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Jyotisha, Qureshi R, Qureshi IA. Exploration of membrane-bound ecto-phosphatase to identify potential therapeutic target for leishmaniasis. Int J Biol Macromol 2025; 307:141820. [PMID: 40057095 DOI: 10.1016/j.ijbiomac.2025.141820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Revised: 03/03/2025] [Accepted: 03/05/2025] [Indexed: 03/15/2025]
Abstract
Leishmaniasis, caused by leishmanial parasites, is a major health concern worldwide that emphasizes on the exploration of novel therapeutic targets. Membrane-bound ecto-phosphatase of Leishmania donovani (LdMAcP) is essential for parasite virulence and absence of its ortholog in human makes it an attractive drug target. Hence, LdMAcP was cloned and purified to homogeneity that exhibited optimal catalytic efficiency at acidic pH. Analysis of secondary structure established the presence of appropriate secondary structural content with more α-helices, whereas quenching studies delineated the tryptophan residues to be predominantly situated within the hydrophobic regions. Additionally, LdMAcP elicited immune responses by upregulating pro-inflammatory cytokines and nitric oxide production. Structural studies revealed that LdMAcP shares a common α/β fold with other HAP superfamily members, while docking studies displayed binding of its inhibitor sanguinarine to the catalytic pocket with superior affinity than pNPP. Molecular dynamics simulations confirmed that LdMAcP complexes with pNPP and sanguinarine demonstrate enhanced stability compared to the apo form of the enzyme. Further analysis showed LdMAcP-sanguinarine complex to possess more negative binding energy as compared to its complex with pNPP. Altogether, the study underscores comprehensive insight of structural and immunomodulatory features of LdMAcP, offering its potential therapeutic application against leishmaniasis.
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Affiliation(s)
- Jyotisha
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Rahila Qureshi
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India.
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2
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Yanagi KS, Jochim B, Kunjo SO, Breen P, Ruvkun G, Lehrbach N. Mutations in nucleotide metabolism genes bypass proteasome defects in png-1/NGLY1-deficient Caenorhabditis elegans. PLoS Biol 2024; 22:e3002720. [PMID: 38991033 PMCID: PMC11265709 DOI: 10.1371/journal.pbio.3002720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 07/23/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The conserved SKN-1A/Nrf1 transcription factor regulates the expression of proteasome subunit genes and is essential for maintenance of adequate proteasome function in animal development, aging, and stress responses. Unusual among transcription factors, SKN-1A/Nrf1 is a glycoprotein synthesized in the endoplasmic reticulum (ER). N-glycosylated SKN-1A/Nrf1 exits the ER and is deglycosylated in the cytosol by the PNG-1/NGLY1 peptide:N-glycanase. Deglycosylation edits the protein sequence of SKN-1A/Nrf1 by converting N-glycosylated asparagine residues to aspartate, which is necessary for SKN-1A/Nrf1 transcriptional activation of proteasome subunit genes. Homozygous loss-of-function mutations in the peptide:N-glycanase (NGLY1) gene cause NGLY1 deficiency, a congenital disorder of deglycosylation. There are no effective treatments for NGLY1 deficiency. Since SKN-1A/Nrf1 is a major client of NGLY1, the resulting proteasome deficit contributes to NGLY1 disease. We sought to identify targets for mitigation of proteasome dysfunction in NGLY1 deficiency that might indicate new avenues for treatment. We isolated mutations that suppress the sensitivity to proteasome inhibitors caused by inactivation of the NGLY1 ortholog PNG-1 in Caenorhabditis elegans. We identified multiple suppressor mutations affecting 3 conserved genes: rsks-1, tald-1, and ent-4. We show that the suppressors act through a SKN-1/Nrf-independent mechanism and confer proteostasis benefits consistent with amelioration of proteasome dysfunction. ent-4 encodes an intestinal nucleoside/nucleotide transporter, and we show that restriction of nucleotide availability is beneficial, whereas a nucleotide-rich diet exacerbates proteasome dysfunction in PNG-1/NGLY1-deficient C. elegans. Our findings suggest that dietary or pharmacological interventions altering nucleotide availability have the potential to mitigate proteasome insufficiency in NGLY1 deficiency and other diseases associated with proteasome dysfunction.
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Affiliation(s)
- Katherine S. Yanagi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Briar Jochim
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Sheikh Omar Kunjo
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nicolas Lehrbach
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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Wu Z, Zhang J, Wu Y, Chen M, Hu H, Gao X, Li C, Li M, Zhang Y, Lin X, Yang Q, Chen L, Chen K, Zheng L, Zhu A. Gelsenicine disrupted the intestinal barrier of Caenorhabditis elegans. Chem Biol Interact 2024; 395:111036. [PMID: 38705443 DOI: 10.1016/j.cbi.2024.111036] [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: 03/18/2024] [Revised: 04/23/2024] [Accepted: 05/03/2024] [Indexed: 05/07/2024]
Abstract
Gelsemium elegans Benth. (G. elegans) is a traditional medicinal herb that has anti-inflammatory, analgesic, sedative, and detumescence effects. However, it can also cause intestinal side effects such as abdominal pain and diarrhea. The toxicological mechanisms of gelsenicine are still unclear. The objective of this study was to assess enterotoxicity induced by gelsenicine in the nematodes Caenorhabditis elegans (C. elegans). The nematodes were treated with gelsenicine, and subsequently their growth, development, and locomotion behavior were evaluated. The targets of gelsenicine were predicted using PharmMapper. mRNA-seq was performed to verify the predicted targets. Intestinal permeability, ROS generation, and lipofuscin accumulation were measured. Additionally, the fluorescence intensities of GFP-labeled proteins involved in oxidative stress and unfolded protein response in endoplasmic reticulum (UPRER) were quantified. As a result, the treatment of gelsenicine resulted in the inhibition of nematode lifespan, as well as reductions in body length, width, and locomotion behavior. A total of 221 targets were predicted by PharmMapper, and 731 differentially expressed genes were screened out by mRNA-seq. GO and KEGG enrichment analysis revealed involvement in redox process and transmembrane transport. The permeability assay showed leakage of blue dye from the intestinal lumen into the body cavity. Abnormal mRNAs expression of gem-4, hmp-1, fil-2, and pho-1, which regulated intestinal development, absorption and catabolism, transmembrane transport, and apical junctions, was observed. Intestinal lipofuscin and ROS were increased, while sod-2 and isp-1 expressions were decreased. Multiple proteins in SKN-1/DAF-16 pathway were found to bind stably with gelsenicine in a predictive model. There was an up-regulation in the expression of SKN-1:GFP, while the nuclear translocation of DAF-16:GFP exhibited abnormality. The UPRER biomarker HSP-4:GFP was down-regulated. In conclusion, the treatment of gelsenicine resulted in the increase of nematode intestinal permeability. The toxicological mechanisms underlying this effect involved the disruption of intestinal barrier integrity, an imbalance between oxidative and antioxidant processes mediated by the SKN-1/DAF-16 pathway, and abnormal unfolded protein reaction.
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Affiliation(s)
- Zekai Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China
| | - Jian Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350108, China
| | - Yajiao Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China
| | - Mengting Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China
| | - Hong Hu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350108, China
| | - Xinyue Gao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China
| | - Chutao Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China
| | - Maodong Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Youbo Zhang
- State key laboratory of Natural and Biomimetic Drugs and Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xiaohuang Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China
| | - Qiaomei Yang
- Department of Gynecology, Fujian Maternity and Child Health Hospital (Fujian Obstetrics and Gynecology Hospital, Fuzhou, 350001, China
| | - Li Chen
- Department of Gynecology, Fujian Maternity and Child Health Hospital (Fujian Obstetrics and Gynecology Hospital, Fuzhou, 350001, China
| | - Kunqi Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China.
| | - Lifeng Zheng
- Department of Orthopedics, the First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China.
| | - An Zhu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108, China.
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Liu J, Murray JI. Mechanisms of lineage specification in Caenorhabditis elegans. Genetics 2023; 225:iyad174. [PMID: 37847877 PMCID: PMC11491538 DOI: 10.1093/genetics/iyad174] [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: 08/26/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
The studies of cell fate and lineage specification are fundamental to our understanding of the development of multicellular organisms. Caenorhabditis elegans has been one of the premiere systems for studying cell fate specification mechanisms at single cell resolution, due to its transparent nature, the invariant cell lineage, and fixed number of somatic cells. We discuss the general themes and regulatory mechanisms that have emerged from these studies, with a focus on somatic lineages and cell fates. We next review the key factors and pathways that regulate the specification of discrete cells and lineages during embryogenesis and postembryonic development; we focus on transcription factors and include numerous lineage diagrams that depict the expression of key factors that specify embryonic founder cells and postembryonic blast cells, and the diverse somatic cell fates they generate. We end by discussing some future perspectives in cell and lineage specification.
