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Aguoru NA, Kirk RS, Walker AJ. Molecular insights into the heat shock proteins of the human parasitic blood fluke Schistosoma mansoni. Parasit Vectors 2022; 15:365. [PMID: 36229862 PMCID: PMC9559072 DOI: 10.1186/s13071-022-05500-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022] Open
Abstract
Background Heat shock proteins (HSPs) are evolutionarily conserved proteins, produced by cells in response to hostile environmental conditions, that are vital to organism homeostasis. Here, we undertook the first detailed molecular bioinformatic analysis of these important proteins and mapped their tissue expression in the human parasitic blood fluke, Schistosoma mansoni, one of the causative agents of the neglected tropical disease human schistosomiasis. Methods Using bioinformatic tools we classified and phylogenetically analysed HSP family members in schistosomes, and performed transcriptomic, phosphoproteomic, and interactomic analysis of the S. mansoni HSPs. In addition, S. mansoni HSP protein expression was mapped in intact parasites using immunofluorescence. Results Fifty-five HSPs were identified in S. mansoni across five HSP families; high conservation of HSP sequences were apparent across S. mansoni, Schistosoma haematobium and Schistosoma japonicum, with S. haematobium HSPs showing greater similarity to S. mansoni than those of S. japonicum. For S. mansoni, differential HSP gene expression was evident across the various parasite life stages, supporting varying roles for the HSPs in the different stages, and suggesting that they might confer some degree of protection during life stage transitions. Protein expression patterns of HSPs were visualised in intact S. mansoni cercariae, 3 h and 24 h somules, and adult male and female worms, revealing HSPs in the tegument, cephalic ganglia, tubercles, testes, ovaries as well as other important organs. Analysis of putative HSP protein-protein associations highlighted proteins that are involved in transcription, modification, stability, and ubiquitination; functional enrichment analysis revealed functions for HSP networks in S. mansoni including protein export for HSP 40/70, and FOXO/mTOR signalling for HSP90 networks. Finally, a total of 76 phosphorylation sites were discovered within 17 of the 55 HSPs, with 30 phosphorylation sites being conserved with those of human HSPs, highlighting their likely core functional significance. Conclusions This analysis highlights the fascinating biology of S. mansoni HSPs and their likely importance to schistosome function, offering a valuable and novel framework for future physiological investigations into the roles of HSPs in schistosomes, particularly in the context of survival in the host and with the aim of developing novel anti-schistosome therapeutics. Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05500-7.
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Affiliation(s)
- Nancy A Aguoru
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, Surrey, UK
| | - Ruth S Kirk
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, Surrey, UK
| | - Anthony J Walker
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, Surrey, UK.
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2
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Djhsp60 Is Required for Planarian Regeneration and Homeostasis. Biomolecules 2022; 12:biom12060808. [PMID: 35740934 PMCID: PMC9221281 DOI: 10.3390/biom12060808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
HSP60, a well-known mitochondrial chaperone, is essential for mitochondrial homeostasis. HSP60 deficiency causes dysfunction of the mitochondria and is lethal to animal survival. Here, we used freshwater planarian as a model system to investigate and uncover the roles of HSP60 in tissue regeneration and homeostasis. HSP60 protein is present in all types of cells in planarians, but it is relatively rich in stem cells and head neural cells. Knockdown of HSP60 by RNAi causes head regression and the loss of regenerating abilities, which is related to decrease in mitotic cells and inhibition of stem cell-related genes. RNAi-HSP60 disrupts the structure of the mitochondria and inhibits the mitochondrial-related genes, which mainly occur in intestinal tissues. RNAi-HSP60 also damages the integrity of intestinal tissues and downregulates intestine-expressed genes. More interestingly, RNAi-HSP60 upregulates the expression of the cathepsin L-like gene, which may be the reason for head regression and necrotic-like cell death. Taking these points together, we propose a model illustrating the relationship between neoblasts and intestinal cells, and also highlight the essential role of the intestinal system in planarian regeneration and tissue homeostasis.
