1
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Vora M, Dietz J, Wing Z, Liu J, Rongo C, Savage-Dunn C. Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597576. [PMID: 38895257 PMCID: PMC11185707 DOI: 10.1101/2024.06.05.597576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Smads and their transcription factor partners mediate the transcriptional responses of target cells to secreted ligands of the Transforming Growth Factor-β (TGF-β) family, including those of the conserved bone morphogenetic protein (BMP) family, yet only a small number of direct target genes have been well characterized. In C. elegans, the BMP2/4 ortholog DBL-1 regulates multiple biological functions, including body size, via a canonical receptor-Smad signaling cascade. Here, we identify functional binding sites for SMA-3/Smad and its transcriptional partner SMA-9/Schnurri based on ChIP-seq peaks (identified by modEncode) and expression differences of nearby genes identified from RNA-seq analysis of corresponding mutants. We found that SMA-3 and SMA-9 have both overlapping and unique target genes. At a genome-wide scale, SMA-3/Smad acts as a transcriptional activator, whereas SMA-9/Schnurri direct targets include both activated and repressed genes. Mutations in sma-9 partially suppress the small body size phenotype of sma-3, suggesting some level of antagonism between these factors and challenging the prevailing model for Schnurri function. A functional analysis of target genes revealed a novel role in body size for genes involved in one-carbon metabolism and in the endoplasmic reticulum (ER) secretory pathway, including the disulfide reductase dpy-11. Our findings indicate that Smads and SMA-9/Schnurri have previously unappreciated complex genetic and genomic regulatory interactions that in turn regulate the secretion of extracellular components like collagen into the cuticle to mediate body size regulation.
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Affiliation(s)
- Mehul Vora
- Waksman Institute, Dept. of Genetics, Rutgers University, NJ, USA
- ModOmics Ltd, Southampton, UK
| | - Jonathan Dietz
- Waksman Institute, Dept. of Genetics, Rutgers University, NJ, USA
| | - Zachary Wing
- Department of Biology, Queens College, CUNY, NY, USA
| | - Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, NY, USA
| | | | - Cathy Savage-Dunn
- Department of Biology, Queens College, CUNY, NY, USA
- PhD Program in Biology, the Graduate Center, CUNY, NY, USA
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2
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Schön JL, Groß VE, Post WB, Daum A, Matúš D, Pilz J, Schnorr R, Horn S, Bäumers M, Weidtkamp-Peters S, Hughes S, Schöneberg T, Prömel S. The adhesion GPCR and PCP component flamingo (FMI-1) alters body size and regulates the composition of the extracellular matrix. Matrix Biol 2024; 128:1-10. [PMID: 38378098 DOI: 10.1016/j.matbio.2024.02.005] [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: 10/13/2023] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
The extracellular matrix (ECM) is a network of macromolecules that presents a vital scaffold for cells and enables multiple ways of cellular communication. Thus, it is essential for many physiological processes such as development, tissue morphogenesis, homeostasis, the shape and partially the size of the body and its organs. To ensure these, the composition of the ECM is tissue-specific and highly dynamic. ECM homeostasis is therefore tightly controlled by several mechanisms. Here, we show that FMI-1, the homolog of the Adhesion GPCR Flamingo/CELSR/ADGRC in the nematode Caenorhabditis elegans, modulates the composition of the ECM by controlling the production both of ECM molecules such as collagens and also of ECM modifying enzymes. Thereby, FMI-1 affects the morphology and functionality of the nematode´s cuticle, which is mainly composed of ECM, and also modulates the body size. Mechanistic analyses highlight the fact that FMI-1 exerts its function from neurons non-cell autonomously (trans) solely via its extracellular N terminus. Our data support a model, by which the activity of the receptor, which has a well-described role in the planar cell polarity (PCP) pathway, involves the PCP molecule VANG-1, but seems to be independent of the DBL-1/BMP pathway.
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Affiliation(s)
- Johanna Lena Schön
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany; Department of Dermatology, Venereology and Allergology, Leipzig University Medical Center, Leipzig University, Leipzig, Germany
| | - Victoria Elisabeth Groß
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Willem Berend Post
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexandra Daum
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Matúš
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany; Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
| | - Johanna Pilz
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Rene Schnorr
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Miriam Bäumers
- Center for Advanced Imaging, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Samantha Hughes
- A-LIFE, Section Environmental Health and Toxicology, Free University Amsterdam, Amsterdam, the Netherlands
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany; School of Medicine, University of Global Health Equity, Kigali, Rwanda
| | - Simone Prömel
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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3
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Woodruff GC, Willis JH, Johnson E, Phillips PC. Widespread changes in gene expression accompany body size evolution in nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564729. [PMID: 37961435 PMCID: PMC10635002 DOI: 10.1101/2023.10.30.564729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including C. elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologs with divergent dynamics across this developmental period between the two species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with TGF-β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. Widespread transcriptional divergence between these species is unexpected and may be a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group.
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Affiliation(s)
- Gavin C Woodruff
- University of Oregon, Eugene, Oregon, USA
- Current institution: University of Oklahoma, Norman, Oklahoma, USA
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4
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Godoy LF, Hochbaum D. Transcriptional and spatiotemporal regulation of the dauer program. Transcription 2023; 14:27-48. [PMID: 36951297 PMCID: PMC10353326 DOI: 10.1080/21541264.2023.2190295] [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: 10/31/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/24/2023] Open
Abstract
Caenorhabditis elegans can enter a diapause stage called "dauer" when it senses that the environment is not suitable for development. This implies a detour from the typical developmental trajectory and requires a tight control of the developmental clock and a massive tissue remodeling. In the last decades, core components of the signaling pathways that govern the dauer development decision have been identified, but the tissues where they function for the acquisition of dauer-specific traits are still under intense study. Growing evidence demonstrates that these pathways engage in complex cross-talk and feedback loops. In this review, we summarize the current knowledge regarding the transcriptional regulation of the dauer program and the relevant tissues for its achievement. A better understanding of this process will provide insight on how developmental plasticity is achieved and how development decisions are under a robust regulation to ensure an all-or-nothing response. Furthermore, this developmental decision can also serve as a simplified model for relevant developmental disorders.Abbreviations: AID Auxin Induced Degron DA dafachronic acid Daf-c dauer formation constitutive Daf-d dauer formation defective DTC Distal Tip Cells ECM modified extracellular matrix GPCRs G protein-coupled receptors IIS insulin/IGF-1 signaling ILPs insulin-like peptides LBD Ligand Binding Domain PDL4 Post Dauer L4 TGF-β transforming growth factor beta WT wild-type.
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Affiliation(s)
- Luciana F Godoy
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD) Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Daniel Hochbaum
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD) Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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5
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Reich H, Savage-Dunn C. Signaling circuits and the apical extracellular matrix in aging: connections identified in the nematode Caenorhabditis elegans. Am J Physiol Cell Physiol 2023; 325:C1201-C1211. [PMID: 37721005 PMCID: PMC10861026 DOI: 10.1152/ajpcell.00195.2023] [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: 05/09/2023] [Revised: 08/24/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Numerous conserved signaling pathways play critical roles in aging, including insulin/IGF-1, TGF-β, and Wnt pathways. Some of these pathways also play prominent roles in the formation and maintenance of the extracellular matrix. The nematode Caenorhabditis elegans has been an enduringly productive system for the identification of conserved mechanisms of biological aging. Recent studies in C. elegans highlight the regulatory circuits between conserved signaling pathways and the extracellular matrix, revealing a bidirectional relationship between these factors and providing a platform to address how regulation of and by the extracellular matrix can impact lifespan and organismal health during aging. These discoveries provide new opportunities for clinical advances and novel therapeutic strategies.
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Affiliation(s)
- Hannah Reich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
- PhD Program in Biology, The Graduate Center, City University of New York, New York, New York, United States
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6
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Madhu B, Lakdawala MF, Gumienny TL. The DBL-1/TGF-β signaling pathway tailors behavioral and molecular host responses to a variety of bacteria in Caenorhabditis elegans. eLife 2023; 12:e75831. [PMID: 37750680 PMCID: PMC10567113 DOI: 10.7554/elife.75831] [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: 12/07/2021] [Accepted: 09/25/2023] [Indexed: 09/27/2023] Open
Abstract
Generating specific, robust protective responses to different bacteria is vital for animal survival. Here, we address the role of transforming growth factor β (TGF-β) member DBL-1 in regulating signature host defense responses in Caenorhabditis elegans to human opportunistic Gram-negative and Gram-positive pathogens. Canonical DBL-1 signaling is required to suppress avoidance behavior in response to Gram-negative, but not Gram-positive bacteria. We propose that in the absence of DBL-1, animals perceive some bacteria as more harmful. Animals activate DBL-1 pathway activity in response to Gram-negative bacteria and strongly repress it in response to select Gram-positive bacteria, demonstrating bacteria-responsive regulation of DBL-1 signaling. DBL-1 signaling differentially regulates expression of target innate immunity genes depending on the bacterial exposure. These findings highlight a central role for TGF-β in tailoring a suite of bacteria-specific host defenses.