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Affiliation(s)
- Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Williams RTP, King DC, Mastroianni IR, Hill JL, Apenes NW, Ramirez G, Miner EC, Moore A, Coleman K, Nishimura EO. Transcriptome profiling of the Caenorhabditis elegans intestine reveals that ELT-2 negatively and positively regulates intestinal gene expression within the context of a gene regulatory network. Genetics 2023; 224:iyad088. [PMID: 37183501 PMCID: PMC10411582 DOI: 10.1093/genetics/iyad088] [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: 03/06/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/16/2023] Open
Abstract
ELT-2 is the major transcription factor (TF) required for Caenorhabditis elegans intestinal development. ELT-2 expression initiates in embryos to promote development and then persists after hatching through the larval and adult stages. Though the sites of ELT-2 binding are characterized and the transcriptional changes that result from ELT-2 depletion are known, an intestine-specific transcriptome profile spanning developmental time has been missing. We generated this dataset by performing Fluorescence Activated Cell Sorting on intestine cells at distinct developmental stages. We analyzed this dataset in conjunction with previously conducted ELT-2 studies to evaluate the role of ELT-2 in directing the intestinal gene regulatory network through development. We found that only 33% of intestine-enriched genes in the embryo were direct targets of ELT-2 but that number increased to 75% by the L3 stage. This suggests additional TFs promote intestinal transcription especially in the embryo. Furthermore, only half of ELT-2's direct target genes were dependent on ELT-2 for their proper expression levels, and an equal proportion of those responded to elt-2 depletion with over-expression as with under-expression. That is, ELT-2 can either activate or repress direct target genes. Additionally, we observed that ELT-2 repressed its own promoter, implicating new models for its autoregulation. Together, our results illustrate that ELT-2 impacts roughly 20-50% of intestine-specific genes, that ELT-2 both positively and negatively controls its direct targets, and that the current model of the intestinal regulatory network is incomplete as the factors responsible for directing the expression of many intestinal genes remain unknown.
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Affiliation(s)
- Robert T P Williams
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - David C King
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Izabella R Mastroianni
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica L Hill
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Nicolai W Apenes
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriela Ramirez
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - E Catherine Miner
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Andrew Moore
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Karissa Coleman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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Wen Z, Zhang Z, Aimulajiang K, Aleem MT, Feng J, Liang M, Lu M, Xu L, Song X, Li X, Yan R. Histidine acid phosphatase domain-containing protein from Haemonchus contortus is a stimulatory antigen for the Th1 immune response of goat PBMCs. Parasit Vectors 2022; 15:282. [PMID: 35933400 PMCID: PMC9356432 DOI: 10.1186/s13071-022-05411-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background Histidine acid phosphatase (HAP), a member of the histidine phosphatase superfamily, is widely found in parasites and is also a potential vaccine antigen or drug target. However, the biological function of HAP in Haemonchus contortus is still unclear. Methods We cloned the HAP gene from H. contortus (Hc-HAP) and expressed the purified recombinant Hc-HAP (rHc-HAP) protein. The transcription of the Hc-HAP gene in the eggs, infective third-stage larvae (L3s), exsheathed third-stage larvae (xL3s) and adults (females/males) was analyzed by quantitative real-time-PCR (qPCR). An immunofluorescence assay was also used to detect the localization of Hc-HAP expression in adult worms. The effect of rHc-HAP on the function of peripheral blood mononuclear cells (PBMCs) was observed by co-culture of rHc-HAP protein with goat PBMCs. Results The qPCR results revealed that the Hc-HAP gene was transcribed at a higher level in the L3 and xL3 stages that there were gender differences in transcription at the adult stage, with females exhibiting higher transcription than males. Moreover, Hc-HAP was mainly expressed in adult intestinal microvilli. Additionally, western blot results revealed that rHc-HAP could be detected in goat sera artificially infected with H. contortus. In the experiments, rHc-HAP bound to goat PBMCs and released nitric oxide. The rHc-HAP also induced the expression of interferon gamma (IFN-γ) and the phosphorylated STAT 1 transcription factor, while inhibiting interleukin-4 expression. Conclusions The results shows that rHc-HAP stimulated the IFN-γ/STAT1 signaling pathway and enabled polarization of PBMCs toward T-helper 1 immune responses. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05411-7.
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Affiliation(s)
- Zhaohai Wen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhaoying Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Kalibixiati Aimulajiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.,State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, 830011, Xinjiang, People's Republic of China
| | - Muhammad Tahir Aleem
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiajun Feng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Meng Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Mingmin Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Lixin Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xiaokai Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xiangrui Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Ruofeng Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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Silva H, Anjo SI, Manadas B, Abrantes I, Fonseca L, Cardoso JMS. Comparative Analysis of Bursaphelenchus xylophilus Secretome Under Pinus pinaster and P. pinea Stimuli. FRONTIERS IN PLANT SCIENCE 2021; 12:668064. [PMID: 34046053 PMCID: PMC8144518 DOI: 10.3389/fpls.2021.668064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/29/2021] [Indexed: 05/19/2023]
Abstract
The pinewood nematode (PWN), Bursaphelenchus xylophilus, the pine wilt disease's (PWD) causal agent, is a migratory endoparasitic nematode skilled to feed on pine tissues and on fungi that colonize the trees. In order to study B. xylophilus secretomes under the stimulus of pine species with different susceptibilities to disease, nematodes were exposed to aqueous pine extracts from Pinus pinaster (high-susceptible host) and P. pinea (low-susceptible host). Sequential windowed acquisition of all theoretical mass spectra (SWATH-MS) was used to determine relative changes in protein amounts between B. xylophilus secretions, and a total of 776 secreted proteins were quantified in both secretomes. From these, 22 proteins were found increased in the B. xylophilus secretome under the P. pinaster stimulus and 501 proteins increased under the P. pinea stimulus. Functional analyses of the 22 proteins found increased in the P. pinaster stimulus showed that proteins with peptidase, hydrolase, and antioxidant activities were the most represented. On the other hand, gene ontology (GO) enrichment analysis of the 501 proteins increased under the P. pinea stimulus revealed an enrichment of proteins with binding activity. The differences detected in the secretomes highlighted the diverse responses from the nematode to overcome host defenses with different susceptibilities and provide new clues on the mechanism behind the pathogenicity of this plant-parasitic nematode. Proteomic data are available via ProteomeXchange with identifier PXD024011.
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Affiliation(s)
- Hugo Silva
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Sandra I. Anjo
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Luís Fonseca
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Joana M. S. Cardoso
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
- *Correspondence: Joana M. S. Cardoso,
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Eurmsirilerd E, Maduro MF. Evolution of Developmental GATA Factors in Nematodes. J Dev Biol 2020; 8:jdb8040027. [PMID: 33207804 PMCID: PMC7712238 DOI: 10.3390/jdb8040027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
GATA transcription factors are found in animals, plants, and fungi. In animals, they have important developmental roles in controlling specification of cell identities and executing tissue-specific differentiation. The Phylum Nematoda is a diverse group of vermiform animals that inhabit ecological niches all over the world. Both free-living and parasitic species are known, including those that cause human infectious disease. To date, GATA factors in nematodes have been studied almost exclusively in the model system C. elegans and its close relatives. In this study, we use newly available sequences to identify GATA factors across the nematode phylum. We find that most species have fewer than six GATA factors, but some species have 10 or more. Comparisons of gene and protein structure suggest that there were at most two GATA factors at the base of the phylum, which expanded by duplication and modification to result in a core set of four factors. The high degree of structural similarity with the corresponding orthologues in C. elegans suggests that the nematode GATA factors share similar functions in development.
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Affiliation(s)
- Ethan Eurmsirilerd
- Undergraduate Program in Biology, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA;
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Morris F. Maduro
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Correspondence:
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AlKhaleefa A, Snider FL, Duff HJ, McGhee JD. -Using the C. elegans lem-2 Gene to Reconstruct the Human LEMD2 Mutation Associated with Hutterite-type Cataract/Cardiomyopathy. MICROPUBLICATION BIOLOGY 2020; 2020. [PMID: 32666044 PMCID: PMC7351585 DOI: 10.17912/micropub.biology.000273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ayaa AlKhaleefa
- 1. Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
| | - Frances L Snider
- 1. Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
| | - Henry J Duff
- Cardiac Sciences, Libin Cardiology Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
| | - James D McGhee
- 1. Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
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10
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Radeke LJ, Herman MA. Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia. BMC Microbiol 2020; 20:170. [PMID: 32560629 PMCID: PMC7304212 DOI: 10.1186/s12866-020-01771-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Background Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans, being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans. Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Results Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. Conclusions Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.
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Affiliation(s)
- Leah J Radeke
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Michael A Herman
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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Ma J, Gao B, Wang R, Li X, Chen S. Transcriptome analyses of Ditylenchus destructor in responses to cold and desiccation stress. Genet Mol Biol 2020; 43:e20180057. [PMID: 32232317 PMCID: PMC7198036 DOI: 10.1590/1678-4685-gmb-2018-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/03/2019] [Indexed: 11/22/2022] Open
Abstract
The objective of this study was to identify molecular responses in Ditylenchus destructor to cold and desiccation by means of transcriptomes analyses. A total of 102,517 unigenes were obtained, with an average length of 1,076 bp, in which 58,453 (57%) had a functional annotation. A total of 1154 simple sequence repeats (SSRs) distributed over 1078 unigenes were detected. Gene expression profiles in response to cold and desiccation stress and the expression of specific stress-related genes were compared. Gene ontology analysis and pathway-based analysis were used to further investigate the functions of the differentially expressed genes. The reliability of the sequencing data was verified through quantitative real-time PCR analysis of 19 stress-related genes. RNA interference used to further assess the functions of the cold-related unigenes 15628 and 15596 showed that the knockdown of each of these genes led to decreased cold tolerance of D. destructor. Hence, this study revealed molecular processes and pathways active in cold- or dessication-treated nematodes. The transcriptome profiles presented in this study provide insight into the transcriptome complexity and will contribute to further understand stress tolerance in D. destructor.