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3
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Allen JM, Balagtas M, Barajas E, Cano Macip C, Alvarez Zepeda S, Iberkleid I, Duncan EM, Zayas RM. RNAi Screen of RING/U-Box Domain Ubiquitin Ligases Identifies Critical Regulators of Tissue Regeneration in Planarians. Front Cell Dev Biol 2022; 9:803419. [PMID: 35127720 PMCID: PMC8807557 DOI: 10.3389/fcell.2021.803419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 11/30/2022] Open
Abstract
Regenerative processes depend on the interpretation of signals to coordinate cell behaviors. The role of ubiquitin-mediated signaling is known to be important in many cellular and biological contexts, but its role in regeneration is not well understood. To investigate how ubiquitylation impacts tissue regeneration in vivo, we are studying planarians that are capable of regenerating after nearly any injury using a population of stem cells. Here we used RNAi to screen RING/U-box E3 ubiquitin ligases that are highly expressed in planarian stem cells and stem cell progeny. RNAi screening identified nine genes with functions in regeneration, including the spliceosomal factor prpf19 and histone modifier rnf2; based on their known roles in developmental processes, we further investigated these two genes. We found that prpf19 was required for animal survival but not for stem cell maintenance, suggesting a role in promoting cell differentiation. Because RNF2 is the catalytic subunit of the Polycomb Repressive Complex 1 (PRC1), we also examined other putative members of this complex (CBX and PHC). We observed a striking phenotype of regional tissue misspecification in cbx and phc RNAi planarians. To identify genes regulated by PRC1, we performed RNA-seq after knocking down rnf2 or phc. Although these proteins are predicted to function in the same complex, we found that the set of genes differentially expressed in rnf2 versus phc RNAi were largely non-overlapping. Using in situ hybridization, we showed that rnf2 regulates gene expression levels within a tissue type, whereas phc is necessary for the spatial restriction of gene expression, findings consistent with their respective in vivo phenotypes. This work not only uncovered roles for RING/U-box E3 ligases in stem cell regulation and regeneration, but also identified differential gene targets for two putative PRC1 factors required for maintaining cell-type-specific gene expression in planarians.
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Affiliation(s)
- John M Allen
- Department of Biology, San Diego State University, San Diego, CA, United States
- Deparment of Biology, University of Kentucky, Lexington, KY, United States
| | - Madison Balagtas
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Elizabeth Barajas
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Carolina Cano Macip
- Department of Biology, San Diego State University, San Diego, CA, United States
| | | | - Ionit Iberkleid
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Elizabeth M Duncan
- Deparment of Biology, University of Kentucky, Lexington, KY, United States
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA, United States
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4
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Gutiérrez-Gutiérrez Ó, Felix DA, Salvetti A, Amro EM, Thems A, Pietsch S, Koeberle A, Rudolph KL, González-Estévez C. Regeneration in starved planarians depends on TRiC/CCT subunits modulating the unfolded protein response. EMBO Rep 2021; 22:e52905. [PMID: 34190393 PMCID: PMC8344900 DOI: 10.15252/embr.202152905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/15/2021] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
Planarians are able to stand long periods of starvation by maintaining adult stem cell pools and regenerative capacity. The molecular pathways that are needed for the maintenance of regeneration during starvation are not known. Here, we show that down‐regulation of chaperonin TRiC/CCT subunits abrogates the regeneration capacity of planarians during starvation, but TRiC/CCT subunits are dispensable for regeneration in fed planarians. Under starvation, they are required to maintain mitotic fidelity and for blastema formation. We show that TRiC subunits modulate the unfolded protein response (UPR) and are required to maintain ATP levels in starved planarians. Regenerative defects in starved CCT‐depleted planarians can be rescued by either chemical induction of mild endoplasmic reticulum stress, which leads to induction of the UPR, or by the supplementation of fatty acids. Together, these results indicate that CCT‐dependent UPR induction promotes regeneration of planarians under food restriction.
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Affiliation(s)
| | - Daniel A Felix
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Elias M Amro
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Anne Thems
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Stefan Pietsch
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Andreas Koeberle
- Chair of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany.,Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - K Lenhard Rudolph
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
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5
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Wang C, Yang ZZ, Guo FH, Shi S, Han XS, Zeng A, Lin H, Jing Q. Heat shock protein DNAJA1 stabilizes PIWI proteins to support regeneration and homeostasis of planarian Schmidtea mediterranea. J Biol Chem 2019; 294:9873-9887. [PMID: 31076507 DOI: 10.1074/jbc.ra118.004445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 04/25/2019] [Indexed: 12/16/2022] Open
Abstract
PIWI proteins are key regulators of germline and somatic stem cells throughout different evolutionary lineages. However, how PIWI proteins themselves are regulated remains largely unknown. To identify candidate proteins that interact with PIWI proteins and regulate their stability, here we established a yeast two-hybrid (Y2H) assay in the planarian species Schmidtea mediterranea We show that DNAJA1, a heat shock protein 40 family member, interacts with the PIWI protein SMEDWI-2, as validated by the Y2H screen and co-immunoprecipitation assays. We found that DNAJA1 is enriched in planarian adult stem cells, the nervous system, and intestinal tissues. DNAJA1-knockdown abolished planarian regeneration and homeostasis, compromised stem cell maintenance and PIWI-interacting RNA (piRNA) biogenesis, and deregulated SMEDWI-1/2 target genes. Mechanistically, we observed that DNAJA1 is required for the stability of SMEDWI-1 and SMEDWI-2 proteins. Furthermore, we noted that human DNAJA1 binds to Piwi-like RNA-mediated gene silencing 1 (PIWIL1) and is required for PIWIL1 stability in human gastric cancer cells. In summary, our results reveal not only an evolutionarily conserved functional link between PIWI and DNAJA1 that is essential for PIWI protein stability and piRNA biogenesis, but also an important role of DNAJA1 in the control of proteins involved in stem cell regulation.
