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Rodrigo AP, Lopes A, Pereira R, Anjo SI, Manadas B, Grosso AR, Baptista PV, Fernandes AR, Costa PM. Endogenous Fluorescent Proteins in the Mucus of an Intertidal Polychaeta: Clues for Biotechnology. Mar Drugs 2022; 20:md20040224. [PMID: 35447897 PMCID: PMC9028460 DOI: 10.3390/md20040224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
The vast ocean holds many unexplored organisms with unique adaptive features that enable them to thrive in their environment. The secretion of fluorescent proteins is one of them, with reports on the presence of such compounds in marine annelids being scarce. The intertidal Eulalia sp. is an example. The worm secretes copious amounts of mucus, that when purified and concentrated extracts, yield strong fluorescence under UV light. Emission has two main maxima, at 400 nm and at 500 nm, with the latter responsible for the blue–greenish fluorescence. Combining proteomics and transcriptomics techniques, we identified ubiquitin, peroxiredoxin, and 14-3-3 protein as key elements in the mucus. Fluorescence was found to be mainly modulated by redox status and pH, being consistently upheld in extracts prepared in Tris-HCl buffer with reducing agent at pH 7 and excited at 330 nm. One of the proteins associated with the fluorescent signal was localized in secretory cells in the pharynx. The results indicate that the secretion of fluorescent proteinaceous complexes can be an important defense against UV for this dweller. Additionally, the internalization of fluorescent complexes by ovarian cancer cells and modulation of fluorescence of redox status bears important considerations for biotechnological application of mucus components as markers.
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Affiliation(s)
- Ana P. Rodrigo
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Correspondence: (A.P.R.); (P.M.C.); Tel.: +351-212-948-300 (A.P.R. & P.M.C.)
| | - Ana Lopes
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
| | - Ricardo Pereira
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
| | - Sandra I. Anjo
- Center for Neuroscience and Cell Biology, University of Coimbra, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; (S.I.A.); (B.M.)
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, University of Coimbra, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; (S.I.A.); (B.M.)
| | - Ana R. Grosso
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro V. Baptista
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alexandra R. Fernandes
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro M. Costa
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Correspondence: (A.P.R.); (P.M.C.); Tel.: +351-212-948-300 (A.P.R. & P.M.C.)
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2
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Maciel EI, Valle Arevalo A, Ziman B, Nobile CJ, Oviedo NJ. Epithelial Infection With Candida albicans Elicits a Multi-System Response in Planarians. Front Microbiol 2021; 11:629526. [PMID: 33519792 PMCID: PMC7840899 DOI: 10.3389/fmicb.2020.629526] [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: 11/15/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Candida albicans is one of the most common fungal pathogens of humans. Prior work introduced the planarian Schmidtea mediterranea as a new model system to study the host response to fungal infection at the organismal level. In the current study, we analyzed host-pathogen changes that occurred in situ during early infection with C. albicans. We found that the transcription factor Bcr1 and its downstream adhesin Als3 are required for C. albicans to adhere to and colonize the planarian epithelial surface, and that adherence of C. albicans triggers a multi-system host response that is mediated by the Dectin signaling pathway. This infection response is characterized by two peaks of stem cell divisions and transcriptional changes in differentiated tissues including the nervous and the excretory systems. This response bears some resemblance to a wound-like response to physical injury; however, it takes place without visible tissue damage and it engages a distinct set of progenitor cells. Overall, we identified two C. albicans proteins that mediate epithelial infection of planarians and a comprehensive host response facilitated by diverse tissues to effectively clear the infection.
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Affiliation(s)
- Eli Isael Maciel
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, United States
| | - Ashley Valle Arevalo
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, United States
| | - Benjamin Ziman
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, United States
| | - Clarissa J Nobile
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Health Sciences Research Institute, University of California, Merced, Merced, CA, United States
| | - Néstor J Oviedo
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Health Sciences Research Institute, University of California, Merced, Merced, CA, United States
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3
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Forsthoefel DJ, Cejda NI, Khan UW, Newmark PA. Cell-type diversity and regionalized gene expression in the planarian intestine. eLife 2020; 9:e52613. [PMID: 32240093 PMCID: PMC7117911 DOI: 10.7554/elife.52613] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.