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Affiliation(s)
- Juan Ma
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences /IPM centre of Hebei Province/ Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
| | - Bo Gao
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences /IPM centre of Hebei Province/ Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
| | - Rongyan Wang
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences /IPM centre of Hebei Province/ Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
| | - Xiuhua Li
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences /IPM centre of Hebei Province/ Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
| | - Shulong Chen
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences /IPM centre of Hebei Province/ Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
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12
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Shao H, Wang D. Long-term and low-dose exposure to nanopolystyrene induces a protective strategy to maintain functional state of intestine barrier in nematode Caenorhabditis elegans. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113649. [PMID: 31767235 DOI: 10.1016/j.envpol.2019.113649] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/01/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Functional state of intestinal barrier plays an important role for environmental animals in being against various toxicants. We investigated GATA transcriptional factor ELT-2-mediated intestinal response to nanopolystyrere in Caenorhabditis elegans. Prolonged exposure to nanopolystyrene (≥1 μg/L) induced an increase in expression of ELT-2, and intestinal RNA interference (RNAi) knockdown of elt-2 caused enhancement in intestinal permeability. Meanwhile, mutation of elt-2 resulted in susceptibility to nanopolystyrene toxicity, and ELT-2 functioned in intestine to regulate the nanopolystyrene toxicity. ERM-1, CLEC-63, and CLEC-85 were identified as targets of ELT-2 in regulating the nanopolystyrene toxicity. ERM-1 was required for maintaining functional state in intestinal barrier, and functioned synergistically with CLEC-63 or CLEC-85 to regulate nanopolystyrene toxicity. Therefore, activation of intestinal ELT-2 by nanopolystyrere could mediate a protective strategy to maintain the functional state of intestinal barrier. During this process, intestinal ELT-2 activated two different molecular signals (ERM-1 signal and CLEC-63/85 signal) for nematodes against the nanopolystyrene toxicity.
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Affiliation(s)
- Huimin Shao
- Medical School, Southeast University, Nanjing, 210009, China
| | - Dayong Wang
- Medical School, Southeast University, Nanjing, 210009, China.
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13
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Maduro MF. Gut development in C. elegans. Semin Cell Dev Biol 2017; 66:3-11. [PMID: 28065852 DOI: 10.1016/j.semcdb.2017.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/28/2016] [Accepted: 01/03/2017] [Indexed: 12/13/2022]
Abstract
The midgut (intestine) of the nematode, C. elegans, is a tube consisting of 20 cells that arises from a single embryonic precursor. Owing to its comparatively simple anatomy and the advantages inherent to the C. elegans system, the gut has been used as a model for organogenesis for more than 25 years. In this review, the salient features of C. elegans gut development are described from the E progenitor through to the 20-cell intestine. The core gene regulatory network that drives specification of the gut, and other genes with roles in organogenesis, lumen morphogenesis and the cell cycle, are also described. Questions for future work are posed.
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Affiliation(s)
- Morris F Maduro
- Biology Department, University of California, Riverside, CA 92521, United States.
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14
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Developmentally programmed germ cell remodelling by endodermal cell cannibalism. Nat Cell Biol 2016; 18:1302-1310. [PMID: 27842058 PMCID: PMC5129868 DOI: 10.1038/ncb3439] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/13/2016] [Indexed: 02/06/2023]
Abstract
Primordial germ cells (PGCs) in many species associate intimately with endodermal cells, but the significance of such interactions is largely unexplored. Here, we show that Caenorhabditis elegans PGCs form lobes that are removed and digested by endodermal cells, dramatically altering PGC size and mitochondrial content. We demonstrate that endodermal cells do not scavenge lobes PGCs shed, but rather, actively remove lobes from the cell body. CED-10 (Rac)-induced actin, DYN-1 (dynamin) and LST-4 (SNX9) transiently surround lobe necks and are required within endodermal cells for lobe scission, suggesting that scission occurs through a mechanism resembling vesicle endocytosis. These findings reveal an unexpected role for endoderm in altering the contents of embryonic PGCs, and define a form of developmentally programmed cell remodelling involving intercellular cannibalism. Active roles for engulfing cells have been proposed in several neuronal remodelling events, suggesting that intercellular cannibalism may be a more widespread method used to shape cells than previously thought.
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15
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Du L, Tracy S, Rifkin SA. Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. Dev Biol 2016; 412:160-170. [PMID: 26896592 PMCID: PMC4814310 DOI: 10.1016/j.ydbio.2016.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
Cis-regulatory elements (CREs) are crucial links in developmental gene regulatory networks, but in many cases, it can be difficult to discern whether similar CREs are functionally equivalent. We found that despite similar conservation and binding capability to upstream activators, different GATA cis-regulatory motifs within the promoter of the C. elegans endoderm regulator elt-2 play distinctive roles in activating and modulating gene expression throughout development. We fused wild-type and mutant versions of the elt-2 promoter to a gfp reporter and inserted these constructs as single copies into the C. elegans genome. We then counted early embryonic gfp transcripts using single-molecule RNA FISH (smFISH) and quantified gut GFP fluorescence. We determined that a single primary dominant GATA motif located 527bp upstream of the elt-2 start codon was necessary for both embryonic activation and later maintenance of transcription, while nearby secondary GATA motifs played largely subtle roles in modulating postembryonic levels of elt-2. Mutation of the primary activating site increased low-level spatiotemporally ectopic stochastic transcription, indicating that this site acts repressively in non-endoderm cells. Our results reveal that CREs with similar GATA factor binding affinities in close proximity can play very divergent context-dependent roles in regulating the expression of a developmentally critical gene in vivo.
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Affiliation(s)
- Lawrence Du
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Sharon Tracy
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Scott A Rifkin
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States.
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16
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Asan A, Raiders SA, Priess JR. Morphogenesis of the C. elegans Intestine Involves Axon Guidance Genes. PLoS Genet 2016; 12:e1005950. [PMID: 27035721 PMCID: PMC4817974 DOI: 10.1371/journal.pgen.1005950] [Citation(s) in RCA: 27] [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: 12/14/2015] [Accepted: 03/01/2016] [Indexed: 11/21/2022] Open
Abstract
Genetic and molecular studies have provided considerable insight into how various tissue progenitors are specified in early embryogenesis, but much less is known about how those progenitors create three-dimensional tissues and organs. The C. elegans intestine provides a simple system for studying how a single progenitor, the E blastomere, builds an epithelial tube of 20 cells. As the E descendants divide, they form a primordium that transitions between different shapes over time. We used cell contours, traced from confocal optical z-stacks, to build a 3D graphic reconstruction of intestine development. The reconstruction revealed several new aspects of morphogenesis that extend and clarify previous observations. The first 8 E descendants form a plane of four right cells and four left cells; the plane arises through oriented cell divisions and VANG-1/Van Gogh-dependent repositioning of any non-planar cells. LIN-12/Notch signaling affects the left cells in the E8 primordium, and initiates later asymmetry in cell packing. The next few stages involve cell repositioning and intercalation events that shuttle cells to their final positions, like shifting blocks in a Rubik’s cube. Repositioning involves breaking and replacing specific adhesive contacts, and some of these events involve EFN-4/Ephrin, MAB-20/semaphorin-2a, and SAX-3/Robo. Once cells in the primordium align along a common axis and in the correct order, cells at the anterior end rotate clockwise around the axis of the intestine. The anterior rotation appears to align segments of the developing lumen into a continuous structure, and requires the secreted ligand UNC-6/netrin, the receptor UNC-40/DCC, and an interacting protein called MADD-2. Previous studies showed that rotation requires a second round of LIN-12/Notch signaling in cells on the right side of the primordium, and we show that MADD-2-GFP appears to be downregulated in those cells. This report uses the intestine of the nematode C. elegans as a model system to address how progenitor cells form a three-dimensional organ. The fully formed intestine is a cylindrical tube of only 20 epithelial cells, and all of these cells are descendants of a single cell, the E blastomere. The E descendants form a primordium that changes shape over time as different E descendants divide and move. Cells in the primordium must continually adhere to each other during these movements to maintain the integrity of the primordium. Here, we generated a 3D graphic reconstruction of the developing intestine in order to analyze these events. We found that the cell movements are highly reproducible, suggesting that they are programmed by asymmetric gene expression in the primordium. In particular, we found that the conserved receptor LIN-12/Notch appears to modulate left-right adhesion in the primordium, leading to the asymmetric packing of cells. One of the most remarkable events in intestinal morphogenesis is the circumferential rotation of a subset of cells. We found that rotation appears to have a role in aligning the developing lumen of the intestine, and involves a conserved, UNC-6/netrin signaling pathway that is best known for its roles in the guided growth of neurons.
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Affiliation(s)
- Alparsan Asan
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Stephan A. Raiders
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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17
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Gao X, Tyagi R, Magrini V, Ly A, Jasmer DP, Mitreva M. Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine. RNA Biol 2016; 14:1335-1352. [PMID: 27002534 DOI: 10.1080/15476286.2016.1166333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of Ascaris suum, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among 3 contiguous regions of the adult A. suum intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. A. suum intestinal miRNAs were identified that are conserved with intestinal miRNAs from C. elegans (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, Heligmosomoides polygyrus (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.