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Affiliation(s)
- Chen Wang
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Zhen-Zhen Yang
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Fang-Hao Guo
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Shuo Shi
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Shuai Han
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - An Zeng
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
| | - Haifan Lin
- From the Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China, .,the Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06511
| | - Qing Jing
- the CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China, and
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6
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De Miguel-Bonet MDM, Ahad S, Hartenstein V. Role of neoblasts in the patterned postembryonic growth of the platyhelminth Macrostomum lignano. NEUROGENESIS 2018; 5:e14699441-e14699449. [PMID: 30083565 DOI: 10.1080/23262133.2018.1469944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 03/29/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
Neoblasts are motile pluripotent stem cells unique to the flatworm phyla Platyhelminthes and Acoela. The role of neoblasts in tissue regeneration has received much attention in recent studies. Here we review data pertinent to the structure and embryonic origin of these stem cells, and their participation in normal cell turnover. Next, we present data proving that neoblasts also account for the addition of cells during postembryonic growth. Bromodeoxyuridine (BrdU) pulse chase experiments demonstrate that the incorporation of neoblast-derived cells into the different tissues of the juvenile worm follows a stereotyped pattern, whereby cells within the parenchymal layer (muscle, gland) incorporate new cells most rapidly, followed by the epidermal domain surrounding the mouth, dorsal epidermis, and, lastly, the nervous system.
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Affiliation(s)
| | - Sally Ahad
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
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7
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Felix DA, Gutiérrez-Gutiérrez Ó, Espada L, Thems A, González-Estévez C. It is not all about regeneration: Planarians striking power to stand starvation. Semin Cell Dev Biol 2018; 87:169-181. [PMID: 29705301 DOI: 10.1016/j.semcdb.2018.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/11/2018] [Accepted: 04/25/2018] [Indexed: 12/12/2022]
Abstract
All living forms, prokaryotes as eukaryotes, have some means of adaptation to food scarcity, which extends the survival chances under extreme environmental conditions. Nowadays we know that dietary interventions, including fasting, extends lifespan of many organisms and can also protect against age-related diseases including in humans. Therefore, the capacity of adapting to periods of food scarcity may have evolved billions of years ago not only to allow immediate organismal survival but also to be able to extend organismal lifespan or at least to lead to a healthier remaining lifespan. Planarians have been the center of attention since more than two centuries because of their astonishing power of full body regeneration that relies on a large amount of adult stem cells or neoblasts. However, they also present an often-overlooked characteristic. They are able to stand long time starvation. Planarians have adapted to periods of fasting by shrinking or degrowing. Here we will review the published data about starvation in planarians and conclude with the possibility of starvation being one of the processes that rejuvenate the planarian, thus explaining the historical notion of non-ageing planarians.
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Affiliation(s)
- Daniel A Felix
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Óscar Gutiérrez-Gutiérrez
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Lilia Espada
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Anne Thems
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Cristina González-Estévez
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
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8
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Insight into stem cell regulation from sub-lethally irradiated worms. Gene 2018; 662:37-45. [PMID: 29627527 DOI: 10.1016/j.gene.2018.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/24/2018] [Accepted: 04/05/2018] [Indexed: 12/30/2022]
Abstract
Despite the significant advances in the comprehension of stem cell control network, the nature of extrinsic signals regulating their dynamic remains to be understood. In this paper, we take advantage of the stem cell repopulation process that follows low-dose X-ray treatment in planarians to identify genes, preferentially enriched in differentiated cells, whose expression is activated during the process. Genetic silencing of some of them impaired the stem cell repopulation, suggesting a tight extrinsic control of stem cell activity.