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Affiliation(s)
- David J Forsthoefel
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Nicholas I Cejda
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
| | - Umair W Khan
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Phillip A Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
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4
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Wilden B, Majdi N, Kuhlicke U, Neu TR, Traunspurger W. Flatworm mucus as the base of a food web. BMC Ecol 2019; 19:15. [PMID: 30925873 PMCID: PMC6441204 DOI: 10.1186/s12898-019-0231-2] [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: 05/26/2018] [Accepted: 03/23/2019] [Indexed: 11/10/2022] Open
Abstract
Background By altering their habitats, engineering species can improve their own fitness. However, the effect of this strategy on the fitness of coexisting species or on the structure of the respective food web is poorly understood. In this study, bacteria and bacterivorous nematodes with short (Caenorhabditis elegans) and long (Plectus acuminatus) life cycles were exposed to the mucus secreted by the freshwater flatworm Polycelis tenuis. The growth, reproduction, and feeding preferences of the nematodes in the presence/absence of the mucus were then determined. In addition, confocal laser scanning microscopy (CLSM) was used to examine the structural footprint of the mucus and the mucus colonization dynamics of bacteria and protozoans. Results Mucus exposure resulted in a greater reproductive output in P. acuminatus than in C. elegans. In a cafeteria experiment, both nematode species were attracted by bacteria-rich patches and were not deterred by mucus. CLSM showed that the flatworms spread a layer of polysaccharide-rich mucus ca. 15 µm thick from their tails. Subsequent colonization of the mucus by bacteria and protozoans resulted in an architecture that progressively resembled a complex biofilm. The presence of protozoans reduced nematode reproduction, presumably due to competition for their bacterial food supply. Conclusion Animal secretions such as mucus may have broader, community-level consequences and contribute to fueling microbial food webs. Electronic supplementary material The online version of this article (10.1186/s12898-019-0231-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin Wilden
- Department of Animal Ecology, University of Bielefeld, Konsequenz 45, 33615, Bielefeld, Germany.
| | - Nabil Majdi
- Department of Animal Ecology, University of Bielefeld, Konsequenz 45, 33615, Bielefeld, Germany.,EcoLab, UMR 5245, CNRS, INP, UPS, ENSAT, Université de Toulouse, 118 route de Narbonne, 31062, Toulouse, France
| | - Ute Kuhlicke
- Department River Ecology, Helmholtz Centre of Environmental Research, Brückstr. 3a, 39114, Magdeburg, Germany
| | - Thomas R Neu
- Department River Ecology, Helmholtz Centre of Environmental Research, Brückstr. 3a, 39114, Magdeburg, Germany
| | - Walter Traunspurger
- Department of Animal Ecology, University of Bielefeld, Konsequenz 45, 33615, Bielefeld, Germany
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5
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Jones S, Osman S, Howl J. The planarian Schmidtea mediterranea as a model system for the discovery and characterization of cell-penetrating peptides and bioportides. Chem Biol Drug Des 2019; 93:1036-1049. [PMID: 30790457 DOI: 10.1111/cbdd.13483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/13/2018] [Accepted: 12/27/2018] [Indexed: 12/16/2022]
Abstract
The general utility of the planarian Schmidtea mediterranea, an organism with remarkable regenerative capacity, was investigated as a convenient three-dimensional model to analyse the import of cell-penetrating peptides (CPPs) and bioportides (bioactive CPPs) into complex tissues. The unpigmented planarian blastema, 3 days post head amputation, is a robust platform to assess the penetration of red-fluorescent CPPs into epithelial cells and deeper tissues. Three planarian proteins, Ovo, ZicA and Djeya, which collectively control head remodelling and eye regeneration following decapitation, are a convenient source of novel cationic CPP vectors. One example, Djeya1 (RKLAFRYRRIKELYNSYR), is a particularly efficient and seemingly inert CPP vector that could be further developed to assist the delivery of bioactive payloads across the plasma membrane of eukaryotic cells. Eye regeneration, following head amputation, was utilized in an effort to identify bioportides capable of influencing stem cell-dependent morphogenesis. These investigations identified the tetradecapeptide mastoparan (INLKALAALAKKIL) as a bioportide able to influence the gross morphology of head development. We conclude that, compared with cellular monolayers, the S. mediterranea system provides many advantages and will support the identification of bioportides able to selectively modify the biology of totipotent neoblasts and, presumably, other mammalian stem cell types.
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Affiliation(s)
- Sarah Jones
- Molecular Pharmacology Group, Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
| | - Shaimaa Osman
- Peptide Chemistry Department, National Research Centre, Cairo, Egypt
| | - John Howl
- Molecular Pharmacology Group, Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
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6
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Caruana NJ, Strugnell JM, Faou P, Finn J, Cooke IR. Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae). J Proteome Res 2019; 18:890-899. [PMID: 30628786 DOI: 10.1021/acs.jproteome.8b00569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sepioloidea lineolata, the striped pyjama squid (family Sepiadariidae), is a small species of benthic bobtail squid distributed along the Southern Indo-Pacific coast of Australia. Like other sepiadariid squids, it is known to secrete large volumes of viscous slime when stressed. In order to identify key proteins involved in the function of sepiadariid slimes, we compared the slime proteome of Sepioloidea lineolata with that of a closely related species, Sepiadarium austrinum. Of the 550 protein groups identified in Sepioloidea lineolata slime, 321 had orthologs in Sepiadarium austrinum, and the abundance of these (iBAQ) was highly correlated between species. Both slimes were dominated by a small number of abundant proteins, and several of these were short secreted proteins with no homologues outside the class Cephalopoda. No mucins were identified within either species' slime, suggesting that it is structurally distinct from mucin polymer-based gels found in many vertebrate and echinoderm secretions. The extent of N-glycosylation in the slime of Sepioloidea lineolata was also studied via glycan cleavage with Peptide: N-glycosidase F (PNGase-F). Although very few (four) proteins showed strong evidence of N-glycosylation, we found that treatment with PNGase-F led to a slight increase in peptide identification rates compared with controls.