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Affiliation(s)
- Bhoomi Madhu
- Department of Biology, Texas Woman’s UniversityDentonUnited States
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Mohammed Farhan Lakdawala
- Department of Biology, Texas Woman’s UniversityDentonUnited States
- AbbVie (United States)WorcesterUnited States
| | - Tina L Gumienny
- Department of Biology, Texas Woman’s UniversityDentonUnited States
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7
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Yamamoto KK, Savage-Dunn C. TGF-β pathways in aging and immunity: lessons from Caenorhabditis elegans. Front Genet 2023; 14:1220068. [PMID: 37732316 PMCID: PMC10507863 DOI: 10.3389/fgene.2023.1220068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
The Transforming Growth Factor-β (TGF-β) superfamily of signaling molecules plays critical roles in development, differentiation, homeostasis, and disease. Due to the conservation of these ligands and their signaling pathways, genetic studies in invertebrate systems including the nematode Caenorhabditis elegans have been instrumental in identifying signaling mechanisms. C. elegans is also a premier organism for research in longevity and healthy aging. Here we summarize current knowledge on the roles of TGF-β signaling in aging and immunity.
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Affiliation(s)
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, and PhD Program in Biology, The Graduate Center, City University of New York, New York City, NY, United States
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8
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Liu J, Zhang P, Zheng Z, Afridi MI, Zhang S, Wan Z, Zhang X, Stingelin L, Wang Y, Tu H. GABAergic signaling between enteric neurons and intestinal smooth muscle promotes innate immunity and gut defense in Caenorhabditis elegans. Immunity 2023; 56:1515-1532.e9. [PMID: 37437538 DOI: 10.1016/j.immuni.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/06/2023] [Accepted: 06/07/2023] [Indexed: 07/14/2023]
Abstract
The nervous system is critical for intestinal homeostasis and function, but questions remain regarding its impact on gut immune defense. By screening the major neurotransmitters of C. elegans, we found that γ-aminobutyric acid (GABA) deficiency enhanced susceptibility to pathogenic Pseudomonas aeruginosa PA14 infection. GABAergic signaling between enteric neurons and intestinal smooth muscle promoted gut defense in a PMK-1/p38-dependent, but IIS/DAF-16- and DBL-1/TGF-β-independent, pathway. Transcriptomic profiling revealed that the neuropeptide, FLP-6, acted downstream of enteric GABAergic signaling. Further data determined that FLP-6 was expressed and secreted by intestinal smooth muscle cells and functioned as a paracrine molecule on the intestinal epithelium. FLP-6 suppressed the transcription factors ZIP-10 and KLF-1 that worked in parallel and converged to the PMK-1/p38 pathway in the intestinal epithelia for innate immunity and gut defense. Collectively, these findings uncover an enteric neuron-muscle-epithelium axis that may be evolutionarily conserved in higher organisms.
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Affiliation(s)
- Junqiang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Pei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Zhongfan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Muhammad Irfan Afridi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Shan Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Zhiqing Wan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Xiumei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Lukas Stingelin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Yirong Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China
| | - Haijun Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, Hunan, China.
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9
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Goodman MB, Savage-Dunn C. Reciprocal interactions between transforming growth factor beta signaling and collagens: Insights from Caenorhabditis elegans. Dev Dyn 2022; 251:47-60. [PMID: 34537996 PMCID: PMC8982858 DOI: 10.1002/dvdy.423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/03/2023] Open
Abstract
Studies in genetically tractable organisms such as the nematode Caenorhabditis elegans have led to pioneering insights into conserved developmental regulatory mechanisms. For example, Smad signal transducers for the transforming growth factor beta (TGF-β) superfamily were first identified in C. elegans and in the fruit fly Drosophila. Recent studies of TGF-β signaling and the extracellular matrix (ECM) in C. elegans have forged unexpected links between signaling and the ECM, yielding novel insights into the reciprocal interactions that occur across tissues and spatial scales, and potentially providing new opportunities for the study of biomechanical regulation of gene expression.
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Affiliation(s)
- Miriam B. Goodman
- Department of Molecular and Cellular Physiology, Stanford University, CA 94304
| | - Cathy Savage-Dunn
- Department of Biology, Queens College at the City University of New York, 11367,Correspondence to: >
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10
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Zheng Z, Aihemaiti Y, Liu J, Afridi MI, Yang S, Zhang X, Xu Y, Chen C, Tu H. The bZIP Transcription Factor ZIP-11 Is Required for the Innate Immune Regulation in Caenorhabditis elegans. Front Immunol 2021; 12:744454. [PMID: 34804026 PMCID: PMC8602821 DOI: 10.3389/fimmu.2021.744454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
Innate immunity is the first line of host defense against pathogen infection in metazoans. However, the molecular mechanisms of the complex immune regulatory network are not fully understood. Based on a transcriptome profiling of the nematode Caenorhabditis elegans, we found that a bZIP transcription factor ZIP-11 was up-regulated upon Pseudomonas aeruginosa PA14 infection. The tissue specific RNAi knock-down and rescue data revealed that ZIP-11 acts in intestine to promote host resistance against P. aeruginosa PA14 infection. We further showed that intestinal ZIP-11 regulates innate immune response through constituting a feedback loop with the conserved PMK-1/p38 mitogen-activated protein signaling pathway. Intriguingly, ZIP-11 interacts with a CCAAT/enhancer-binding protein, CEBP-2, to mediate the transcriptional response to P. aeruginosa PA14 infection independently of PMK-1/p38 pathway. In addition, human homolog ATF4 can functionally substitute for ZIP-11 in innate immune regulation of C. elegans. Our findings indicate that the ZIP-11/ATF4 genetic program activates local innate immune response through conserved PMK-1/p38 and CEBP-2/C/EBPγ immune signals in C. elegans, raising the possibility that a similar process may occur in other organisms.
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Affiliation(s)
- Zhongfan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Yilixiati Aihemaiti
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Junqiang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Muhammad Irfan Afridi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Shengmei Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Xiumei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Yongfu Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Chunhong Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
| | - Haijun Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
- Shenzhen Research Institute, Hunan University, Shenzhen, China
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11
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Clark JF, Ciccarelli EJ, Kayastha P, Ranepura G, Yamamoto KK, Hasan MS, Madaan U, Meléndez A, Savage-Dunn C. BMP pathway regulation of insulin signaling components promotes lipid storage in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009836. [PMID: 34634043 PMCID: PMC8530300 DOI: 10.1371/journal.pgen.1009836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/21/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022] Open
Abstract
A small number of peptide growth factor ligands are used repeatedly in development and homeostasis to drive programs of cell differentiation and function. Cells and tissues must integrate inputs from these diverse signals correctly, while failure to do so leads to pathology, reduced fitness, or death. Previous work using the nematode C. elegans identified an interaction between the bone morphogenetic protein (BMP) and insulin/IGF-1-like signaling (IIS) pathways in the regulation of lipid homeostasis. The molecular components required for this interaction, however, were not fully understood. Here we report that INS-4, one of 40 insulin-like peptides (ILPs), is regulated by BMP signaling to modulate fat accumulation. Furthermore, we find that the IIS transcription factor DAF-16/FoxO, but not SKN-1/Nrf, acts downstream of BMP signaling in lipid homeostasis. Interestingly, BMP activity alters sensitivity of these two transcription factors to IIS-promoted cytoplasmic retention in opposite ways. Finally, we probe the extent of BMP and IIS interactions by testing additional IIS functions including dauer formation, aging, and autophagy induction. Coupled with our previous work and that of other groups, we conclude that BMP and IIS pathways have at least three modes of interaction: independent, epistatic, and antagonistic. The molecular interactions we identify provide new insight into mechanisms of signaling crosstalk and potential therapeutic targets for IIS-related pathologies such as diabetes and metabolic syndrome.