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9
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Ma K, Zhang H, Zhang Y, Song G, Wu M, Chen G. Identification of a HSP40 gene involved in planarian regeneration. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Guo Q, Zhao G, Ni J, Guo Y, Zhang Y, Tian Q, Zhang S. Down-regulate of Djrfc2 causes tissues hypertrophy during planarian regeneration. Biochem Biophys Res Commun 2017; 493:1224-1229. [DOI: 10.1016/j.bbrc.2017.09.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 09/07/2017] [Indexed: 01/13/2023]
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11
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Gutiérrez-Gutiérrez Ó, Felix DA, González-Estévez C. Planarian finds time(less) to fight infection. Virulence 2017; 8:1043-1048. [PMID: 28277898 DOI: 10.1080/21505594.2017.1300735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Daniel A Felix
- a Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) , Jena , Germany
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12
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Plusquin M, De Mulder K, Van Belleghem F, DeGheselle O, Pirotte N, Willems M, Cuypers A, Salvenmoser W, Ladurner P, Artois T, Smeets K. Toxic effects of cadmium on flatworm stem cell dynamics: A transcriptomic and ultrastructural elucidation of underlying mechanisms. ENVIRONMENTAL TOXICOLOGY 2016; 31:1217-1228. [PMID: 25846626 DOI: 10.1002/tox.22129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 02/06/2015] [Accepted: 02/15/2015] [Indexed: 06/04/2023]
Abstract
Stem cells or undifferentiated cells can cope more easily with external stresses. To evaluate the impact of toxic compounds on stem cell dynamics in vivo, in relation to other biological responses, we use the carcinogenic element cadmium and the regenerating model organism Macrostomum lignano. Through both BrdU and anti-histone H3 immunostainings, cadmium-induced effects were investigated at different stages of the stem cell cycle. A 24-h exposure to 100 and 250 μM CdCl2 significantly decreased the number of stem cells (neoblasts) in mitosis, whereas the number of cells in the S phase remained unchanged. After this short-term exposure, the ultrastructure of the neoblasts was minimally affected in contrast to the epidermal tissues. These results were supported by gene expression data: transcripts of cdc2 and pig3 were significantly upregulated during all treatments. Both genes are involved in the cell cycle progression and are transcribed in the gonadal region, where stem cells are highly represented. Based on a substantial increase in gene expression of heat shock proteins (HSP) and their high activity in the gonadal region, we hypothesize that these proteins are key players in the protection of stem cells against external stresses. Apart from the strong HSP induction, other protective processes including cell division, apoptosis and anti-oxidative defence, were also activated. We, therefore, conclude that the protection of stem cells against external stressors may be based on the interplay between stem cell maintenance, i.e. repair and recovery through division, on one hand and apoptosis on the other hand. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1217-1228, 2016.
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Affiliation(s)
- Michelle Plusquin
- Centre for Environmental Sciences, Department Biology, Hasselt University, Agoralaan, Diepenbeek, Belgium
| | - Katrien De Mulder
- Institute of Zoology, Center of Molecular Bioscience Innsbruck, University of Innsbruck, Innrain, Innsbruck, Austria
| | - Frank Van Belleghem
- Centre for Environmental Sciences, Department Biology, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Faculty of Management, Science and Technology, Open Universiteit, Valkenburgerweg 177, Heerlen, The Netherlands
| | - Olivier DeGheselle
- Centre for Environmental Sciences, Department Biology, Hasselt University, Agoralaan, Diepenbeek, Belgium
| | - Nicky Pirotte
- Centre for Environmental Sciences, Department Biology, Hasselt University, Agoralaan, Diepenbeek, Belgium
| | - Maxime Willems
- Pharmaceutical Technology, Ghent University, St. Pietersnieuwstraat, Gent, Belgium
| | - Ann Cuypers
- Centre for Environmental Sciences, Department Biology, Hasselt University, Agoralaan, Diepenbeek, Belgium
| | - Willi Salvenmoser
- Institute of Zoology, Center of Molecular Bioscience Innsbruck, University of Innsbruck, Innrain, Innsbruck, Austria
| | - Peter Ladurner
- Institute of Zoology, Center of Molecular Bioscience Innsbruck, University of Innsbruck, Innrain, Innsbruck, Austria
| | - Tom Artois
- Centre for Environmental Sciences, Department Biology, Hasselt University, Agoralaan, Diepenbeek, Belgium
| | - Karen Smeets
- Centre for Environmental Sciences, Department Biology, Hasselt University, Agoralaan, Diepenbeek, Belgium
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13
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Ong TH, Romanova EV, Roberts-Galbraith RH, Yang N, Zimmerman TA, Collins JJ, Lee JE, Kelleher NL, Newmark PA, Sweedler JV. Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea. J Biol Chem 2016; 291:8109-20. [PMID: 26884331 PMCID: PMC4825013 DOI: 10.1074/jbc.m115.709196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
Tissue regeneration is a complex process that involves a mosaic of molecules that vary spatially and temporally. Insights into the chemical signaling underlying this process can be achieved with a multiplex and untargeted chemical imaging method such as mass spectrometry imaging (MSI), which can enablede novostudies of nervous system regeneration. A combination of MSI and multivariate statistics was used to differentiate peptide dynamics in the freshwater planarian flatwormSchmidtea mediterraneaat different time points during cephalic ganglia regeneration. A protocol was developed to makeS. mediterraneatissues amenable for MSI. MS ion images of planarian tissue sections allow changes in peptides and unknown compounds to be followed as a function of cephalic ganglia regeneration. In conjunction with fluorescence imaging, our results suggest that even though the cephalic ganglia structure is visible after 6 days of regeneration, the original chemical composition of these regenerated structures is regained only after 12 days. Differences were observed in many peptides, such as those derived from secreted peptide 4 and EYE53-1. Peptidomic analysis further identified multiple peptides from various known prohormones, histone proteins, and DNA- and RNA-binding proteins as being associated with the regeneration process. Mass spectrometry data also facilitated the identification of a new prohormone, which we have named secreted peptide prohormone 20 (SPP-20), and is up-regulated during regeneration in planarians.