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Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture , James Cook University , Townsville , QLD 4811 , Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Julian Finn
- Sciences , Museums Victoria , Carlton , VIC 3053 , Australia
| | - Ira R Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia.,Department of Molecular and Cell Biology , James Cook University , Townsville , QLD 4811 , Australia
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7
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Abstract
This article serves as a brief primer on planaria for behavior scientists. In the 1950s and 1960s, McConnell's planarian laboratory posited that conditioned behavior could transfer after regeneration, and through cannibalization of trained planaria. These studies, the responses, and replications have been collectively referred to as the "planarian controversy." Successful behavioral assays still require refinement with this organism, but they could add valuable insight into our conceptualization of memory and learning. We discuss how the planarian's distinctive biology enables an examination of biobehavioral interaction models, and what behavior scientists must consider if they are to advance behavioral research with this organism. Suggestions for academics interested in building planaria learning laboratories are offered.
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Affiliation(s)
- Neil Deochand
- Health and Human Services Department, University of Cincinnati, 450H Teachers-Dyer Complex, Cincinnati, OH 45221 USA
| | - Mack S. Costello
- Department of Psychology, Rider University, 2083 Lawrenceville Road, Lawrenceville, NJ 08648 USA
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8
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Swapna LS, Molinaro AM, Lindsay-Mosher N, Pearson BJ, Parkinson J. Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. Genome Biol 2018; 19:124. [PMID: 30143032 PMCID: PMC6109357 DOI: 10.1186/s13059-018-1498-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. RESULTS In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic functional annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that the TRAF gene family has been greatly expanded in planarians. We further provide a single-cell RNA sequencing analysis of 2000 cells, revealing both known and novel cell types defined by unique signatures of gene expression. Among these are a novel mesenchymal cell population as well as a cell type involved in eye regeneration. Integration of our metabolic reconstruction further reveals the extent to which given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles. CONCLUSIONS In general, S. mediterranea displays a high level of gene and pathway conservation compared with other model systems, rendering it a viable model to study the roles of these pathways in stem cell biology and regeneration.
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Affiliation(s)
| | - Alyssa M Molinaro
- Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nicole Lindsay-Mosher
- Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Bret J Pearson
- Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Ontario Institute for Cancer Research, Toronto, ON, Canada.
| | - John Parkinson
- Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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9
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Wu XJ, Dinguirard N, Sabat G, Lui HD, Gonzalez L, Gehring M, Bickham-Wright U, Yoshino TP. Proteomic analysis of Biomphalaria glabrata plasma proteins with binding affinity to those expressed by early developing larval Schistosoma mansoni. PLoS Pathog 2017; 13:e1006081. [PMID: 28520808 PMCID: PMC5433772 DOI: 10.1371/journal.ppat.1006081] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 11/20/2016] [Indexed: 11/19/2022] Open
Abstract
Interactions between early developing Schistosoma mansoni larval stages and the hemolymph of its snail intermediate host represent the first molecular encounter with the snail’s immune system. To gain a more comprehensive understanding of this early parasite-host interaction, biotinylated sporocyst tegumental membrane (Mem) proteins and larval transformation proteins (LTP) were affixed to streptavidin-agarose beads and used as affinity matrices to enrich for larval-reactive plasma proteins from susceptible (NMRI) and resistant (BS-90) strains of the snail Biomphalaria glabrata. Nano-LC/MS-MS proteomic analyses of isolated plasma proteins revealed a diverse array of 94 immune-and nonimmune-related plasma proteins. Included among the immune-related subset were pattern recognition receptors (lectins, LPS-binding protein, thioester-containing proteins-TEPs), stress proteins (HSP60 and 70), adhesion proteins (dermatopontins), metalloproteases (A Disintegrin And Metalloproteinase (ADAM), ADAM-related Zn proteinases), cytotoxins (biomphalysin) and a Ca2+-binding protein (neo-calmodulin). Variable immunoglobulin and lectin domain (VIgL) gene family members, including fibrinogen-related proteins (FREPs), galectin-related proteins (GREPs) and C-type lectin-related proteins (CREPs), were the most prevalent of larval-reactive immune lectins present in plasma. FREPs were highly represented, although only a subset of FREP subfamilies (FREP 2, 3 and 12) were identified, suggesting potential selectivity in the repertoire of plasma lectins recognizing larval glycoconjugates. Other larval-binding FREP-like and CREP-like proteins possessing a C-terminal fibrinogen-related