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Affiliation(s)
- James F. Clark
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York City, New York, United States of America
| | - Emma J. Ciccarelli
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York City, New York, United States of America
| | - Peter Kayastha
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
| | - Gehan Ranepura
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
| | - Katerina K. Yamamoto
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York City, New York, United States of America
| | - Muhammad S. Hasan
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
| | - Uday Madaan
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York City, New York, United States of America
| | - Alicia Meléndez
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York City, New York, United States of America
| | - Cathy Savage-Dunn
- Biology Department, Queens College, City University of New York (CUNY), New York City, New York, United States of America
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York City, New York, United States of America
- * E-mail:
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12
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Mørch MGM, Møller KV, Hesselager MO, Harders RH, Kidmose CL, Buhl T, Fuursted K, Bendixen E, Shen C, Christensen LG, Poulsen CH, Olsen A. The TGF-β ligand DBL-1 is a key player in a multifaceted probiotic protection against MRSA in C. elegans. Sci Rep 2021; 11:10717. [PMID: 34021197 PMCID: PMC8139972 DOI: 10.1038/s41598-021-89831-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/30/2021] [Indexed: 02/04/2023] Open
Abstract
Worldwide the increase in multi-resistant bacteria due to misuse of traditional antibiotics is a growing threat for our health. Finding alternatives to traditional antibiotics is thus timely. Probiotic bacteria have numerous beneficial effects and could offer safer alternatives to traditional antibiotics. Here, we use the nematode Caenorhabditis elegans (C. elegans) to screen a library of different lactobacilli to identify potential probiotic bacteria and characterize their mechanisms of action. We show that pretreatment with the Lactobacillus spp. Lb21 increases lifespan of C. elegans and results in resistance towards pathogenic methicillin-resistant Staphylococcus aureus (MRSA). Using genetic analysis, we find that Lb21-mediated MRSA resistance is dependent on the DBL-1 ligand of the TGF-β signaling pathway in C. elegans. This response is evolutionarily conserved as we find that Lb21 also induces the TGF-β pathway in porcine epithelial cells. We further characterize the host responses in an unbiased proteome analysis and identify 474 proteins regulated in worms fed Lb21 compared to control food. These include fatty acid CoA synthetase ACS-22, aspartic protease ASP-6 and vitellogenin VIT-2 which are important for Lb21-mediated MRSA resistance. Thus, Lb21 exerts its probiotic effect on C. elegans in a multifactorial manner. In summary, our study establishes a mechanistic basis for the antimicrobial potential of lactobacilli.
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Affiliation(s)
- Maria G M Mørch
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katrine V Møller
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Rikke H Harders
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Caroline L Kidmose
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Therese Buhl
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Chong Shen
- Gut Immunology Lab, Health & Biosciences , IFF , Brabrand , Denmark
| | | | | | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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13
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George AK, Behera J, Homme RP, Tyagi N, Tyagi SC, Singh M. Rebuilding Microbiome for Mitigating Traumatic Brain Injury: Importance of Restructuring the Gut-Microbiome-Brain Axis. Mol Neurobiol 2021; 58:3614-3627. [PMID: 33774742 PMCID: PMC8003896 DOI: 10.1007/s12035-021-02357-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/10/2021] [Indexed: 12/20/2022]
Abstract
Traumatic brain injury (TBI) is a damage to the brain from an external force that results in temporary or permanent impairment in brain functions. Unfortunately, not many treatment options are available to TBI patients. Therefore, knowledge of the complex interplay between gut microbiome (GM) and brain health may shed novel insights as it is a rapidly expanding field of research around the world. Recent studies show that GM plays important roles in shaping neurogenerative processes such as blood-brain-barrier (BBB), myelination, neurogenesis, and microglial maturation. In addition, GM is also known to modulate many aspects of neurological behavior and cognition; however, not much is known about the role of GM in brain injuries. Since GM has been shown to improve cellular and molecular functions via mitigating TBI-induced pathologies such as BBB permeability, neuroinflammation, astroglia activation, and mitochondrial dysfunction, herein we discuss how a dysbiotic gut environment, which in fact, contributes to central nervous system (CNS) disorders during brain injury and how to potentially ward off these harmful effects. We further opine that a better understanding of GM-brain (GMB) axis could help assist in designing better treatment and management strategies in future for the patients who are faced with limited options.
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Affiliation(s)
- Akash K George
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA.,Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Jyotirmaya Behera
- Bone Biology Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Rubens P Homme
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA.,Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Neetu Tyagi
- Bone Biology Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Suresh C Tyagi
- Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA. .,Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA.
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14
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Caenorhabditis elegans saposin-like spp-9 is involved in specific innate immune responses. Genes Immun 2020; 21:301-310. [PMID: 32770079 DOI: 10.1038/s41435-020-0108-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 11/08/2022]
Abstract
Animals counter specific environmental challenges with a combination of broad and tailored host responses. One protein family enlisted in the innate immune response includes the saposin-like antimicrobial proteins. We investigated the expression of a Caenorhabditis elegans saposin-like gene, spp-9, in response to different stresses. spp-9 expression was detected in the intestine and six amphid neurons, including AWB and AWC. spp-9 expression is increased in response to starvation stress. In addition, we discovered pathogen-specific regulation of spp-9 that was not clearly demarcated by Gram nature of the bacterial challenge. Multiple molecular innate immune response pathways, including DBL-1/TGF-β-like, insulin-like, and p38/MAPK, regulate expression of spp-9. Our results suggest spp-9 is involved in targeted responses to a variety of abiotic and bacterial challenges that are coordinated by multiple signaling pathways.
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15
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Madaan U, Faure L, Chowdhury A, Ahmed S, Ciccarelli EJ, Gumienny TL, Savage-Dunn C. Feedback regulation of BMP signaling by Caenorhabditis elegans cuticle collagens. Mol Biol Cell 2020; 31:825-832. [PMID: 32049594 PMCID: PMC7185965 DOI: 10.1091/mbc.e19-07-0390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cellular responsiveness to environment, including changes in extracellular matrix (ECM), is critical for normal processes such as development and wound healing, but can go awry, as in oncogenesis and fibrosis. One type of molecular pathway contributing to this responsiveness is the BMP signaling pathway. Owing to their broad and potent functions, BMPs and their pathways are regulated at multiple levels. In Caenorhabditis elegans, the BMP ligand DBL-1 is a regulator of body size. We previously showed that DBL-1/BMP signaling determines body size through transcriptional regulation of cuticle collagen genes. We now identify feedback regulation of DBL-1/BMP through analysis of four DBL-1–regulated collagen genes. Inactivation of any of these genes reduces DBL-1/BMP signaling, measured by a pathway activity reporter. Furthermore, depletion of these collagens reduces GFP::DBL-1 fluorescence and acts unexpectedly at the level of dbl-1 transcription. We conclude that cuticle, a specialized ECM, impinges on DBL-1/BMP expression and signaling. Interestingly, the feedback regulation of DBL-1/BMP signaling by collagens is likely to be contact independent due to physical separation of the cuticle from DBL-1–expressing cells in the ventral nerve cord. Our results provide an entry point into a novel regulatory mechanism for BMP signaling, with broader implications for mechanical regulation of gene expression.
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Affiliation(s)
- Uday Madaan
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367.,PhD Program in Biology, The Graduate Center, City University of New York, NY 10016
| | - Lionel Faure
- Department of Biology, Texas Woman's University, Denton, TX 76204
| | - Albar Chowdhury
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367
| | - Shahrear Ahmed
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367
| | - Emma J Ciccarelli
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367.,PhD Program in Biology, The Graduate Center, City University of New York, NY 10016
| | - Tina L Gumienny
- Department of Biology, Texas Woman's University, Denton, TX 76204
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367.,PhD Program in Biology, The Graduate Center, City University of New York, NY 10016
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16
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Abstract
The microscopic nematode Caenorhabditis elegans has emerged as a powerful system to characterize evolutionarily ancient mechanisms of pathogen sensing, innate immune activation, and protective host responses. Experimentally, C. elegans can be infected with a wide variety of human pathogens, as well as with natural pathogens of worms that were isolated from wild-caught nematodes. Here, we focus on an experimental model of bacterial pathogenesis that utilizes the human opportunistic bacterial pathogen Pseudomonas aeruginosa and present an algorithm that can be used to study mechanisms of immune function in nematodes. An initial comparison of the susceptibility of a C. elegans mutant to P. aeruginosa infection with its normal lifespan permits an understanding of a mutant's effect on pathogen susceptibility in the context of potential pleotropic consequences on general worm fitness. Assessing the behavior of nematodes in the presence of P. aeruginosa can also help determine if a gene of interest modulates pathogen susceptibility by affecting the host's ability to avoid a pathogen. In addition, quantification of the pathogen load in the C. elegans intestine during infection, characterization of immune effector transcription that are regulated by host defense pathways and an initial assessment of tissue specificity of immune gene function can refine hypotheses about the mechanism of action of a gene of interest. Together, these protocols offer one approach to characterize novel host defense mechanisms in a simple metazoan host.