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Affiliation(s)
- Ta-Hsuan Ong
- From the Department of Chemistry, and the Beckman Institute
| | | | - Rachel H Roberts-Galbraith
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
| | - Ning Yang
- From the Department of Chemistry, and the Beckman Institute
| | | | - James J Collins
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
| | - Ji Eun Lee
- From the Department of Chemistry, and the Beckman Institute
| | - Neil L Kelleher
- the Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60611
| | - Phillip A Newmark
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
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14
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Geng X, Wang G, Qin Y, Zang X, Li P, Geng Z, Xue D, Dong Z, Ma K, Chen G, Xu C. iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians. PLoS One 2015; 10:e0132045. [PMID: 26131905 PMCID: PMC4488856 DOI: 10.1371/journal.pone.0132045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 06/09/2015] [Indexed: 02/07/2023] Open
Abstract
The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
| | - Gaiping Wang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Yanli Qin
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Pengfei Li
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Zhi Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Deming Xue
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Zimei Dong
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Kexue Ma
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Guangwen Chen
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
- * E-mail: (CSX); (GWC)
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
- * E-mail: (CSX); (GWC)
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15
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Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF. Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. BMC Genomics 2015; 16:361. [PMID: 25952370 PMCID: PMC4494696 DOI: 10.1186/s12864-015-1533-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/13/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking. RESULTS Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC. CONCLUSIONS DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.
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Affiliation(s)
- Gustavo Rodríguez-Esteban
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - Alejandro González-Sastre
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - José Ignacio Rojo-Laguna
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - Emili Saló
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - Josep F Abril
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
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16
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Henderson JM, Nisperos SV, Weeks J, Ghulam M, Marín I, Zayas RM. Identification of HECT E3 ubiquitin ligase family genes involved in stem cell regulation and regeneration in planarians. Dev Biol 2015; 404:21-34. [PMID: 25956527 DOI: 10.1016/j.ydbio.2015.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 03/14/2015] [Accepted: 04/27/2015] [Indexed: 12/28/2022]
Abstract
E3 ubiquitin ligases constitute a large family of enzymes that modify specific proteins by covalently attaching ubiquitin polypeptides. This post-translational modification can serve to regulate protein function or longevity. In spite of their importance in cell physiology, the biological roles of most ubiquitin ligases remain poorly understood. Here, we analyzed the function of the HECT domain family of E3 ubiquitin ligases in stem cell biology and tissue regeneration in planarians. Using bioinformatic searches, we identified 17 HECT E3 genes that are expressed in the Schmidtea mediterranea genome. Whole-mount in situ hybridization experiments showed that HECT genes were expressed in diverse tissues and most were expressed in the stem cell population (neoblasts) or in their progeny. To investigate the function of all HECT E3 ligases, we inhibited their expression using RNA interference (RNAi) and determined that orthologs of huwe1, wwp1, and trip12 had roles in tissue regeneration. We show that huwe1 RNAi knockdown led to a significant expansion of the neoblast population and death by lysis. Further, our experiments showed that wwp1 was necessary for both neoblast and intestinal tissue homeostasis as well as uncovered an unexpected role of trip12 in posterior tissue specification. Taken together, our data provide insights into the roles of HECT E3 ligases in tissue regeneration and demonstrate that planarians will be a useful model to evaluate the functions of E3 ubiquitin ligases in stem cell regulation.