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Affiliation(s)
- Xin Gao
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Rahul Tyagi
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Vincent Magrini
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Amy Ly
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Douglas P Jasmer
- b Department of Veterinary Microbiology and Pathology , Washington State University , Pullman , WA , USA
| | - Makedonka Mitreva
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA.,c Department of Internal Medicine , Washington University School of Medicine , St. Louis , MO , USA
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18
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Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH. Methods 2015; 98:42-49. [PMID: 26564238 DOI: 10.1016/j.ymeth.2015.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 12/30/2022] Open
Abstract
Advances in fluorescent probe design and synthesis have allowed the uniform in situ labeling of individual RNA molecules. In a technique referred to as single molecule RNA FISH (smRNA FISH), the labeled RNA molecules can be imaged as diffraction-limited spots and counted using image analysis algorithms. Single RNA counting has provided valuable insights into the process of gene regulation. This microscopy-based method has often revealed a high cell-to-cell variability in expression levels, which has in turn led to a growing interest in investigating the biological significance of gene expression noise. Here we describe the application of the smRNA FISH technique to samples of Caenorhabditis elegans, a well-characterized model organism.
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19
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Banerjee S, Versaw WK, Garcia LR. Imaging Cellular Inorganic Phosphate in Caenorhabditis elegans Using a Genetically Encoded FRET-Based Biosensor. PLoS One 2015; 10:e0141128. [PMID: 26484766 PMCID: PMC4615621 DOI: 10.1371/journal.pone.0141128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/05/2015] [Indexed: 01/02/2023] Open
Abstract
Inorganic phosphate (Pi) has central roles in metabolism, cell signaling and energy conversion. The distribution of Pi to each cell and cellular compartment of an animal must be tightly coordinated with its dietary supply and with the varied metabolic demands of individual cells. An analytical method for monitoring Pi dynamics with spatial and temporal resolution is therefore needed to gain a comprehensive understanding of mechanisms governing the transport and recycling of this essential nutrient. Here we demonstrate the utility of a genetically encoded FRET-based Pi sensor to assess cellular Pi levels in the nematode Caenorhabditis elegans. The sensor was expressed in different cells and tissues of the animal, including head neurons, tail neurons, pharyngeal muscle, and the intestine. Cytosolic Pi concentrations were monitored using ratiometric imaging. Injection of phosphate buffer into intestinal cells confirmed that the sensor was responsive to changes in Pi concentration in vivo. Live Pi imaging revealed cell-specific and developmental stage-specific differences in cytosolic Pi concentrations. In addition, cellular Pi levels were perturbed by food deprivation and by exposure to the respiratory inhibitor cyanide. These results suggest that Pi concentration is a sensitive indicator of metabolic status. Moreover, we propose that live Pi imaging in C. elegans is a powerful approach to discern mechanisms that govern Pi distribution in individual cells and throughout an animal.
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Affiliation(s)
- Swayoma Banerjee
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843-3258, United States of America
| | - Wayne K. Versaw
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843-3258, United States of America
| | - L. Rene Garcia
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843-3258, United States of America
- Howard Hughes Medical Institute, College Station, TX, 77843-3258, United States of America
- * E-mail:
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20
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Ackley BD. Wnt-signaling and planar cell polarity genes regulate axon guidance along the anteroposterior axis in C. elegans. Dev Neurobiol 2014; 74:781-96. [PMID: 24214205 PMCID: PMC4167394 DOI: 10.1002/dneu.22146] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 09/18/2013] [Accepted: 11/02/2013] [Indexed: 11/10/2022]
Abstract
During the development of the nervous system, neurons encounter signals that inform their outgrowth and polarization. Understanding how these signals combinatorially function to pattern the nervous system is of considerable interest to developmental neurobiologists. The Wnt ligands and their receptors have been well characterized in polarizing cells during asymmetric cell division. The planar cell polarity (PCP) pathway is also critical for cell polarization in the plane of an epithelium. The core set of PCP genes include members of the conserved Wnt-signaling pathway, such as Frizzled and Disheveled, but also the cadherin-domain protein Flamingo. In Drosophila, the Fat and Dachsous cadherins also function in PCP, but in parallel to the core PCP components. C. elegans also have two Fat-like and one Dachsous-like cadherins, at least one of which, cdh-4, contributes to neural development. In C. elegans Wnt ligands and the conserved PCP genes have been shown to regulate a number of different events, including embryonic cell polarity, vulval morphogenesis, and cell migration. As is also observed in vertebrates, the Wnt and PCP genes appear to function to primarily provide information about the anterior to posterior axis of development. Here, we review the recent work describing how mutations in the Wnt and core PCP genes affect axon guidance and synaptogenesis in C. elegans.
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Affiliation(s)
- Brian D Ackley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
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21
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Armstrong SD, Babayan SA, Lhermitte-Vallarino N, Gray N, Xia D, Martin C, Kumar S, Taylor DW, Blaxter ML, Wastling JM, Makepeace BL. Comparative analysis of the secretome from a model filarial nematode (Litomosoides sigmodontis) reveals maximal diversity in gravid female parasites. Mol Cell Proteomics 2014; 13:2527-44. [PMID: 24958169 DOI: 10.1074/mcp.m114.038539] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Filarial nematodes (superfamily Filarioidea) are responsible for an annual global health burden of ∼6.3 million disability-adjusted life-years, which represents the greatest single component of morbidity attributable to helminths affecting humans. No vaccine exists for the major filarial diseases, lymphatic filariasis and onchocerciasis; in part because research on protective immunity against filariae has been constrained by the inability of the human-parasitic species to complete their lifecycles in laboratory mice. However, the rodent filaria Litomosoides sigmodontis has become a popular experimental model, as BALB/c mice are fully permissive for its development and reproduction. Here, we provide a comprehensive analysis of excretory-secretory products from L. sigmodontis across five lifecycle stages and identifications of host proteins associated with first-stage larvae (microfilariae) in the blood. Applying intensity-based quantification, we determined the abundance of 302 unique excretory-secretory proteins, of which 64.6% were present in quantifiable amounts only from gravid adult female nematodes. This lifecycle stage, together with immature microfilariae, released four proteins that have not previously been evaluated as vaccine candidates: a predicted 28.5 kDa filaria-specific protein, a zonadhesin and SCO-spondin-like protein, a vitellogenin, and a protein containing six metridin-like ShK toxin domains. Female nematodes also released two proteins derived from the obligate Wolbachia symbiont. Notably, excretory-secretory products from all parasite stages contained several uncharacterized members of the transthyretin-like protein family. Furthermore, biotin labeling revealed that redox proteins and enzymes involved in purinergic signaling were enriched on the adult nematode cuticle. Comparison of the L. sigmodontis adult secretome with that of the human-infective filarial nematode Brugia malayi (reported previously in three independent published studies) identified differences that suggest a considerable underlying diversity of potential immunomodulators. The molecules identified in L. sigmodontis excretory-secretory products show promise not only for vaccination against filarial infections, but for the amelioration of allergy and autoimmune diseases.
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Affiliation(s)
- Stuart D Armstrong
- From the ‡Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Simon A Babayan
- §Centre for Immunity, Infection & Evolution and Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | | | - Nick Gray
- §Centre for Immunity, Infection & Evolution and Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Dong Xia
- From the ‡Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Coralie Martin
- ¶UMR 7245 MCAM CNRS, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - Sujai Kumar
- §Centre for Immunity, Infection & Evolution and Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - David W Taylor
- ‖Division of Pathway Medicine, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Mark L Blaxter
- §Centre for Immunity, Infection & Evolution and Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Jonathan M Wastling
- From the ‡Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK; **The National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool L3 5RF, UK
| | - Benjamin L Makepeace
- From the ‡Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK;
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22
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Pettersson S, Forchheimer R, Larsson JÅ. Meta-Boolean models of asymmetric division patterns in the C. elegans intestinal lineage: Implications for the posterior boundary of intestinal twist. WORM 2013; 2:e23701. [PMID: 24058861 PMCID: PMC3670462 DOI: 10.4161/worm.23701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 01/14/2013] [Indexed: 11/24/2022]
Abstract
The intestine of Caenorhabditis elegans is derived from 20 cells that are organized into nine intestinal rings. During embryogenesis, three of the rings rotate approximately 90 degrees in a process known as intestinal twist. The underlying mechanisms for this morphological event are not fully known, but it has been demonstrated that both left-right and anterior-posterior asymmetry is required for intestinal twist to occur. We have recently presented a rule-based meta-Boolean tree model intended to describe complex lineages. In this report we apply this model to the E lineage of C. elegans, specifically targeting the asymmetric anterior-posterior division patterns within the lineage. The resulting model indicates that cells with the same factor concentration are located next to each other in the intestine regardless of lineage origin. In addition, the shift in factor concentrations coincides with the boundary for intestinal twist. When modeling lit-1 mutant data according to the same principle, the factor distributions in each cell are altered, yet the concurrence between the shift in concentration and intestinal twist remains. This pattern suggests that intestinal twist is controlled by a threshold mechanism. In the current paper we present the factor concentrations for all possible combinations of symmetric and asymmetric divisions in the E lineage and relate these to the potential threshold by studying existing data for wild-type and mutant embryos. Finally, we discuss how the resulting models can serve as a basis for experimental design in order to reveal the underlying mechanisms of intestinal twist.
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Affiliation(s)
- Sofia Pettersson
- Division of Information Coding; Department of Electrical Engineering; Linköping University; Linköping, Sweden
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23
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Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. ACTA ACUST UNITED AC 2013:1-34. [PMID: 23801596 DOI: 10.1895/wormbook.1.45.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.
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Affiliation(s)
- Valerie Reinke
- Department of Genetics, Yale University, New Haven, CT 06520, USA.