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Affiliation(s)
- Kyle J Foster
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Deborah L McEwan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Read Pukkila-Worley
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA.
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17
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Lakdawala MF, Madhu B, Faure L, Vora M, Padgett RW, Gumienny TL. Genetic interactions between the DBL-1/BMP-like pathway and dpy body size-associated genes in Caenorhabditis elegans. Mol Biol Cell 2019; 30:3151-3160. [PMID: 31693440 PMCID: PMC6938244 DOI: 10.1091/mbc.e19-09-0500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/22/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022] Open
Abstract
Bone morphogenetic protein (BMP) signaling pathways control many developmental and homeostatic processes, including cell size and extracellular matrix remodeling. An understanding of how this pathway itself is controlled remains incomplete. To identify novel regulators of BMP signaling, we performed a forward genetic screen in Caenorhabditis elegans for genes involved in body size regulation, a trait under the control of BMP member DBL-1. We isolated mutations that suppress the long phenotype of lon-2, a gene that encodes a negative regulator that sequesters DBL-1. This screen was effective because we isolated alleles of several core components of the DBL-1 pathway, demonstrating the efficacy of the screen. We found additional alleles of previously identified but uncloned body size genes. Our screen also identified widespread involvement of extracellular matrix proteins in DBL-1 regulation of body size. We characterized interactions between the DBL-1 pathway and extracellular matrix and other genes that affect body morphology. We discovered that loss of some of these genes affects the DBL-1 pathway, and we provide evidence that DBL-1 signaling affects many molecular and cellular processes associated with body size. We propose a model in which multiple body size factors are controlled by signaling through the DBL-1 pathway and by DBL-1-independent processes.
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Affiliation(s)
| | - Bhoomi Madhu
- Department of Biology, Texas Woman’s University, Denton, TX 76204-5799
| | - Lionel Faure
- Department of Biology, Texas Woman’s University, Denton, TX 76204-5799
| | - Mehul Vora
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020
| | - Richard W. Padgett
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020
- Waksman Institute of Microbiology Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854-8020
- Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ 08854-8020
| | - Tina L. Gumienny
- Department of Biology, Texas Woman’s University, Denton, TX 76204-5799
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18
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BMP Signaling Determines Body Size via Transcriptional Regulation of Collagen Genes in Caenorhabditis elegans. Genetics 2018; 210:1355-1367. [PMID: 30274988 DOI: 10.1534/genetics.118.301631] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/25/2018] [Indexed: 01/10/2023] Open
Abstract
Body size is a tightly regulated phenotype in metazoans that depends on both intrinsic and extrinsic factors. While signaling pathways are known to control organ and body size, the downstream effectors that mediate their effects remain poorly understood. In the nematode Caenorhabditis elegans, a Bone Morphogenetic Protein (BMP)-related signaling pathway is the major regulator of growth and body size. We investigated the transcriptional network through which the BMP pathway regulates body size and identified cuticle collagen genes as major effectors of growth control. We demonstrate that cuticle collagens can act as positive regulators (col-41), negative regulators (col-141), or dose-sensitive regulators (rol-6) of body size. Moreover, we find a requirement of BMP signaling for stage-specific expression of cuticle collagen genes. We show that the Smad signal transducers directly bind conserved Smad-binding elements in regulatory regions of col-141 and col-142, but not of col-41 Hence, cuticle collagen genes may be directly and indirectly regulated via the BMP pathway. Our work thus connects a conserved signaling pathway with its critical downstream effectors, advancing insight into how body size is specified. Since collagen mutations and misregulation are implicated in numerous human genetic disorders and injury sequelae, understanding how collagen gene expression is regulated has broad implications.
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19
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Clark JF, Meade M, Ranepura G, Hall DH, Savage-Dunn C. Caenorhabditis elegans DBL-1/BMP Regulates Lipid Accumulation via Interaction with Insulin Signaling. G3 (BETHESDA, MD.) 2018; 8:343-351. [PMID: 29162682 PMCID: PMC5765361 DOI: 10.1534/g3.117.300416] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/18/2017] [Indexed: 11/23/2022]
Abstract
Metabolic homeostasis is coordinately controlled by diverse inputs. Understanding these regulatory networks is vital to combating metabolic disorders. The nematode Caenorhabditis elegans has emerged as a powerful, genetically tractable model system for the discovery of lipid regulatory mechanisms. Here we introduce DBL-1, the C. elegans homolog of bone morphogenetic protein 2/4 (BMP2/4), as a significant regulator of lipid homeostasis. We used neutral lipid staining and a lipid droplet marker to demonstrate that both increases and decreases in DBL-1/BMP signaling result in reduced lipid stores and lipid droplet count. We find that lipid droplet size, however, correlates positively with the level of DBL-1/BMP signaling. Regulation of lipid accumulation in the intestine occurs through non-cell-autonomous signaling, since expression of SMA-3, a Smad signal transducer, in the epidermis (hypodermis) is sufficient to rescue the loss of lipid accumulation. Finally, genetic evidence indicates that DBL-1/BMP functions upstream of Insulin/IGF-1 Signaling in lipid metabolism. We conclude that BMP signaling regulates lipid metabolism in C. elegans through interorgan signaling to the Insulin pathway, shedding light on a less well-studied regulatory mechanism for metabolic homeostasis.
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Affiliation(s)
- James F Clark
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York, New York 10016
- Biology Department, Queens College, CUNY, Flushing, New York 11367
| | - Michael Meade
- Biology Department, Queens College, CUNY, Flushing, New York 11367
| | - Gehan Ranepura
- Biology Department, Queens College, CUNY, Flushing, New York 11367
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, New York, New York 10461
| | - Cathy Savage-Dunn
- Ph.D. Program in Biology, The Graduate Center, City University of New York (CUNY), New York, New York 10016
- Biology Department, Queens College, CUNY, Flushing, New York 11367
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20
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Shen Q, Toulabi LB, Shi H, Nicklow EE, Liu J. The forkhead transcription factor UNC-130/FOXD integrates both BMP and Notch signaling to regulate dorsoventral patterning of the C. elegans postembryonic mesoderm. Dev Biol 2018; 433:75-83. [PMID: 29155044 PMCID: PMC5722696 DOI: 10.1016/j.ydbio.2017.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 11/17/2022]
Abstract
The proper development of a multicellular organism requires precise spatial and temporal coordination of cell intrinsic and cell extrinsic regulatory mechanisms. Both Notch signaling and bone morphogenetic protein (BMP) signaling function to regulate the proper development of the C. elegans postembryonic mesoderm. We have identified the C. elegans FOXD transcription factor UNC-130 as a major target functioning downstream of both BMP signaling and Notch signaling to regulate dorsoventral patterning of the postembryonic mesoderm. We showed that unc-130 expression in the postembryonic M lineage is asymmetric: its absence of expression in the dorsal side of the M lineage requires the antagonism of BMP signaling by the zinc finger transcription factor SMA-9, while its expression in the ventral side of the M lineage is activated by LIN-12/Notch signaling. We further showed that the regulation of UNC-130 expression by BMP signaling and Notch signaling is specific to the M lineage, as the ventral expression of UNC-130 in the embryonically-derived bodywall muscles was not affected in either BMP pathway or Notch pathway mutants. Finally, we showed that the function of UNC-130 in the M lineage is independent of UNC-129, a gene previously shown to function downstream of and be repressed by UNC-130 for axon guidance. Our studies uncovered a new function of UNC-130/FOXD in the C. elegans postembryonic mesoderm, and identify UNC-130 as a critical factor that integrates two independent spatial cues for the proper patterning and fate specification of the C. elegans postembryonic mesoderm.
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Affiliation(s)
- Qinfang Shen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Leila B Toulabi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Herong Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Erin E Nicklow
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States.
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21
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Kato M, Kashem MA, Cheng C. An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans. Aging (Albany NY) 2017; 8:1979-2005. [PMID: 27623524 PMCID: PMC5076448 DOI: 10.18632/aging.101029] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/19/2016] [Indexed: 12/22/2022]
Abstract
Adaptation to an environmental or metabolic perturbation is a feature of the evolutionary process. Recent insights into microRNA function suggest that microRNAs serve as key players in a robust adaptive response against stress in animals through their capacity to fine-tune gene expression. However, it remains largely unclear how a microRNA-modulated downstream mechanism contributes to the process of homeostatic adaptation. Here we show that loss of an intestinally expressed microRNA gene, mir-60, in the nematode C. elegans promotes an adaptive response to chronic - a mild and long-term - oxidative stress exposure. The pathway involved appears to be unique since the canonical stress-responsive factors, such as DAF-16/FOXO, are dispensable for mir-60 loss to enhance oxidative stress resistance. Gene expression profiles revealed that genes encoding lysosomal proteases and those involved in xenobiotic metabolism and pathogen defense responses are up-regulated by the loss of mir-60. Detailed genetic studies and computational microRNA target prediction suggest that endocytosis components and a bZip transcription factor gene zip-10, which functions in innate immune response, are directly modulated by miR-60 in the intestine. Our findings suggest that the mir-60 loss facilitates adaptive response against chronic oxidative stress by ensuring the maintenance of cellular homeostasis.
