million years of evolution. Integrating sequence conservation, gene expression data, gene function, epigenetic marks, and other genomic features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos, which provided further evidence of putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results suggest that ancient genomic functional associations are far more common than previously thought—involving ∼12% of the ancestral bilaterian genome—and that cis-regulatory constraints are crucial in determining metazoan genome architecture.
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Affiliation(s)
- Manuel Irimia
- Department of Biology, Stanford University, Stanford, California 94305, USA
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20
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Li X, Johnson RW, Park D, Chin-Sang I, Chamberlin HM. Somatic gonad sheath cells and Eph receptor signaling promote germ-cell death in C. elegans. Cell Death Differ 2012; 19:1080-9. [PMID: 22240896 PMCID: PMC3354057 DOI: 10.1038/cdd.2011.192] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 11/07/2011] [Accepted: 11/07/2011] [Indexed: 02/07/2023] Open
Abstract
Programmed cell death eliminates unwanted cells during normal development and physiological homeostasis. While cell interactions can influence apoptosis as they do other types of cell fate, outside of the adaptive immune system little is known about the intercellular cues that actively promote cell death in healthy cells. We used the Caenorhabditis elegans germline as a model to investigate the extrinsic regulators of physiological apoptosis. Using genetic and cell biological methods, we show that somatic gonad sheath cells, which also act as phagocytes of dying germ cells, promote death in the C. elegans germline through VAB-1/Eph receptor signaling. We report that the germline apoptosis function of VAB-1 impacts specific cell death pathways, and may act in parallel to extracellular signal-regulated kinase MAPK signaling. This work defines a non-autonomous, pro-apoptotic signaling for efficient physiological cell death, and highlights the dynamic nature of intercellular communication between dying cells and the phagocytes that remove them.
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Affiliation(s)
- X Li
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - R W Johnson
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - D Park
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - I Chin-Sang
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - H M Chamberlin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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21
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Murata D, Nomura KH, Dejima K, Mizuguchi S, Kawasaki N, Matsuishi-Nakajima Y, Ito S, Gengyo-Ando K, Kage-Nakadai E, Mitani S, Nomura K. GPI-anchor synthesis is indispensable for the germline development of the nematode Caenorhabditis elegans. Mol Biol Cell 2012; 23:982-95. [PMID: 22298425 PMCID: PMC3302757 DOI: 10.1091/mbc.e10-10-0855] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 11/28/2011] [Accepted: 01/23/2012] [Indexed: 11/11/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI)-anchor attachment is one of the most common posttranslational protein modifications. Using the nematode Caenorhabditis elegans, we determined that GPI-anchored proteins are present in germline cells and distal tip cells, which are essential for the maintenance of the germline stem cell niche. We identified 24 C. elegans genes involved in GPI-anchor synthesis. Inhibition of various steps of GPI-anchor synthesis by RNA interference or gene knockout resulted in abnormal development of oocytes and early embryos, and both lethal and sterile phenotypes were observed. The piga-1 gene (orthologue of human PIGA) codes for the catalytic subunit of the phosphatidylinositol N-acetylglucosaminyltransferase complex, which catalyzes the first step of GPI-anchor synthesis. We isolated piga-1-knockout worms and found that GPI-anchor synthesis is indispensable for the maintenance of mitotic germline cell number. The knockout worms displayed 100% lethality, with decreased mitotic germline cells and abnormal eggshell formation. Using cell-specific rescue of the null allele, we showed that expression of piga-1 in somatic gonads and/or in germline is sufficient for normal embryonic development and the maintenance of the germline mitotic cells. These results clearly demonstrate that GPI-anchor synthesis is indispensable for germline formation and for normal development of oocytes and eggs.
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Affiliation(s)
- Daisuke Murata
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8581, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuko H. Nomura
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Katsufumi Dejima
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Souhei Mizuguchi
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Nana Kawasaki
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Yukari Matsuishi-Nakajima
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Satsuki Ito
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Keiko Gengyo-Ando
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Eriko Kage-Nakadai
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Shohei Mitani
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - Kazuya Nomura
- Department of Biological Sciences, Faculty of Sciences 33, Kyushu University, Fukuoka 812-8581, Japan
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8581, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
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Tolkin T, Christiaen L. Development and Evolution of the Ascidian Cardiogenic Mesoderm. Curr Top Dev Biol 2012; 100:107-42. [DOI: 10.1016/b978-0-12-387786-4.00011-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Achilleos A, Wehman AM, Nance J. PAR-3 mediates the initial clustering and apical localization of junction and polarity proteins during C. elegans intestinal epithelial cell polarization. Development 2010; 137:1833-42. [PMID: 20431121 DOI: 10.1242/dev.047647] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The apicobasal polarity of epithelial cells is critical for organ morphogenesis and function, and loss of polarity can promote tumorigenesis. Most epithelial cells form when precursor cells receive a polarization cue, develop distinct apical and basolateral domains and assemble junctions near their apical surface. The scaffolding protein PAR-3 regulates epithelial cell polarity, but its cellular role in the transition from precursor cell to polarized epithelial cell has not been determined in vivo. Here, we use a targeted protein-degradation strategy to remove PAR-3 from C. elegans embryos and examine its cellular role as intestinal precursor cells become polarized epithelial cells. At initial stages of polarization, PAR-3 accumulates in cortical foci that contain E-cadherin, other adherens junction proteins, and the polarity proteins PAR-6 and PKC-3. Using live imaging, we show that PAR-3 foci move apically and cluster, and that PAR-3 is required to assemble E-cadherin into foci and for foci to accumulate at the apical surface. We propose that PAR-3 facilitates polarization by promoting the initial clustering of junction and polarity proteins that then travel and accumulate apically. Unexpectedly, superficial epidermal cells form apical junctions in the absence of PAR-3, and we show that PAR-6 has a PAR-3-independent role in these cells to promote apical junction maturation. These findings indicate that PAR-3 and PAR-6 function sequentially to position and mature apical junctions, and that the requirement for PAR-3 can vary in different types of epithelial cells.
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Affiliation(s)
- Annita Achilleos
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute for Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA
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