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24
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McGhee JD. TheCaenorhabditis elegansintestine. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:347-67. [DOI: 10.1002/wdev.93] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Melo JA, Ruvkun G. Inactivation of conserved C. elegans genes engages pathogen- and xenobiotic-associated defenses. Cell 2012; 149:452-66. [PMID: 22500807 DOI: 10.1016/j.cell.2012.02.050] [Citation(s) in RCA: 305] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 01/02/2012] [Accepted: 02/23/2012] [Indexed: 12/18/2022]
Abstract
The nematode C. elegans is attracted to nutritious bacteria and is repelled by pathogens and toxins. Here we show that RNAi and toxin-mediated disruption of core cellular activities, including translation, respiration, and protein turnover, stimulate behavioral avoidance of normally attractive bacteria. RNAi of these and other essential processes induces expression of detoxification and innate immune effectors, even in the absence of toxins or pathogens. Disruption of core processes in non-neuronal tissues was sufficient to stimulate aversion behavior, revealing a neuroendocrine axis of control that additionally required serotonergic and Jnk kinase signaling pathways. We propose that surveillance pathways overseeing core cellular activities allow animals to detect invading pathogens that deploy toxins and virulence factors to undermine vital host functions. Variation in cellular surveillance and endocrine pathways controlling behavior, detoxification, and immunity selected by past toxin or microbial interactions could underlie aberrant responses to foods, medicines, and microbes.
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Affiliation(s)
- Justine A Melo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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Romney SJ, Newman BS, Thacker C, Leibold EA. HIF-1 regulates iron homeostasis in Caenorhabditis elegans by activation and inhibition of genes involved in iron uptake and storage. PLoS Genet 2011; 7:e1002394. [PMID: 22194696 PMCID: PMC3240588 DOI: 10.1371/journal.pgen.1002394] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 10/10/2011] [Indexed: 12/31/2022] Open
Abstract
Caenorhabditis elegans ftn-1 and ftn-2, which encode the iron-storage protein ferritin, are transcriptionally inhibited during iron deficiency in intestine. Intestinal specific transcription is dependent on binding of ELT-2 to GATA binding sites in an iron-dependent enhancer (IDE) located in ftn-1 and ftn-2 promoters, but the mechanism for iron regulation is unknown. Here, we identify HIF-1 (hypoxia-inducible factor -1) as a negative regulator of ferritin transcription. HIF-1 binds to hypoxia-response elements (HREs) in the IDE in vitro and in vivo. Depletion of hif-1 by RNA interference blocks transcriptional inhibition of ftn-1 and ftn-2 reporters, and ftn-1 and ftn-2 mRNAs are not regulated in a hif-1 null strain during iron deficiency. An IDE is also present in smf-3 encoding a protein homologous to mammalian divalent metal transporter-1. Unlike the ftn-1 IDE, the smf-3 IDE is required for HIF-1–dependent transcriptional activation of smf-3 during iron deficiency. We show that hif-1 null worms grown under iron limiting conditions are developmentally delayed and that depletion of FTN-1 and FTN-2 rescues this phenotype. These data show that HIF-1 regulates intestinal iron homeostasis during iron deficiency by activating and inhibiting genes involved in iron uptake and storage. Due to its presence in proteins involved in hemoglobin synthesis, DNA synthesis, and mitochondrial respiration, eukaryotic cells require iron for survival. Excess iron can lead to oxidative damage, while iron deficiency reduces cell growth and causes cell death. Dysregulation of iron homeostasis in humans caused by iron deficiency or excess leads to anemia, diabetes, and neurodegenerative disorders. All organisms have thus developed mechanisms to sense, acquire, and store iron. We use Caenorhabditis elegans as a model organism to study mechanisms of iron regulation. Our previous studies show that the iron-storage protein ferritin (FTN-1, FTN-2) is transcriptionally inhibited in intestine during iron deficiency, but the mechanisms regulating iron regulation are not known. Here, we find that hypoxia-inducible factor 1 (HIF-1) transcriptionally inhibits ftn-1 and ftn-2 during iron deficiency. We also show that HIF-1 activates the iron uptake gene smf-3. Transcriptional activation and inhibition by HIF-1 is dependent on an iron enhancer in the promoters of these genes. HIF-1 is a known transcriptional activator, but its role in transcriptional inhibition is not well understood. Our data show that HIF-1 regulates iron homeostasis by activating and inhibiting iron uptake and storage genes, and they provide insight into HIF-1 transcriptional inhibition.
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Affiliation(s)
- Steven Joshua Romney
- Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Ben S. Newman
- University of Washington, Seattle, Washington, United States of America
| | - Colin Thacker
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Elizabeth A. Leibold
- Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Sinclair J, Hamza I. A novel heme-responsive element mediates transcriptional regulation in Caenorhabditis elegans. J Biol Chem 2010; 285:39536-43. [PMID: 20938051 DOI: 10.1074/jbc.m110.167619] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hemes are prosthetic groups that participate in diverse biochemical pathways across phylogeny. Although heme can also regulate broad physiological processes by directly modulating gene expression in Metazoa, the regulatory pathways for sensing and responding to heme are not well defined. Caenorhabditis elegans is a heme auxotroph and relies solely on environmental heme for sustenance. Worms respond to heme availability by regulating heme-responsive genes such as hrg-1, an intestinal heme transporter that is up-regulated by >60-fold during heme depletion. To identify the mechanism for the heme-dependent regulation of hrg-1, we interrogated the hrg-1 promoter. Deletion and mutagenesis studies of the hrg-1 promoter revealed a 23-bp heme-responsive element that is both necessary and sufficient for heme-dependent regulation of hrg-1. Furthermore, our studies show that the heme regulation of hrg-1 is mediated by both activation and repression in conjunction with ELT-2 and ELT-4, transcription factors that specify intestinal expression.
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Affiliation(s)
- Jason Sinclair
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
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28
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Kormish JD, Gaudet J, McGhee JD. Development of the C. elegans digestive tract. Curr Opin Genet Dev 2010; 20:346-54. [PMID: 20570129 DOI: 10.1016/j.gde.2010.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/20/2010] [Accepted: 04/24/2010] [Indexed: 12/11/2022]
Abstract
The C. elegans digestive tract (pharynx, intestine, and rectum) contains only approximately 100 cells but develops under the control of the same types of transcription factors (e.g. FoxA and GATA factors) that control digestive tract development in far more complex animals. The GATA-factor dominated core regulatory hierarchy directing development of the homogenous clonal intestine from oocyte to mature organ is now known with some degree of certainty, setting the stage for more biochemical experiments to understand developmental mechanisms. The FoxA-factor dominated development of the pharynx (and rectum) is less well understood but is beginning to reveal how transcription factor combinations produce unique cell types within organs.
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Affiliation(s)
- Jay D Kormish
- Department of Molecular Biology and Biochemistry, Department of Medical Genetics, Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
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Owraghi M, Broitman-Maduro G, Luu T, Roberson H, Maduro MF. Roles of the Wnt effector POP-1/TCF in the C. elegans endomesoderm specification gene network. Dev Biol 2009; 340:209-21. [PMID: 19818340 DOI: 10.1016/j.ydbio.2009.09.042] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 09/23/2009] [Accepted: 09/25/2009] [Indexed: 10/20/2022]
Abstract
In C. elegans the 4-cell stage blastomere EMS is an endomesodermal precursor. Its anterior daughter, MS, makes primarily mesodermal cells, while its posterior daughter E generates the entire intestine. The gene regulatory network underlying specification of MS and E has been the subject of study for more than 15 years. A key component of the specification of the two cells is the involvement of the Wnt/beta-catenin asymmetry pathway, which through its nuclear effector POP-1, specifies MS and E as different from each other. Loss of pop-1 function results in the mis-specification of MS as an E-like cell, because POP-1 directly represses the end-1 and end-3 genes in MS, which would otherwise promote an endoderm fate. A long-standing question has been whether POP-1 plays a role in specifying MS fate beyond repression of endoderm fate. This question has been difficult to ask because the only chromosomal lesions that remove both end-1 and end-3 are large deletions removing hundreds of genes. Here, we report the construction of bona fide end-1 end-3 double mutants. In embryos lacking activity of end-1, end-3 and pop-1 together, we find that MS fate is partially restored, while E expresses early markers of MS fate and adopts characteristics of both MS and C. Our results suggest that POP-1 is not critical for MS specification beyond repression of endoderm specification, and reveal that Wnt-modified POP-1 and END-1/3 further reinforce E specification by repressing MS fate in E. By comparison, a previous work suggested that in the related nematode C. briggsae, Cb-POP-1 is not required to repress endoderm specification in MS, in direct contrast with Ce-POP-1, but is critical for repression of MS fate in E. The findings reported here shed new light on the flexibility of combinatorial control mechanisms in endomesoderm specification in Caenorhabditis.
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Affiliation(s)
- Melissa Owraghi
- Department of Biology, University of California, 2121A Genomics Building, Riverside, Riverside, CA 92521, USA
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Maduro MF. Structure and evolution of the C. elegans embryonic endomesoderm network. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:250-60. [PMID: 18778800 PMCID: PMC2688470 DOI: 10.1016/j.bbagrm.2008.07.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 07/29/2008] [Indexed: 12/19/2022]
Abstract
The specification of the Caenorhabditis elegans endomesoderm has been the subject of study for more than 15 years. Specification of the 4-cell stage endomesoderm precursor, EMS, occurs as a result of the activation of a transcription factor cascade that starts with SKN-1, coupled with input from the Wnt/beta-catenin asymmetry pathway through the nuclear effector POP-1. As development proceeds, transiently-expressed cell fate factors are succeeded by stable, tissue/organ-specific regulators. The pathway is complex and uses motifs found in all transcriptional networks. Here, the regulators that function in the C. elegans endomesoderm network are described. An examination of the motifs in the network suggests how they may have evolved from simpler gene interactions. Flexibility in the network is evident from the multitude of parallel functions that have been identified and from apparent changes in parts of the corresponding network in Caenorhabditis briggsae. Overall, the complexities of C. elegans endomesoderm specification build a picture of a network that is robust, complex, and still evolving.