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Affiliation(s)
- Jordana M Henderson
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Sean V Nisperos
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Joi Weeks
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Mahjoobah Ghulam
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
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17
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Natarajan N, Ramakrishnan P, Lakshmanan V, Palakodeti D, Rangiah K. A quantitative metabolomics peek into planarian regeneration. Analyst 2015; 140:3445-64. [PMID: 25815385 DOI: 10.1039/c4an02037e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The fresh water planarian species Schmidtea mediterranea is an emerging stem cell model because of its capability to regenerate a whole animal from a small piece of tissue. It is one of the best model systems to address the basic mechanisms essential for regeneration. Here, we are interested in studying the roles of various amines, thiols and nucleotides in planarian regeneration, stem cell function and growth. We developed mass spectrometry based quantitative methods and validated the differential enrichment of 35 amines, 7 thiol metabolites and 4 nucleotides from both intact and regenerating planarians. Among the amines, alanine in sexual and asparagine in asexual are the highest (>1000 ng/mg) in the intact planarians. The levels of thiols such as cysteine and GSH are 651 and 1107 ng mg(-1) in planarians. Among the nucleotides, the level of cGMP is the lowest (0.03 ng mg(-1)) and the level of AMP is the highest (187 ng mg(-1)) in both of the planarian strains. We also noticed increasing levels of amines in both anterior and posterior regenerating planarians. The blastema from day 3 regenerating planarians also showed higher amounts of many amines. Interestingly, the thiol (cysteine and GSH) levels are well maintained during planarian regeneration. This suggests an inherent and effective mechanism to control induced oxidative stress because of the robust regeneration and stem cell proliferation. Like in intact planarians, the level of cGMP is also very low in regenerating planarians. Surprisingly, the levels of amines and thiols in head regenerating blastemas are ∼3 times higher compared to those for tail regenerating blastemas. Thus our results strongly indicate the potential roles of amines, thiols and nucleotides in planarian regeneration.
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Affiliation(s)
- Nivedita Natarajan
- Metabolomics Facility, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bangalore-560065, India.
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18
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Protein expression profiling in head fragments during planarian regeneration after amputation. Dev Genes Evol 2015; 225:79-93. [PMID: 25697422 DOI: 10.1007/s00427-015-0494-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
Following amputation, a planarian tail fragment can regrow into a complete organism including a well-organized brain within about 2-3 weeks, thus restoring the structure and function to presurgical levels. Despite the enormous potential of these animals for regenerative medicine, our understanding of the exact mechanism of planarian regeneration is incomplete. To better understand the molecular nature of planarian head regeneration, we applied two-dimensional electrophoresis (2-DE)/matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)/time-of-flight mass spectrometry (TOF MS) technique to analyze the dynamic proteomic expression profiles over the course of 6 to 168 h post-decapitation. This approach identified a total of 141 differentially expressed proteins, 47 of which exhibited exceptionally high fold changes (≥3-fold change). Of these, Rx protein, an important regulator of head and brain development, was considered to be closely related to planarian head regeneration because of its exceptional high expression almost throughout the time course of regeneration process. Functional annotation analysis classified the 141 proteins into eight categories: (1) signaling, (2) Ca(2+) binding and translocation, (3) transcription and translation, (4) cytoskeleton, (5) metabolism, (6) cell protection, (7) tissue differentiation, and (8) cell cycle. Signaling pathway analysis indicated that Wnt1/Ca(2+) signaling pathway was activated during head regeneration. Integrating the analyses of proteome expression profiling, functional annotation, and signaling pathway, amputation-induced head reformation requires some mechanisms to promote cell proliferation and differentiation, including differential regulation of proapoptotic and antiapoptotic proteins, and the regulation of proliferation and differentiation-related proteins. Importantly, Wnt1/Ca(2+) signaling pathway upregulates Rx expression, finally facilitating the differentiation of neoblasts into various cell types. Taken together, our study demonstrated that proteomic analysis approach used by us is a powerful tool in understanding molecular process related to head regeneration of planarian.