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Affiliation(s)
- Masaomi Kato
- The Laboratory of Ageing, Centenary Institute, Camperdown, NSW 2050, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Mohammed Abul Kashem
- The Laboratory of Ageing, Centenary Institute, Camperdown, NSW 2050, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Chao Cheng
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
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22
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Inter-organ signalling by HRG-7 promotes systemic haem homeostasis. Nat Cell Biol 2017; 19:799-807. [PMID: 28581477 PMCID: PMC5594749 DOI: 10.1038/ncb3539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 04/27/2017] [Indexed: 12/17/2022]
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23
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Abstract
Transforming growth factor β (TGF-β) and related ligands have potent effects on an enormous diversity of biological functions in all animals examined. Because of the strong conservation of TGF-β family ligand functions and signaling mechanisms, studies from multiple animal systems have yielded complementary and synergistic insights. In the nematode Caenorhabditis elegans, early studies were instrumental in the elucidation of TGF-β family signaling mechanisms. Current studies in C. elegans continue to identify new functions for the TGF-β family in this organism as well as new conserved mechanisms of regulation.
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Affiliation(s)
- Cathy Savage-Dunn
- Department of Biology, Queens College, and the Graduate Center, New York, New York 11367
| | - Richard W Padgett
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08854-8020
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24
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Microsporidia Intracellular Development Relies on Myc Interaction Network Transcription Factors in the Host. G3-GENES GENOMES GENETICS 2016; 6:2707-16. [PMID: 27402359 PMCID: PMC5015929 DOI: 10.1534/g3.116.029983] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microsporidia are ubiquitous parasites that infect a wide range of animal hosts, and these fungal-related microbes undergo their entire replicative lifecycle inside of host cells. Despite being widespread in the environment and causing medical and agricultural harm, virtually nothing is known about the host factors important to facilitate their growth and development inside of host cells. Here, we perform a genetic screen to identify host transcription factors important for development of the microsporidian pathogen Nematocida parisii inside intestinal cells of its natural host, the nematode Caenorhabditis elegans. Through this screen, we identified the C. elegans Myc family of transcription factors as key host regulators of microsporidia growth and development. The Mad-like transcription factor MDL-1, and the Max-like transcription factors MXL-1 and MXL-2 promote pathogen levels, while the Myc-Mondo-like transcription factor MML-1 inhibits pathogen levels. We used epistasis analysis to show that MDL-1 and MXL-1, which are thought to function as a heterodimer, appear to be acting canonically. In contrast, MXL-2 and MML-1, which are also thought to function as a heterodimer, appear to be acting in separate pathways (noncanonically) in the context of pathogen infection. We also found that both MDL-1::GFP and MML-1::GFP are expressed in intestinal cells during infection. These findings provide novel insight into the host transcription factors that regulate microsporidia development.
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25
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Fluid dynamics alter Caenorhabditis elegans body length via TGF-β/DBL-1 neuromuscular signaling. NPJ Microgravity 2016; 2:16006. [PMID: 28725724 PMCID: PMC5515535 DOI: 10.1038/npjmgrav.2016.6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 12/14/2015] [Accepted: 01/10/2016] [Indexed: 01/12/2023] Open
Abstract
Skeletal muscle wasting is a major obstacle for long-term space exploration. Similar to astronauts, the nematode Caenorhabditis elegans displays negative muscular and physical effects when in microgravity in space. It remains unclear what signaling molecules and behavior(s) cause these negative alterations. Here we studied key signaling molecules involved in alterations of C. elegans physique in response to fluid dynamics in ground-based experiments. Placing worms in space on a 1G accelerator increased a myosin heavy chain, myo-3, and a transforming growth factor-β (TGF-β), dbl-1, gene expression. These changes also occurred when the fluid dynamic parameters viscosity/drag resistance or depth of liquid culture were increased on the ground. In addition, body length increased in wild type and body wall cuticle collagen mutants, rol-6 and dpy-5, grown in liquid culture. In contrast, body length did not increase in TGF-β, dbl-1, or downstream signaling pathway, sma-4/Smad, mutants. Similarly, a D1-like dopamine receptor, DOP-4, and a mechanosensory channel, UNC-8, were required for increased dbl-1 expression and altered physique in liquid culture. As C. elegans contraction rates are much higher when swimming in liquid than when crawling on an agar surface, we also examined the relationship between body length enhancement and rate of contraction. Mutants with significantly reduced contraction rates were typically smaller. However, in dop-4, dbl-1, and sma-4 mutants, contraction rates still increased in liquid. These results suggest that neuromuscular signaling via TGF-β/DBL-1 acts to alter body physique in response to environmental conditions including fluid dynamics.
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26
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Characterization of innate immunity genes in the parasitic nematode Brugia malayi. Symbiosis 2016; 68:145-155. [PMID: 27110057 PMCID: PMC4826884 DOI: 10.1007/s13199-015-0374-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/24/2015] [Indexed: 01/11/2023]
Abstract
The filarial nematode Brugia malayi is one of the causative agents of lymphatic filariasis, a neglected tropical disease that affects 120 million people worldwide. The limited effectiveness of available anthelmintics and the absence of a vaccine have prompted extensive research on the interaction between Brugia and its obligate bacterial endosymbiont, Wolbachia. Recent studies suggest that Wolbachia is able to manipulate its nematode host immunity but relatively little is known about the immune system of filarial nematodes. Therefore, elucidation of the mechanisms underlying the immune system of B. malayi may be useful for understanding how the symbiotic relationship is maintained and help in the identification of new drug targets. In order to characterize the main genetic pathways involved in B. malayi immunity, we exposed adult female worms to two bacterial lysates (Escherichia coli and Bacillus amyloliquefaciens), dsRNA and dsDNA. We performed transcriptome sequencing of worms exposed to each immune elicitor at two different timepoints. Gene expression analysis of untreated and immune-challenged worms was performed to characterize gene expression patterns associated with each type of immune stimulation. Our results indicate that different immune elicitors produced distinct expression patterns in B. malayi, with changes in the expression of orthologs of well-characterized C. elegans immune pathways such as insulin, TGF-β, and p38 MAPK pathways, as well as C-type lectins and several stress-response genes.