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Affiliation(s)
- Morris F Maduro
- Department of Biology, University of California, Riverside, CA 92521, USA.
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31
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McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, Khattra J, Hirst M, Jones SJM, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, Kalb JM. ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol 2009; 327:551-65. [PMID: 19111532 PMCID: PMC2706090 DOI: 10.1016/j.ydbio.2008.11.034] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 11/17/2008] [Indexed: 12/14/2022]
Abstract
Starting with SAGE-libraries prepared from C. elegans FAC-sorted embryonic intestine cells (8E-16E cell stage), from total embryos and from purified oocytes, and taking advantage of the NextDB in situ hybridization data base, we define sets of genes highly expressed from the zygotic genome, and expressed either exclusively or preferentially in the embryonic intestine or in the intestine of newly hatched larvae; we had previously defined a similarly expressed set of genes from the adult intestine. We show that an extended TGATAA-like sequence is essentially the only candidate for a cis-acting regulatory motif common to intestine genes expressed at all stages. This sequence is a strong ELT-2 binding site and matches the sequence of GATA-like sites found to be important for the expression of every intestinal gene so far analyzed experimentally. We show that the majority of these three sets of highly expressed intestinal-specific/intestinal-enriched genes respond strongly to ectopic expression of ELT-2 within the embryo. By flow-sorting elt-2(null) larvae from elt-2(+) larvae and then preparing Solexa/Illumina-SAGE libraries, we show that the majority of these genes also respond strongly to loss-of-function of ELT-2. To test the consequences of loss of other transcription factors identified in the embryonic intestine, we develop a strain of worms that is RNAi-sensitive only in the intestine; however, we are unable (with one possible exception) to identify any other transcription factor whose intestinal loss-of-function causes a phenotype of comparable severity to the phenotype caused by loss of ELT-2. Overall, our results support a model in which ELT-2 is the predominant transcription factor in the post-specification C. elegans intestine and participates directly in the transcriptional regulation of the majority (>80%) of intestinal genes. We present evidence that ELT-2 plays a central role in most aspects of C. elegans intestinal physiology: establishing the structure of the enterocyte, regulating enzymes and transporters involved in digestion and nutrition, responding to environmental toxins and pathogenic infections, and regulating the downstream intestinal components of the daf-2/daf-16 pathway influencing aging and longevity.
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Affiliation(s)
- James D McGhee
- Department of Biochemistry and Molecular Biology, Department of Medical Genetics, Genes and Development Research Group, University of Calgary, Calgary, Alberta, Canada T2N 4N1.
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glo-3, a novel Caenorhabditis elegans gene, is required for lysosome-related organelle biogenesis. Genetics 2008; 180:857-71. [PMID: 18780725 DOI: 10.1534/genetics.108.093534] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Gut granules are specialized lysosome-related organelles that act as sites of fat storage in Caenorhabditis elegans intestinal cells. We identified mutations in a gene, glo-3, that functions in the formation of embryonic gut granules. Some glo-3(-) alleles displayed a complete loss of embryonic gut granules, while other glo-3(-) alleles had reduced numbers of gut granules. A subset of glo-3 alleles led to mislocalization of gut granule contents into the intestinal lumen, consistent with a defect in intracellular trafficking. glo-3(-) embryos lacking gut granules developed into adults containing gut granules, indicating that glo-3(+) function may be differentially required during development. We find that glo-3(+) acts in parallel with or downstream of the AP-3 complex and the PGP-2 ABC transporter in gut granule biogenesis. glo-3 encodes a predicted membrane-associated protein that lacks obvious sequence homologs outside of nematodes. glo-3 expression initiates in embryonic intestinal precursors and persists almost exclusively in intestinal cells through adulthood. GLO-3GFP localizes to the gut granule membrane, suggesting it could play a direct role in the trafficking events at the gut granule. smg-1(-) suppression of glo-3(-) nonsense alleles indicates that the C-terminal half of GLO-3, predicted to be present in the cytoplasm, is not necessary for gut granule formation. Our studies identify GLO-3 as a novel player in the formation of lysosome-related organelles.
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Bao Z, Zhao Z, Boyle TJ, Murray JI, Waterston RH. Control of cell cycle timing during C. elegans embryogenesis. Dev Biol 2008; 318:65-72. [PMID: 18430415 PMCID: PMC2442716 DOI: 10.1016/j.ydbio.2008.02.054] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 02/10/2008] [Accepted: 02/29/2008] [Indexed: 01/08/2023]
Abstract
As a fundamental process of development, cell proliferation must be coordinated with other processes such as fate differentiation. Through statistical analysis of individual cell cycle lengths of the first 8 out of 10 rounds of embryonic cell division in Caenorhabditis elegans, we identified synchronous and invariantly ordered divisions that are tightly associated with fate differentiation. Our results suggest a three-tier model for fate control of cell cycle pace: the primary control of cell cycle pace is established by lineage and the founder cell fate, then fine-tuned by tissue and organ differentiation within each lineage, then further modified by individualization of cells as they acquire unique morphological and physiological roles in the variant body plan. We then set out to identify the pace-setting mechanisms in different fates. Our results suggest that ubiquitin-mediated degradation of CDC-25.1 is a rate-determining step for the E (gut) and P(3) (muscle and germline) lineages but not others, even though CDC-25.1 and its apparent decay have been detected in all lineages. Our results demonstrate the power of C. elegans embryogenesis as a model to dissect the interaction between differentiation and proliferation, and an effective approach combining genetic and statistical analysis at single-cell resolution.
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Affiliation(s)
- Zhirong Bao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Anokye-Danso F, Anyanful A, Sakube Y, Kagawa H. Transcription factors GATA/ELT-2 and forkhead/HNF-3/PHA-4 regulate the tropomyosin gene expression in the pharynx and intestine of Caenorhabditis elegans. J Mol Biol 2007; 379:201-11. [PMID: 18448117 DOI: 10.1016/j.jmb.2007.11.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Revised: 11/27/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
Abstract
Gene regulation during development is an important biological activity that leads to synthesis of biomolecules at specific locations and specific times. The single tropomyosin gene of Caenorhabditis elegans, tmy-1/lev-11, produces four isoforms of protein: two from the external promoter and two from the internal promoter. We investigated the internal promoter of tropomyosin to identify sequences that regulate expression of tmy-1 in the pharynx and intestine. By promoter deletion of tmy-1 reporters as well as by database analyses, a 100-bp fragment that contained binding sequences for a GATA factor, for a chicken CdxA homolog, and for a forkhead factor was identified. Both the forkhead and CdxA binding sequences contributed to pharyngeal and intestinal expression. In addition, the GATA site also influenced intestinal expression of tmy-1 reporter. We showed that ELT-2 and PHA-4 proteins interact directly with the GATA and forkhead binding sequences, respectively, in gel mobility shift assays. RNA interference knockdown of elt-2 diminished tmy-1::gfp expression in the intestine. In contrast to RNA interference knockdown of pha-4, expression of tmy-1::gfp in pha-4;smg-1 mutants was slightly weaker than that of the wild type. Ectopic expression of PHA-4 and ELT-2 by heat shock was sufficient to elicit widespread expression of tmy-1::lacZ reporter in embryos. We found no indication of a synergistic relation between ELT-2 and PHA-4. Based on our data, PHA-4 and CdxA function as general transcription factors for pharyngeal and intestinal regulation of tmy-1. We present models by which ELT-2, PHA-4, and CdxA orchestrate expression from the internal promoter of tmy-1.
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Affiliation(s)
- Frederick Anokye-Danso
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
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35
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Romney SJ, Thacker C, Leibold EA. An iron enhancer element in the FTN-1 gene directs iron-dependent expression in Caenorhabditis elegans intestine. J Biol Chem 2007; 283:716-25. [PMID: 18024960 DOI: 10.1074/jbc.m707043200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ferritin is a ubiquitous protein that sequesters iron and protects cells from iron toxicity. Caenorhabditis elegans express two ferritins, FTN-1 and FTN-2, which are transcriptionally regulated by iron. To identify the cis-acting sequences and proteins required for iron-dependent regulation of ftn-1 and ftn-2 expression, we generated transcriptional GFP reporters corresponding to 5 '-upstream sequences of the ftn-1 and ftn-2 genes. We identified a conserved 63-bp sequence, the iron-dependent element (IDE), that is required for iron-dependent regulation of a ftn-1 GFP reporter in intestine. The IDE contains two GATA-binding motifs and three octameric direct repeats. Site-directed mutagenesis of the GATA sequences, singly or in combination, reduces ftn-1 GFP reporter expression in the intestine. In vitro DNA mobility shift assays show that the intestine-specific GATA protein ELT-2 binds to both GATA sequences. Inhibition of ELT-2 function by RNA interference blocks ftn-1 GFP reporter expression in vivo. Insertion of the IDE into the promoter region of a heterologous reporter activates iron-dependent transcription in intestine. These data demonstrate that the activation of ftn-1 and ftn-2 transcription by iron requires ELT-2 and that the IDE functions as an iron-dependent enhancer in intestine.