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19
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20
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Vicente J, Saenz-de-Juano M, Jiménez-Trigos E, Viudes-de-Castro M, Peñaranda D, Marco-Jiménez F. Rabbit morula vitrification reduces early foetal growth and increases losses throughout gestation. Cryobiology 2013; 67:321-6. [DOI: 10.1016/j.cryobiol.2013.09.165] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/28/2022]
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21
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SILAC Proteomics of Planarians Identifies Ncoa5 as a Conserved Component of Pluripotent Stem Cells. Cell Rep 2013; 5:1142-55. [DOI: 10.1016/j.celrep.2013.10.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/09/2013] [Accepted: 10/21/2013] [Indexed: 12/19/2022] Open
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22
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Elliott SA, Sánchez Alvarado A. The history and enduring contributions of planarians to the study of animal regeneration. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2013; 2:301-26. [PMID: 23799578 PMCID: PMC3694279 DOI: 10.1002/wdev.82] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Having an almost unlimited capacity to regenerate tissues lost to age and injury, planarians have long fascinated naturalists. In the Western hemisphere alone, their documented history spans more than 200 years. Planarians were described in the early 19th century as being 'immortal under the edge of the knife', and initial investigation of these remarkable animals was significantly influenced by studies of regeneration in other organisms and from the flourishing field of experimental embryology in the late 19th and early 20th centuries. This review strives to place the study of planarian regeneration into a broader historical context by focusing on the significance and evolution of knowledge in this field. It also synthesizes our current molecular understanding of the mechanisms of planarian regeneration uncovered since this animal's relatively recent entrance into the molecular-genetic age.
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Affiliation(s)
- Sarah A Elliott
- Howard Hughes Medical Institute and Stowers Institute for Medical Research, Kansas City, MO, USA.
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23
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Franco C, Soares R, Pires E, Koci K, Almeida AM, Santos R, Coelho AV. Understanding regeneration through proteomics. Proteomics 2013; 13:686-709. [DOI: 10.1002/pmic.201200397] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 12/29/2022]
Affiliation(s)
- Catarina Franco
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Elisabete Pires
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Kamila Koci
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - André M. Almeida
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
- Instituto de Investigação Científica Tropical; Lisboa Portugal
| | - Romana Santos
- Unidade de Investigação em Ciências Orais e Biomédicas, Faculdade de Medicina Dentária; Universidade de Lisboa; Portugal
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
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24
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Saenz-de-Juano MD, Marco-Jiménez F, Peñaranda DS, Joly T, Vicente JS. Effects of Slow Freezing Procedure on Late Blastocyst Gene Expression and Survival Rate in Rabbit1. Biol Reprod 2012; 87:91. [DOI: 10.1095/biolreprod.112.100677] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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25
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Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biol 2012; 13:R19. [PMID: 22439894 PMCID: PMC3439970 DOI: 10.1186/gb-2012-13-3-r19] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 03/08/2012] [Accepted: 03/22/2012] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Planarian stem cells, or neoblasts, drive the almost unlimited regeneration capacities of freshwater planarians. Neoblasts are traditionally described by their morphological features and by the fact that they are the only proliferative cell type in asexual planarians. Therefore, they can be specifically eliminated by irradiation. Irradiation, however, is likely to induce transcriptome-wide changes in gene expression that are not associated with neoblast ablation. This has affected the accurate description of their specific transcriptomic profile. RESULTS We introduce the use of Smed-histone-2B RNA interference (RNAi) for genetic ablation of neoblast cells in Schmidtea mediterranea as an alternative to irradiation. We characterize the rapid, neoblast-specific phenotype induced by Smed-histone-2B RNAi, resulting in neoblast ablation. We compare and triangulate RNA-seq data after using both irradiation and Smed-histone-2B RNAi over a time course as means of neoblast ablation. Our analyses show that Smed-histone-2B RNAi eliminates neoblast gene expression with high specificity and discrimination from gene expression in other cellular compartments. We compile a high confidence list of genes downregulated by both irradiation and Smed-histone-2B RNAi and validate their expression in neoblast cells. Lastly, we analyze the overall expression profile of neoblast cells. CONCLUSIONS Our list of neoblast genes parallels their morphological features and is highly enriched for nuclear components, chromatin remodeling factors, RNA splicing factors, RNA granule components and the machinery of cell division. Our data reveal that the regulation of planarian stem cells relies on posttranscriptional regulatory mechanisms and suggest that planarians are an ideal model for this understudied aspect of stem cell biology.