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Kaplan REW, Chen Y, Moore BT, Jordan JM, Maxwell CS, Schindler AJ, Baugh LR. dbl-1/TGF-β and daf-12/NHR Signaling Mediate Cell-Nonautonomous Effects of daf-16/FOXO on Starvation-Induced Developmental Arrest. PLoS Genet 2015; 11:e1005731. [PMID: 26656736 PMCID: PMC4676721 DOI: 10.1371/journal.pgen.1005731] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/18/2015] [Indexed: 11/23/2022] Open
Abstract
Nutrient availability has profound influence on development. In the nematode C. elegans, nutrient availability governs post-embryonic development. L1-stage larvae remain in a state of developmental arrest after hatching until they feed. This “L1 arrest” (or "L1 diapause") is associated with increased stress resistance, supporting starvation survival. Loss of the transcription factor daf-16/FOXO, an effector of insulin/IGF signaling, results in arrest-defective and starvation-sensitive phenotypes. We show that daf-16/FOXO regulates L1 arrest cell-nonautonomously, suggesting that insulin/IGF signaling regulates at least one additional signaling pathway. We used mRNA-seq to identify candidate signaling molecules affected by daf-16/FOXO during L1 arrest. dbl-1/TGF-β, a ligand for the Sma/Mab pathway, daf-12/NHR and daf-36/oxygenase, an upstream component of the daf-12 steroid hormone signaling pathway, were up-regulated during L1 arrest in a daf-16/FOXO mutant. Using genetic epistasis analysis, we show that dbl-1/TGF-β and daf-12/NHR steroid hormone signaling pathways are required for the daf-16/FOXO arrest-defective phenotype, suggesting that daf-16/FOXO represses dbl-1/TGF-β, daf-12/NHR and daf-36/oxygenase. The dbl-1/TGF-β and daf-12/NHR pathways have not previously been shown to affect L1 development, but we found that disruption of these pathways delayed L1 development in fed larvae, consistent with these pathways promoting development in starved daf-16/FOXO mutants. Though the dbl-1/TGF-β and daf-12/NHR pathways are epistatic to daf-16/FOXO for the arrest-defective phenotype, disruption of these pathways does not suppress starvation sensitivity of daf-16/FOXO mutants. This observation uncouples starvation survival from developmental arrest, indicating that DAF-16/FOXO targets distinct effectors for each phenotype and revealing that inappropriate development during starvation does not cause the early demise of daf-16/FOXO mutants. Overall, this study shows that daf-16/FOXO promotes developmental arrest cell-nonautonomously by repressing pathways that promote larval development. Animals must cope with feast and famine in the wild. Environmental fluctuations require a balancing act between development in favorable conditions and survival during starvation. Disruption of the pathways that govern this balance can lead to cancer, where cells proliferate when they should not, and metabolic diseases, where nutrient sensing is impaired. In the roundworm Caenorhabditis elegans, larval development is controlled by nutrient availability. Larvae are able to survive starvation by stopping development and starting again after feeding. Stopping and starting development in this multicellular animal requires signaling to coordinate development across tissues and organs. How such coordination is accomplished is poorly understood. Insulin/insulin-like growth factor (IGF) signaling governs larval development in response to nutrient availability. Here we show that insulin/IGF signaling activity in one tissue can affect the development of other tissues, suggesting regulation of additional signaling pathways. We identified two pathways that promote development in fed larvae and are repressed by lack of insulin/IGF signaling in starved larvae. Repression of these pathways is crucial to stopping development throughout the animal during starvation. These three pathways are widely conserved and associated with disease, suggesting the nutrient-dependent regulatory network they comprise is important to human health.
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Affiliation(s)
- Rebecca E. W. Kaplan
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Yutao Chen
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Brad T. Moore
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - James M. Jordan
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Colin S. Maxwell
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Adam J. Schindler
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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Yin J, Madaan U, Park A, Aftab N, Savage-Dunn C. Multiple cis elements and GATA factors regulate a cuticle collagen gene in Caenorhabditis elegans. Genesis 2015; 53:278-84. [PMID: 25711168 DOI: 10.1002/dvg.22847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 01/05/2023]
Abstract
The cuticle of the nematode Caenorhabditis elegans is a specialized extracellular matrix whose major component is collagen. Cuticle collagens are encoded by a large multigene family consisting of more than 150 members. Cuticle collagen genes are expressed in epidermis (hypodermis) and may be stage-specific or cyclically expressed. We identified cuticle collagen genes as transcriptional targets of the DBL-1 TGF-β-related signaling pathway. These studies prompted us to investigate the cis-regulatory sequences required for transcription of one of the target genes, col-41. We generated reporter constructs that reproduce stage- and tissue-specific expression of fluorescent markers. We identify four conserved sequence elements that are required for transcription of reporters. Finally, we provide evidence that col-41 expression is controlled by a sequence element containing two GATA sites and by the epidermal GATA transcription factors ELT-1 and ELT-3.
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Affiliation(s)
- Jianghua Yin
- Department of Biology, Queens College, CUNY, Flushing, New York; The Graduate Center, CUNY, New York, New York
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Schultz RD, Bennett EE, Ellis EA, Gumienny TL. Regulation of extracellular matrix organization by BMP signaling in Caenorhabditis elegans. PLoS One 2014; 9:e101929. [PMID: 25013968 PMCID: PMC4094471 DOI: 10.1371/journal.pone.0101929] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/13/2014] [Indexed: 12/22/2022] Open
Abstract
In mammals, Bone Morphogenetic Protein (BMP) pathway signaling is important for the growth and homeostasis of extracellular matrix, including basement membrane remodeling, scarring, and bone growth. A conserved BMP member in Caenorhabditis elegans, DBL-1, regulates body length in a dose-sensitive manner. Loss of DBL-1 pathway signaling also results in increased anesthetic sensitivity. However, the physiological basis of these pleiotropic phenotypes is largely unknown. We created a DBL-1 over-expressing strain and show that sensitivity to anesthetics is inversely related to the dose of DBL-1. Using pharmacological, genetic analyses, and a novel dye permeability assay for live, microwave-treated animals, we confirm that DBL-1 is required for the barrier function of the cuticle, a specialized extracellular matrix. We show that DBL-1 signaling is required to prevent animals from forming tail-entangled aggregates in liquid. Stripping lipids off the surface of wild-type animals recapitulates this phenotype. Finally, we find that DBL-1 signaling affects ultrastructure of the nematode cuticle in a dose-dependent manner, as surface lipid content and cuticular organization are disrupted in animals with genetically altered DBL-1 levels. We propose that the lipid layer coating the nematode cuticle normally prevents tail entanglement, and that reduction of this layer by loss of DBL-1 signaling promotes aggregation. This work provides a physiological mechanism that unites the DBL-1 signaling pathway roles of not only body size regulation and drug responsiveness, but also the novel Hoechst 33342 staining and aggregation phenotypes, through barrier function, content, and organization of the cuticle.
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Affiliation(s)
- Robbie D. Schultz
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, Texas, United States of America
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
| | - Emily E. Bennett
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, Texas, United States of America
| | - E. Ann Ellis
- Microscopy & Imaging Center, Texas A&M University, College Station, Texas, United States of America
| | - Tina L. Gumienny
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, Texas, United States of America
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
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Julien-Gau I, Schmidt M, Kurz CL. f57f4.4p::gfp as a fluorescent reporter for analysis of the C. elegans response to bacterial infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 42:132-137. [PMID: 24012871 DOI: 10.1016/j.dci.2013.08.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Host defense mechanisms are multi-layered and involve constitutive as well as inducible components. The dissection of these complex processes can be greatly facilitated using a reporter gene strategy with a transparent animal. In this study, we use Caenorhabditis elegans as a model host and introduce a new pathogen-inducible fluorescent reporter involving the promoter of f57f4.4, a gene encoding a putative component of the glycocalyx. We show that this reporter construct does not respond to heavy metal or hypertonic environments, but is specifically and locally induced in the intestine upon Photorhabus luminescens and Pseudomonas aeruginosa infections. We further demonstrate that its upregulation requires live pathogens as well as elements of the nematode p38 MAP kinase and TGF-beta pathways. In addition to introducing a new tool for the study of the interactions between C. elegans and a pathogen, our results suggest a role for the glycocalyx in gut immunity.
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Affiliation(s)
- Ingrid Julien-Gau
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, UM2, Case 906, 13288 Marseille Cedex 9, France; INSERM, U1104, 13288 Marseille, France; CNRS, UMR7280, 13288 Marseille, France
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Diepeveen ET, Roth O, Salzburger W. Immune-related functions of the Hivep gene family in East African cichlid fishes. G3 (BETHESDA, MD.) 2013; 3:2205-17. [PMID: 24142922 PMCID: PMC3852383 DOI: 10.1534/g3.113.008839] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/07/2013] [Indexed: 01/20/2023]
Abstract
Immune-related genes are often characterized by adaptive protein evolution. Selection on immune genes can be particularly strong when hosts encounter novel parasites, for instance, after the colonization of a new habitat or upon the exploitation of vacant ecological niches in an adaptive radiation. We examined a set of new candidate immune genes in East African cichlid fishes. More specifically, we studied the signatures of selection in five paralogs of the human immunodeficiency virus type I enhancer-binding protein (Hivep) gene family, tested their involvement in the immune defense, and related our results to explosive speciation and adaptive radiation events in cichlids. We found signatures of long-term positive selection in four Hivep paralogs and lineage-specific positive selection in Hivep3b in two radiating cichlid lineages. Exposure of the cichlid Astatotilapia burtoni to a vaccination with Vibrio anguillarum bacteria resulted in a positive correlation between immune response parameters and expression levels of three Hivep loci. This work provides the first evidence for a role of Hivep paralogs in teleost immune defense and links the signatures of positive selection to host-pathogen interactions within an adaptive radiation.
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Affiliation(s)
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes, Helmholtz Centre of Ocean Research Kiel (GEOMAR), D-24105 Kiel, Germany
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Abstract
Transforming Growth Factor-β (TGF-β) superfamily ligands regulate many aspects of cell identity, function, and survival in multicellular animals. Genes encoding five TGF-β family members are present in the genome of C. elegans. Two of the ligands, DBL-1 and DAF-7, signal through a canonical receptor-Smad signaling pathway; while a third ligand, UNC-129, interacts with a noncanonical signaling pathway. No function has yet been associated with the remaining two ligands. Here we summarize these signaling pathways and their biological functions.