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Affiliation(s)
- S Joshua Romney
- Eccles Program in Human Molecular Biology and Genetics, University of Utah, Salt Lake City 84112, USA
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Neves A, English K, Priess JR. Notch-GATA synergy promotes endoderm-specific expression of ref-1 in C. elegans. Development 2007; 134:4459-68. [PMID: 18003741 DOI: 10.1242/dev.008680] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Notch signaling pathway is involved in a wide variety of cell-fate decisions during development. The diverse behavior of Notch-activated cells is thought to depend on tissue- or cell-type-specific transcription factors, yet the identities of such factors and the mechanism of cooperation with the Notch pathway are largely unknown. We identify here an enhancer in the promoter of ref-1, a C. elegans Notch target, which promotes Notch-dependent expression in mesodermal and endodermal cells. The enhancer contains predicted binding sites for the Notch transcriptional effector LAG-1/CSL that are essential for expression, a non-CSL site required for mesodermal expression, and four predicted binding sites for GATA transcription factors that are required for endodermal expression. We show that endodermal expression involves the GATA transcription factor ELT-2, and that ELT-2 can bind LAG-1/CSL in vitro. In many types of Notch-activated embryonic cells, ectopic ELT-2 is sufficient to drive expression of reporters containing the enhancer.
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Affiliation(s)
- Alexandre Neves
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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37
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Burmeister C, Lüersen K, Heinick A, Hussein A, Domagalski M, Walter RD, Liebau E. Oxidative stress in Caenorhabditis elegans: protective effects of the Omega class glutathione transferase (GSTO-1). FASEB J 2007; 22:343-54. [PMID: 17901115 DOI: 10.1096/fj.06-7426com] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To elucidate the function of Omega class glutathione transferases (GSTs) (EC 2.5.1.18) in multicellular organisms, the GSTO-1 from Caenorhabditis elegans (GSTO-1; C29E4.7) was investigated. Disc diffusion assays using Escherichia coli overexpressing GSTO-1 provided a test of resistance to long-term exposure under oxidative stress. After affinity purification, the recombinant GSTO-1 had minimal catalytic activity toward classic GST substrates but displayed significant thiol oxidoreductase and dehydroascorbate reductase activity. Microinjection of the GSTO-1-promoter green fluorescent protein construct and immunolocalization by electron microscopy localized the protein exclusively in the intestine of all postembryonic stages of C. elegans. Deletion analysis identified an approximately 300-nucleotide sequence upstream of the ATG start site necessary for GSTO-1 expression. Site-specific mutagenesis of a GATA transcription factor binding motif in the minimal promoter led to the loss of reporter expression. Similarly, RNA interference (RNAi) of Elt-2 indicated the involvement of this gut-specific transcription factor in GSTO-1 expression. Transcriptional up-regulation under stress conditions of GSTO-1 was confirmed by analyzing promoter-reporter constructs in transgenic C. elegans strains. To investigate the function of GSTO-1 in vivo, transgenic animals overexpressing GSTO-1 were generated exhibiting an increased resistance to juglone-, paraquat-, and cumene hydroperoxide-induced oxidative stress. Specific silencing of the GSTO-1 by RNAi created worms with an increased sensitivity to several prooxidants, arsenite, and heat shock. We conclude that the stress-responsive GSTO-1 plays a key role in counteracting environmental stress.
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Affiliation(s)
- Cora Burmeister
- Institute for Animal Physiology, University of Muenster, Hindenburgplatz 55, Muenster 48143, Germany
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38
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Huang S, Shetty P, Robertson SM, Lin R. Binary cell fate specification duringC. elegansembryogenesis driven by reiterated reciprocal asymmetry of TCF POP-1 and its coactivatorβ-catenin SYS-1. Development 2007; 134:2685-95. [PMID: 17567664 DOI: 10.1242/dev.008268] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
C. elegans embryos exhibit an invariant lineage comprised primarily of a stepwise binary diversification of anterior-posterior (A-P)blastomere identities. This binary cell fate specification requires input from both the Wnt and MAP kinase signaling pathways. The nuclear level of the TCF protein POP-1 is lowered in all posterior cells. We show here that theβ-catenin SYS-1 also exhibits reiterated asymmetry throughout multiple A-P divisions and that this asymmetry is reciprocal to that of POP-1. Furthermore, we show that SYS-1 functions as a coactivator for POP-1, and that the SYS-1-to-POP-1 ratio appears critical for both the anterior and posterior cell fates. A high ratio drives posterior cell fates, whereas a low ratio drives anterior cell fates. We show that the SYS-1 and POP-1 asymmetries are regulated independently, each by a subset of genes in the Wnt/MAP kinase pathways. We propose that two genetic pathways, one increasing SYS-1 and the other decreasing POP-1 levels, robustly elevate the SYS-1-to-POP-1 ratio in the posterior cell, thereby driving A-P differential cell fates.
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Affiliation(s)
- Shuyi Huang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
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Okumura T, Tajiri R, Kojima T, Saigo K, Murakami R. GATAe-dependent and -independent expressions of genes in the differentiated endodermal midgut of Drosophila. Gene Expr Patterns 2007; 7:178-86. [PMID: 16914392 DOI: 10.1016/j.modgep.2006.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 07/05/2006] [Accepted: 07/07/2006] [Indexed: 11/24/2022]
Abstract
Two sequentially-expressed GATA factor genes, serpent (srp) and GATAe, are essential for development of the Drosophila endoderm. The earliest endodermal GATA gene, srp, has been thought to specify the endodermal fate, activating the second GATA gene GATAe, and the latter continues to be expressed in the endodermal midgut throughout life. Previously, we proposed that GATAe establishes and maintains the state of terminal differentiation of the midgut, since some functional genes in the midgut require GATAe activity for their expression. To obtain further evidence of the role of GATAe, we searched for additional genes that are expressed specifically in the midgut in late stages, and examined responses of a total of selected 15 genes to the depletion and overexpression of GATAe. Ten of the 15 genes failed to be expressed in the embryo deficient for GATAe activity, but, the other five genes did not require GATAe. Instead, srp is required for activating the five genes. These observations indicate that GATAe activates a major subset of genes in the midgut, and some other pathway(s) downstream of srp activates other genes.
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Affiliation(s)
- Takashi Okumura
- Department of Biology and Chemistry, Yamaguchi University, Yoshida 1677-1, Yamaguchi 753-8512, Japan
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Kerry S, TeKippe M, Gaddis NC, Aballay A. GATA transcription factor required for immunity to bacterial and fungal pathogens. PLoS One 2006; 1:e77. [PMID: 17183709 PMCID: PMC1762309 DOI: 10.1371/journal.pone.0000077] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Accepted: 11/12/2006] [Indexed: 12/20/2022] Open
Abstract
In the past decade, Caenorhabditis elegans has been used to dissect several genetic pathways involved in immunity; however, little is known about transcription factors that regulate the expression of immune effectors. C. elegans does not appear to have a functional homolog of the key immune transcription factor NF-κB. Here we show that that the intestinal GATA transcription factor ELT-2 is required for both immunity to Salmonella enterica and expression of a C-type lectin gene, clec-67, which is expressed in the intestinal cells and is a good marker of S. enterica infection. We also found that ELT-2 is required for immunity to Pseudomonas aeruginosa, Enterococcus faecalis, and Cryptococcus neoformans. Lack of immune inhibition by DAF-2, which negatively regulates the FOXO transcription factor DAF-16, rescues the hypersusceptibility to pathogens phenotype of elt-2(RNAi) animals. Our results indicate that ELT-2 is part of a multi-pathogen defense pathway that regulates innate immunity independently of the DAF-2/DAF-16 signaling pathway.
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Captan VV, Goszczynski B, McGhee JD. Neither maternal nor zygotic med-1/med-2 genes play a major role in specifying the Caenorhabditis elegans endoderm. Genetics 2006; 175:969-74. [PMID: 17151237 PMCID: PMC1800632 DOI: 10.1534/genetics.106.066662] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The med-1 and med-2 genes encode small, highly similar proteins related to GATA-type transcription factors and have been proposed as necessary for specification of both the mesoderm and the endoderm of Caenorhabditis elegans. However, we have previously presented evidence that neither maternal nor zygotic expression of the med-1/2 genes is necessary to specify the C. elegans endoderm. Contradicting our conclusions, a recent report presented evidence, based on presumed transgene-induced cosuppression, that the med-1/2 genes do indeed show an endoderm-specifying maternal effect. In this article, we reinvestigate med-2(-); med-1(-) embryos using a med-2- specific null allele instead of the chromosomal deficiences used previously and confirm our previous results: the large majority (approximately 84%) of med-2(-); med-1(-) embryos express gut granules. We also reinvestigate the possibility of a maternal med-1/2 effect by direct injection of med dsRNA into sensitized (med-deficient) hermaphrodites using the standard protocol known to be effective in ablating maternal transcripts, but again find no evidence for any significant maternal med-1/2 effect. We do, however, show that expression of gut granules in med-1/2-deficient embryos is exquisitely sensitive to RNAi against the vacuolar ATPase-encoding unc-32 gene [present on the same multicopy med-1(+)-containing transgenic balancer used in support of the maternal med-1/2 effect]. We thus suggest that the experimental evidence for a maternal med-1/2 effect should be reexamined and may instead reflect cosuppression caused by multiple transgenic unc-32 sequences, not med sequences.