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26
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Bocchinfuso DG, Taylor P, Ross E, Ignatchenko A, Ignatchenko V, Kislinger T, Pearson BJ, Moran MF. Proteomic profiling of the planarian Schmidtea mediterranea and its mucous reveals similarities with human secretions and those predicted for parasitic flatworms. Mol Cell Proteomics 2012; 11:681-91. [PMID: 22653920 PMCID: PMC3434776 DOI: 10.1074/mcp.m112.019026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/17/2012] [Indexed: 11/06/2022] Open
Abstract
The freshwater planarian Schmidtea mediterranea has been used in research for over 100 years, and is an emerging stem cell model because of its capability of regenerating large portions of missing body parts. Exteriorly, planarians are covered in mucous secretions of unknown composition, implicated in locomotion, predation, innate immunity, and substrate adhesion. Although the planarian genome has been sequenced, it remains mostly unannotated, challenging both genomic and proteomic analyses. The goal of the current study was to annotate the proteome of the whole planarian and its mucous fraction. The S. mediterranea proteome was analyzed via mass spectrometry by using multidimensional protein identification technology with whole-worm tryptic digests. By using a proteogenomics approach, MS data were searched against an in silico translated planarian transcript database, and by using the Swiss-Prot BLAST algorithm to identify proteins similar to planarian queries. A total of 1604 proteins were identified. The mucous subproteome was defined through analysis of a mucous trail fraction and an extract obtained by treating whole worms with the mucolytic agent N-acetylcysteine. Gene Ontology analysis confirmed that the mucous fractions were enriched with secreted proteins. The S. mediterranea proteome is highly similar to that predicted for the trematode Schistosoma mansoni associated with intestinal schistosomiasis, with the mucous subproteome particularly highly conserved. Remarkably, orthologs of 119 planarian mucous proteins are present in human mucosal secretions and tear fluid. We suggest planarians have potential to be a model system for the characterization of mucous protein function and relevant to parasitic flatworm infections and diseases underlined by mucous aberrancies, such as cystic fibrosis, asthma, and other lung diseases.
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Affiliation(s)
- Donald G. Bocchinfuso
- From the ‡Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Canada
- §Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Paul Taylor
- From the ‡Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Canada
| | - Eric Ross
- ¶Stowers Institute for Medical Research, Kansas City, Missouri
| | | | | | - Thomas Kislinger
- From the ‡Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Canada
- **Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Bret J. Pearson
- §Department of Molecular Genetics, University of Toronto, Toronto, Canada
- ‡‡Developmental and Stem Cell Biology Program, The Hospital for Sick Children; and
| | - Michael F. Moran
- From the ‡Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Canada
- §Department of Molecular Genetics, University of Toronto, Toronto, Canada
- ‖Ontario Cancer Institute, University Health Network
- §§Banting and Best Department of Medical Research, University of Toronto, MaRS Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada
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27
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Wilson RA. The cell biology of schistosomes: a window on the evolution of the early metazoa. PROTOPLASMA 2012; 249:503-518. [PMID: 21976269 DOI: 10.1007/s00709-011-0326-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 09/26/2011] [Indexed: 05/31/2023]
Abstract
This review of schistosome cell biology has a dual purpose; its intent is to alert two separate research communities to the activities of the other. Schistosomes are by far and away the best-characterised platyhelminths, due to their medical and economic importance, but seem to be almost totally ignored by researchers on the free-living lower metazoans. Equally, in their enthusiasm for the parasitic way of life, schistosome researchers seldom pay attention to the work on free-living animals that could inform their molecular investigations. The publication of transcriptomes and/or genomes for Schistosoma mansoni and Schistosoma japonicum, the sponge Archimedon, the cnidarians Nematostella and Hydra and the planarian Schmidtea provide the raw material for comparisons. Apart from interrogation of the databases for molecular similarities, there have been differences in technical approach to these lower metazoans; widespread application of whole mount in situ hybridisation to Schmidtea contrasts with the application of targeted proteomics to schistosomes. Using schistosome cell biology as the template, the key topics of cell adhesion, development, signalling pathways, nerve and muscle, and epithelia, are reviewed, where possible interspersing comparisons with the sponge, cnidarian and planarian data. The biggest jump in the evolution of cellular capabilities appears to be in the transition from a diploblast to triploblast level of organisation associated with development of a mobile and plastic body form.
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Affiliation(s)
- R Alan Wilson
- Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK.
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28
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Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One 2012; 7:e34447. [PMID: 22496805 PMCID: PMC3319590 DOI: 10.1371/journal.pone.0034447] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 03/05/2012] [Indexed: 02/06/2023] Open
Abstract
The planarian Schmidtea mediterranea is a powerful model organism for studying stem cell biology due to its extraordinary regenerative ability mediated by neoblasts, a population of adult somatic stem cells. Elucidation of the S. mediterranea transcriptome and the dynamics of transcript expression will increase our understanding of the gene regulatory programs that regulate stem cell function and differentiation. Here, we have used RNA-Seq to characterize the S. mediterranea transcriptome in sexual and asexual animals and in purified neoblast and differentiated cell populations. Our analysis identified many uncharacterized genes, transcripts, and alternatively spliced isoforms that are differentially expressed in a strain or cell type-specific manner. Transcriptome profiling of purified neoblasts and differentiated cells identified neoblast-enriched transcripts, many of which likely play important roles in regeneration and stem cell function. Strikingly, many of the neoblast-enriched genes are orthologs of genes whose expression is enriched in human embryonic stem cells, suggesting that a core set of genes that regulate stem cell function are conserved across metazoan species.
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