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Affiliation(s)
- Tina L Gumienny
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, TX 77843, USA
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Luo S, Murphy CT. Caenorhabditis elegans reproductive aging: Regulation and underlying mechanisms. Genesis 2011; 49:53-65. [PMID: 21105070 DOI: 10.1002/dvg.20694] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/16/2010] [Accepted: 11/17/2010] [Indexed: 01/04/2023]
Abstract
Female reproductive decline is one of the first aging phenotypes in humans, manifested in increasing rates of infertility, miscarriage, and birth defects in children of mothers over 35. Recently, Caenorhabditis elegans (C. elegans) has been developed as a model to study reproductive aging, and several studies have advanced our knowledge of reproductive aging regulation in this organism. In this review, we describe our current understanding of reproductive cessation in C. elegans, including the relationship between oocyte quality, ovulation rate, progeny number, and reproductive span. We then discuss possible mechanisms of oocyte quality control, and provide an overview of the signaling pathways currently identified to be involved in reproductive span regulation in C. elegans. Finally, we extend the relevance of C. elegans reproductive aging studies to the issue of human female reproductive decline, and we discuss ideas concerning the relationship between reproductive aging and somatic longevity.
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Affiliation(s)
- Shijing Luo
- Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jeresy, USA.
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Luo S, Kleemann GA, Ashraf JM, Shaw WM, Murphy CT. TGF-β and insulin signaling regulate reproductive aging via oocyte and germline quality maintenance. Cell 2010; 143:299-312. [PMID: 20946987 PMCID: PMC2955983 DOI: 10.1016/j.cell.2010.09.013] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 05/17/2010] [Accepted: 08/10/2010] [Indexed: 12/27/2022]
Abstract
Reproductive cessation is perhaps the earliest aging phenotype that humans experience. Similarly, reproduction of Caenorhabditis elegans ceases in mid-adulthood. Although somatic aging has been studied in both worms and humans, mechanisms regulating reproductive aging are not yet understood. Here, we show that TGF-β Sma/Mab and Insulin/IGF-1 signaling regulate C. elegans reproductive aging by modulating multiple aspects of the reproductive process, including embryo integrity, oocyte fertilizability, chromosome segregation fidelity, DNA damage resistance, and oocyte and germline morphology. TGF-β activity regulates reproductive span and germline/oocyte quality noncell-autonomously and is temporally and transcriptionally separable from its regulation of growth. Chromosome segregation, cell cycle, and DNA damage response genes are upregulated in TGF-β mutant oocytes, decline in aged mammalian oocytes, and are critical for oocyte quality maintenance. Our data suggest that C. elegans and humans share many aspects of reproductive aging, including the correlation between reproductive aging and declining oocyte quality and mechanisms determining oocyte quality.
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Affiliation(s)
- Shijing Luo
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Husi H, McAllister F, Angelopoulos N, Butler VJ, Bailey KR, Malone K, MacKay L, Taylor P, Page AP, Turner NJ, Barran PE, Walkinshaw M. Selective Chemical Intervention in the Proteome of Caenorhabditis elegans. J Proteome Res 2010; 9:6060-70. [DOI: 10.1021/pr100427c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Holger Husi
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Fiona McAllister
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nicos Angelopoulos
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Victoria J. Butler
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Kevin R. Bailey
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Kirk Malone
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Logan MacKay
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Paul Taylor
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Antony P. Page
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nicholas J. Turner
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Perdita E. Barran
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Malcolm Walkinshaw
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom, Faculty of Veterinary Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom, and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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Viñuela A, Snoek LB, Riksen JAG, Kammenga JE. Genome-wide gene expression analysis in response to organophosphorus pesticide chlorpyrifos and diazinon in C. elegans. PLoS One 2010; 5:e12145. [PMID: 20808445 PMCID: PMC2922338 DOI: 10.1371/journal.pone.0012145] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 07/08/2010] [Indexed: 11/18/2022] Open
Abstract
Organophosphorus pesticides (OPs) were originally designed to affect the nervous system by inhibiting the enzyme acetylcholinesterase, an important regulator of the neurotransmitter acetylcholine. Over the past years evidence is mounting that these compounds affect many other processes. Little is known, however, about gene expression responses against OPs in the nematode Caenorhabditis elegans. This is surprising because C. elegans is extensively used as a model species in toxicity studies. To address this question we performed a microarray study in C. elegans which was exposed for 72 hrs to two widely used Ops, chlorpyrifos and diazinon, and a low dose mixture of these two compounds. Our analysis revealed transcriptional responses related to detoxification, stress, innate immunity, and transport and metabolism of lipids in all treatments. We found that for both compounds as well as in the mixture, these processes were regulated by different gene transcripts. Our results illustrate intense, and unexpected crosstalk between gene pathways in response to chlorpyrifos and diazinon in C. elegans.
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Affiliation(s)
- Ana Viñuela
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - L. Basten Snoek
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
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Yin J, Yu L, Savage-Dunn C. Alternative trans-splicing of Caenorhabditis elegans sma-9/schnurri generates a short transcript that provides tissue-specific function in BMP signaling. BMC Mol Biol 2010; 11:46. [PMID: 20565799 PMCID: PMC2904332 DOI: 10.1186/1471-2199-11-46] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 06/17/2010] [Indexed: 11/25/2022] Open
Abstract
Background Transcription cofactors related to Drosophila Schnurri facilitate the transcriptional programs regulated by BMP signaling in C. elegans, Drosophila, Xenopus, and mouse. In different systems, Schnurri homologs have been shown to act as either agonists or antagonists of Smad function, and as either positive or negative regulators of transcription. How Schnurri proteins achieve this diversity of activities is not clear. The C. elegans sma-9/schnurri locus undergoes alternative splicing, including an unusual trans-splicing event that could generate two non-overlapping shorter transcripts. Results We demonstrate here that the shorter transcripts are expressed in vivo. Furthermore, we find that one of the short transcripts plays a tissue-specific role in sma-9 function, contributing to the patterning of male-specific sensory rays, but not to the regulation of body size. Based on previous results, we suggest that this transcript encodes a C-terminal SMA-9 isoform that may provide transcriptional activation activity, while full length isoforms may mediate transcriptional repression and/or activation in a context-dependent manner. Conclusion The alternative trans-splicing of sma-9 may contribute to the diversity of functions necessary to mediate tissue-specific outputs of BMP signaling.
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Affiliation(s)
- Jianghua Yin
- Department of Biology, Queens College, and Biochemistry PhD Program, Graduate School and University Center, City University of New York, Flushing, NY 11367, USA
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Roberts AF, Gumienny TL, Gleason RJ, Wang H, Padgett RW. Regulation of genes affecting body size and innate immunity by the DBL-1/BMP-like pathway in Caenorhabditis elegans. BMC DEVELOPMENTAL BIOLOGY 2010; 10:61. [PMID: 20529267 PMCID: PMC2894779 DOI: 10.1186/1471-213x-10-61] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 06/07/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Bone morphogenetic proteins (BMPs) are members of the conserved transforming growth factor beta (TGFbeta superfamily, and play many developmental and homeostatic roles. In C. elegans, a BMP-like pathway, the DBL-1 pathway, controls body size and is involved in innate immunity. How these functions are carried out, though, and what most of the downstream targets of this pathway are, remain unknown. RESULTS We performed a microarray analysis and compared expression profiles of animals lacking the SMA-6 DBL-1 receptor, which decreases pathway signaling, with animals that overexpress DBL-1 ligand, which increases pathway signaling. Consistent with a role for DBL-1 in control of body size, we find positive regulation by DBL-1 of genes involved in physical structure, protein synthesis and degradation, and metabolism. However, cell cycle genes were mostly absent from our results. We also identified genes in a hedgehog-related pathway, which may comprise a secondary signaling pathway downstream of DBL-1 that controls body size. In addition, DBL-1 signaling up-regulates pro-innate immunity genes. We identified a reporter for DBL-1 signaling, which is normally repressed but is up-regulated when DBL-1 signaling is reduced. CONCLUSIONS Our results indicate that body size in C. elegans is controlled in part by regulation of metabolic processes as well as protein synthesis and degradation. This supports the growing body of evidence that suggests cell size is linked to metabolism. Furthermore, this study discovered a possible role for hedgehog-related pathways in transmitting the BMP-like signal from the hypodermis, where the core DBL-1 pathway components are required, to other tissues in the animal. We also identified the up-regulation of genes involved in innate immunity, clarifying the role of DBL-1 in innate immunity. One of the highly regulated genes is expressed at very low levels in wild-type animals, but is strongly up-regulated in Sma/Mab mutants, making it a useful reporter for DBL-1/BMP-like signaling in C. elegans.