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Affiliation(s)
- Vasile V Captan
- Department of Biochemistry and Molecular Biology, Genes and Development Research Group, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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Abstract
The endomesoderm gene regulatory network (GRN) of C. elegans is a rich resource for studying the properties of cell-fate-specification pathways. This GRN contains both cell-autonomous and cell non-autonomous mechanisms, includes network motifs found in other GRNs, and ties maternal factors to terminal differentiation genes through a regulatory cascade. In most cases, upstream regulators and their direct downstream targets are known. With the availability of resources to study close and distant relatives of C. elegans, the molecular evolution of this network can now be examined. Within Caenorhabditis, components of the endomesoderm GRN are well conserved. A cursory examination of the preliminary genome sequences of two parasitic nematodes, Haemonchus contortus and Brugia malayi, suggests that evolution in this GRN is occurring most rapidly for the zygotic genes that specify blastomere identity.
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Affiliation(s)
- Morris F Maduro
- Department of Biology, University of California, Riverside, Riverside, CA 92521, USA.
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McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol 2006; 302:627-45. [PMID: 17113066 DOI: 10.1016/j.ydbio.2006.10.024] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/08/2006] [Accepted: 10/14/2006] [Indexed: 12/18/2022]
Abstract
A SAGE library was prepared from hand-dissected intestines from adult Caenorhabditis elegans, allowing the identification of >4000 intestinally-expressed genes; this gene inventory provides fundamental information for understanding intestine function, structure and development. Intestinally-expressed genes fall into two broad classes: widely-expressed "housekeeping" genes and genes that are either intestine-specific or significantly intestine-enriched. Within this latter class of genes, we identified a subset of highly-expressed highly-validated genes that are expressed either exclusively or primarily in the intestine. Over half of the encoded proteins are candidates for secretion into the intestinal lumen to hydrolyze the bacterial food (e.g. lysozymes, amoebapores, lipases and especially proteases). The promoters of this subset of intestine-specific/intestine-enriched genes were analyzed computationally, using both a word-counting method (RSAT oligo-analysis) and a method based on Gibbs sampling (MotifSampler). Both methods returned the same over-represented site, namely an extended GATA-related sequence of the general form AHTGATAARR, which agrees with experimentally determined cis-acting control sequences found in intestine genes over the past 20 years. All promoters in the subset contain such a site, compared to <5% for control promoters; moreover, our analysis suggests that the majority (perhaps all) of genes expressed exclusively or primarily in the worm intestine are likely to contain such a site in their promoters. There are three zinc-finger GATA-type factors that are candidates to bind this extended GATA site in the differentiating C. elegans intestine: ELT-2, ELT-4 and ELT-7. All evidence points to ELT-2 being the most important of the three. We show that worms in which both the elt-4 and the elt-7 genes have been deleted from the genome are essentially wildtype, demonstrating that ELT-2 provides all essential GATA-factor functions in the intestine. The SAGE analysis also identifies more than a hundred other transcription factors in the adult intestine but few show an RNAi-induced loss-of-function phenotype and none (other than ELT-2) show a phenotype primarily in the intestine. We thus propose a simple model in which the ELT-2 GATA factor directly participates in the transcription of all intestine-specific/intestine-enriched genes, from the early embryo through to the dying adult. Other intestinal transcription factors would thus modulate the action of ELT-2, depending on the worm's nutritional and physiological needs.
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Affiliation(s)
- James D McGhee
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, Canada T2N 4N1.
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44
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Kormish JD, McGhee JD. The C. elegans lethal gut-obstructed gob-1 gene is trehalose-6-phosphate phosphatase. Dev Biol 2005; 287:35-47. [PMID: 16197937 DOI: 10.1016/j.ydbio.2005.08.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 08/18/2005] [Accepted: 08/18/2005] [Indexed: 11/25/2022]
Abstract
We identified the gob-1 (gut-obstructed) gene in a forward genetic screen for intestinal defects in the nematode Caenorhabditis elegans. gob-1 loss of function results in early larval lethality, at least in part because of a blocked intestinal lumen and consequent starvation. The gob-1 gene is first expressed in the 8E cell stage of the embryonic intestine, and the GATA factor ELT-2 is sufficient but not necessary for this early phase of gob-1 expression; gob-1 expression later becomes widespread in embryos, larvae, and adults. GOB-1 is a member of the HAD-like hydrolase superfamily and shows a robust and specific phosphatase activity for the substrate trehalose-6-phosphate. Trehalose is a glucose disaccharide found in bacteria, fungi, plants, insects, and nematodes but not in mammals. Trehalose plays a number of critical roles such as providing flexible energy reserves and contributing to thermal and osmotic stress resistance. In budding yeast and in plants, the intermediate in trehalose synthesis, trehalose-6-phosphate, has additional critical but less well-defined roles in controlling glycolysis and carbohydrate metabolism. Strong loss-of-function mutants in the C. elegans tps-1 and tps-2 genes (which encode the two trehalose phosphate synthases responsible for trehalose-6-phosphate synthesis) completely suppress the lethality associated with gob-1 loss of function. The suppression of gob-1 lethality by ablation of TPS-1 and TPS-2, the upstream enzymes in the trehalose synthesis pathway, suggests that gob-1 lethality results from a toxic build-up of the intermediate trehalose-6-phosphate, not from an absence of trehalose. GOB-1 is the first trehalose-6-phosphate phosphatase to be identified in nematodes and, because of its associated lethality and distinctive sequence properties, provides a new and attractive target for anti-parasitic drugs.
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Affiliation(s)
- Jay D Kormish
- Department of Biochemistry and Molecular Biology, Genes and Development Research Group, University of Calgary Faculty of Medicine, Health Sciences Centre, Calgary, Alberta, Canada T2N 4N1
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Goszczynski B, McGhee JD. Reevaluation of the role of the med-1 and med-2 genes in specifying the Caenorhabditis elegans endoderm. Genetics 2005; 171:545-55. [PMID: 15998721 PMCID: PMC1456770 DOI: 10.1534/genetics.105.044909] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The med-1 and med-2 genes encode a pair of essentially identical GATA factor-related transcription factors that have been proposed to be necessary for specification of the C. elegans endoderm (intestine or E lineage) as well as part of the C. elegans mesoderm. med-1 and med-2 are proposed to be the direct downstream targets and the principal effectors of the maternally provided SKN-1 transcription factor; med-1 and med-2 would thus occupy the pivotal interface between maternal and zygotic control of gene expression. The conclusion that med-1 and med-2 are necessary for C. elegans endoderm specification was based on a partially penetrant (approximately 50%) loss of endoderm markers produced by RNA-mediated interference (RNAi). To determine whether this partial penetrance reflects: (i) inefficient RNAi against early zygotic transcripts, (ii) experimental uncertainty in the expected level of endoderm loss in skn-1 nulls, or (iii) additional redundancy in the pathway of endoderm specification, we constructed worm strains that segregate embryos lacking both the med-1 gene (because of a gene-specific deletion) and the med-2 gene (using either of two chromosomal deficiencies). Contrary to expectations, we observe that only approximately 3-20% of med-2(-); med-1(-) embryos do not express markers of endoderm differentiation. Furthermore, we found no evidence for a maternal contribution of the med genes to endoderm specification. We conclude that the major pathway(s) for endoderm specification in C. elegans must be independent of the med-1 and med-2 genes.
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Affiliation(s)
- Barbara Goszczynski
- Department of Biochemistry and Molecular Biology, Genes and Development Research Group, University of Calgary, Alberta, Canada
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Oskouian B, Mendel J, Shocron E, Lee MA, Fyrst H, Saba JD. Regulation of sphingosine-1-phosphate lyase gene expression by members of the GATA family of transcription factors. J Biol Chem 2005; 280:18403-10. [PMID: 15734735 DOI: 10.1074/jbc.m410928200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sphingosine-1-phosphate is a bioactive sphingolipid that regulates proliferation, differentiation, migration, and apoptosis. Sphingosine-1-phosphate is irreversibly degraded by the highly conserved enzyme sphingosine-1-phosphate lyase. Recent studies have suggested that sphingosine-1-phosphate lyase expression affects animal development and cell fate decisions. Despite its crucial role, mechanisms affecting expression of sphingosine-1-phosphate lyase remain poorly understood. In this study, regulation of sphingosine-1-phosphate lyase gene expression was investigated in Caenorhabditis elegans, where lyase expression is spatially restricted to cells of the developing and adult gut and is essential for normal development. Deletion analysis and generation of transgenic worms combined with fluorescence microscopy identified a 350-nucleotide sequence upstream of the ATG start site necessary for maximal lyase expression in adult worms. Site-specific mutagenesis of a GATA transcription factor-binding motif in the promoter led to loss of reporter expression. Knockdown of the gut-specific GATA transcription factor ELT-2 by RNA interference similarly led to loss of reporter expression. ELT-2 interacted with the GATA factor-binding motif in vitro and was also capable of driving expression of a Caenorhabditis elegans lyase promoter-beta-galactosidase reporter in a heterologous yeast system. These studies demonstrate that ELT-2 regulates sphingosine-1-phosphate lyase expression in vivo. Additionally, we demonstrate that the human sphingosine-1-phosphate lyase gene is regulated by a GATA transcription factor. Overexpression of GATA-4 led to both an increase in activity of a reporter gene as well as an increase in endogenous sphingosine-1-phosphate lyase protein.
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Affiliation(s)
- Babak Oskouian
- Children's Hospital Oakland Research Institute, Oakland, California 94609-1673 and California Institute of Technology, Division of Biology, Pasadena, California 91125, USA
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