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Affiliation(s)
- Andrew F Roberts
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ 08854-8020, USA
- Current Address: International Life Sciences Institute (ILSI) Research Foundation, Washington D.C. 20005, USA
| | - Tina L Gumienny
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ 08854-8020, USA
- Current Address: Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USA
| | - Ryan J Gleason
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Huang Wang
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Richard W Padgett
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ 08854-8020, USA
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39
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Seetharam A, Bai Y, Stuart GW. A survey of well conserved families of C2H2 zinc-finger genes in Daphnia. BMC Genomics 2010; 11:276. [PMID: 20433734 PMCID: PMC2889900 DOI: 10.1186/1471-2164-11-276] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 04/30/2010] [Indexed: 12/15/2022] Open
Abstract
Background A recent comparative genomic analysis tentatively identified roughly 40 orthologous groups of C2H2 Zinc-finger proteins that are well conserved in "bilaterians" (i.e. worms, flies, and humans). Here we extend that analysis to include a second arthropod genome from the crustacean, Daphnia pulex. Results Most of the 40 orthologous groups of C2H2 zinc-finger proteins are represented by just one or two proteins within each of the previously surveyed species. Likewise, Daphnia were found to possess a similar number of orthologs for all of these small orthology groups. In contrast, the number of Sp/KLF homologs tends to be greater and to vary between species. Like the corresponding mammalian Sp/KLF proteins, most of the Drosophila and Daphnia homologs can be placed into one of three sub-groups: Class I-III. Daphnia were found to have three Class I proteins that roughly correspond to their Drosophila counterparts, dSP1, btd, CG5669, and three Class II proteins that roughly correspond to Luna, CG12029, CG9895. However, Daphnia have four additional KLF-Class II proteins that are most similar to the vertebrate KLF1/2/4 proteins, a subset not found in Drosophila. Two of these four proteins are encoded by genes linked in tandem. Daphnia also have three KLF-Class III members, one more than Drosophila. One of these is a likely Bteb2 homolog, while the other two correspond to Cabot and KLF13, a vertebrate homolog of Cabot. Conclusion Consistent with their likely roles as fundamental determinants of bilaterian form and function, most of the 40 groups of C2H2 zinc-finger proteins are conserved in kind and number in Daphnia. However, the KLF family includes several additional genes that are most similar to genes present in vertebrates but missing in Drosophila.
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Affiliation(s)
- Arun Seetharam
- Department of Biology, Indiana State University, Terre Haute, IN 47809, USA
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40
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Abstract
Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses and recommend strategies for effective motif discovery from these data.
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Luo S, Shaw WM, Ashraf J, Murphy CT. TGF-beta Sma/Mab signaling mutations uncouple reproductive aging from somatic aging. PLoS Genet 2009; 5:e1000789. [PMID: 20041217 PMCID: PMC2791159 DOI: 10.1371/journal.pgen.1000789] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 11/24/2009] [Indexed: 01/07/2023] Open
Abstract
Female reproductive cessation is one of the earliest age-related declines humans experience, occurring in mid-adulthood. Similarly, Caenorhabditis elegans' reproductive span is short relative to its total life span, with reproduction ceasing about a third into its 15–20 day adulthood. All of the known mutations and treatments that extend C. elegans' reproductive period also regulate longevity, suggesting that reproductive span is normally linked to life span. C. elegans has two canonical TGF-ß signaling pathways. We recently found that the TGF-ß Dauer pathway regulates longevity through the Insulin/IGF-1 Signaling (IIS) pathway; here we show that this pathway has a moderate effect on reproductive span. By contrast, TGF-ß Sma/Mab signaling mutants exhibit a substantially extended reproductive period, more than doubling reproductive span in some cases. Sma/Mab mutations extend reproductive span disproportionately to life span and act independently of known regulators of somatic aging, such as Insulin/IGF-1 Signaling and Dietary Restriction. This is the first discovery of a pathway that regulates reproductive span independently of longevity and the first identification of the TGF-ß Sma/Mab pathway as a regulator of reproductive aging. Our results suggest that longevity and reproductive span regulation can be uncoupled, although they appear to normally be linked through regulatory pathways. Female reproductive cessation is the earliest aging phenotype humans experience, and its importance as a clinical issue is growing as more women opt to have children later in life. While much work has been done to understand the general aging process, little is currently known about the regulation of reproductive aging. Like longevity, the ability to produce progeny with advanced age is likely to be genetically regulated. Thus, understanding the processes that regulate reproductive aging may allow us to address the problems of maternal age-related infertility and birth defects. C. elegans and humans both have long post-reproductive life spans, leaving open the possibility that their reproductive spans might be extendable. C. elegans has been used previously to discover conserved regulators of aging, and here we use worms to identify a new regulator of reproductive aging, a highly conserved TGF-ß signaling pathway. We find that TGF-ß signaling regulates reproductive aging independently of somatic aging. This is the first identification of a pathway that breaks the coupling that normally links the two processes. Our work will provide new insights into the improvement of human fertility and prevention of age-related birth defects, and it has implications for the evolutionary relationship between reproduction and longevity regulation.
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Affiliation(s)
- Shijing Luo
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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42
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Abstract
Transforming growth factor beta (TGFbeta) pathways are implicated in metazoan development, adult homeostasis and disease. TGFbeta ligands signal via receptor serine/threonine kinases that phosphorylate, and activate, intracellular Smad effectors as well as other signaling proteins. Oligomeric Smad complexes associate with chromatin and regulate transcription, defining the biological response of a cell to TGFbeta family members. Signaling is modulated by negative-feedback regulation via inhibitory Smads. We review here the mechanisms of TGFbeta signal transduction in metazoans and emphasize events crucial for embryonic development.
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43
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Blitz IL, Cho KWY. Finding partners: how BMPs select their targets. Dev Dyn 2009; 238:1321-31. [PMID: 19441058 DOI: 10.1002/dvdy.21984] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The bone morphogenetic protein (BMP) signaling pathway is a conserved and evolutionarily ancient regulatory module affecting a large variety of cellular behaviors. The evolutionary flexibility in using BMP responses presumably arose by co-option of a canonical BMP signaling cascade to regulate the transcription of diverse batteries of target genes. This begs the question of how seemingly interchangeable BMP signaling components elicit widely different outputs in different cell types, an important issue in the context of understanding how BMP signaling integrates with gene regulatory networks to control development. Because a molecular understanding of how BMP signaling activates different batteries of target genes is an essential prerequisite to comprehending the roles of BMPs in regulating cellular responses, here we review the current knowledge of how BMP-regulated target genes are selected by the signal transduction machinery. We highlight recent studies suggesting the evolutionary conservation of BMP target gene regulation signaling by Schnurri family zinc finger proteins. Developmental Dynamics 238:1321-1331, 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology and the Developmental Biology Center, University of California, Irvine, California, USA.
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Vermeirssen V, Joshi A, Michoel T, Bonnet E, Casneuf T, Van de Peer Y. Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. MOLECULAR BIOSYSTEMS 2009; 5:1817-30. [PMID: 19763340 DOI: 10.1039/b908108a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Differential gene expression governs the development, function and pathology of multicellular organisms. Transcription regulatory networks study differential gene expression at a systems level by mapping the interactions between regulatory proteins and target genes. While microarray transcription profiles are the most abundant data for gene expression, it remains challenging to correctly infer the underlying transcription regulatory networks. The reverse-engineering algorithm LeMoNe (learning module networks) uses gene expression profiles to extract ensemble transcription regulatory networks of coexpression modules and their prioritized regulators. Here we apply LeMoNe to a compendium of microarray studies of the worm Caenorhabditis elegans. We obtain 248 modules with a regulation program for 5020 genes and 426 regulators and a total of 24 012 predicted transcription regulatory interactions. Through GO enrichment analysis, comparison with the gene-gene association network WormNet and integration of other biological data, we show that LeMoNe identifies functionally coherent coexpression modules and prioritizes regulators that relate to similar biological processes as the module genes. Furthermore, we can predict new functional relationships for uncharacterized genes and regulators. Based on modules involved in molting, meiosis and oogenesis, ciliated sensory neurons and mitochondrial metabolism, we illustrate the value of LeMoNe as a biological hypothesis generator for differential gene expression in greater detail. In conclusion, through reverse-engineering of C. elegans expression data, we obtained transcription regulatory networks that can provide further insight into metazoan development.
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