domain (FReD) or C-type lectin binding domain, respectively, and an Ig-fold domain also were identified as predicted proteins from the B. glabrata genome, although incomplete sequence data precluded their placement into specific FREP/CREP subfamilies. Similarly, a group of FReD-containing proteins (angiopoeitin-4, ficolin-2) that lacked N-terminal Ig-fold(s) were identified as a distinct group of FREP-like proteins, separate from the VIgL lectin family. Finally, differential appearance of GREPs in BS-90 plasma eluates, and others proteins exclusively found in eluates of the NMRI strain, suggested snail strain differences in the expression of select larval-reactive immune proteins. This hypothesis was supported by the finding that differential gene expression of the GREP in BS-90 and ADAM in NMRI snail strains generally correlated with their patterns of protein expression. In summary, this study is the first to provide a global comparative proteomic analysis of constitutively expressed plasma proteins from susceptible and resistant B. glabrata strains capable of binding early-expressed larval S. mansoni proteins. Identified proteins, especially those exhibiting differential expression, may play a role in determining immune compatibility in this snail host-parasite system. A complete listing of raw peptide data are available via ProteomeXchange using identifier PXD004942. Transmission of the human blood fluke Schistosoma mansoni critically depends on the successful establishment of infections within species of its snail intermediate host, Biomphalaria. One of the most important barriers to infection is the host’s innate immune system, comprised of plasma proteins and immunocytes (hemocytes) circulating in the hemolymph. Although expression of plasma lectin genes appears to be associated with larval resistance in B. glabrata, few studies have attempted an in depth analysis of gene-encoded lectins, and other immune proteins, that are capable of directly binding schistosome larvae. Using affinity matrices linked to schistosome proteins expressed during early larval development, we identified and compared the parasite-reactive plasma proteins from the susceptible NMRI and resistant BS-90 strains of B. glabrata. Proteomic analyses of isolated plasma proteins revealed a diversity immune-related proteins including lectins, pathogen recognition receptors, cytotoxins, adhesion proteins, metalloproteinases, and Ca2+-binding proteins. Of the lectins, the variable immunoglobulin and lectin domain (VIgL) gene family of proteins comprised of fibrinogen-related proteins (FREPs), galectin-related proteins (GREPs) and C-type lectin-related proteins (CREPs), were highly represented, and consistent with their role in host immunity. Two proteins (GREP and a Zn-metalloproteinase) exhibited snail strain-associated protein and gene expression patterns suggesting their involvement in innate immune responses to larval infection. This comparative proteomic analysis of larval S. mansoni-reactive plasma proteins from susceptible and resistant B. glabrata strains represents the first of its kind and provides valuable insights into possible pathogen recognition receptors and other immune factors regulating parasite-host compatibility in this model system.
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Affiliation(s)
- Xiao-Jun Wu
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Nathalie Dinguirard
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Grzegorz Sabat
- Biotechnology Center, Mass Spectrometry/Proteomics Facility, University of Wisconsin, Madison, WI, United States of America
| | - Hong-di Lui
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Laura Gonzalez
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Michael Gehring
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Utibe Bickham-Wright
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Timothy P. Yoshino
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, United States of America
- * E-mail:
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10
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Hayes MJ. Sulphated glycosaminoglycans support an assortment of planarian rhabdite structures. Biol Open 2017; 6:571-581. [PMID: 28302668 PMCID: PMC5450325 DOI: 10.1242/bio.024554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/15/2017] [Indexed: 11/20/2022] Open
Abstract
Planaria are soft-bodied, bilateral flatworms of the phylum Platyhelminthes. They are covered in cilia and use ciliary-gliding to traverse the substratum while hunting. Their body surface is covered in a layer of viscous slime primarily derived from specialised secretory granules known as rhabdites. The slime must somehow stay associated with the surface of the animal in aqueous environments whilst also lubricating the interface of the animal and the surfaces over which the animal moves. The slime prevents damage to the animal's soft body and also contributes to adhesion to the substratum. In order to gain insight into how it might achieve these diverse functions, we performed electron microscopic examination of the slime's structure. Analysis of two freshwater flatworms from the UK Schmidtea polychroa (Schmidt, 1861) and Polycelis tenuis (Ijima, 1884) revealed a high level of organisation of the slime layer and a variety of ejected slime structures. We show that these structures are rich in sulphated glycosaminoglycans (sGAGs). Most of these (269 of 285 examined) appear to be topologically closed spheroids that we name ball-GAGs. Another class appears to burst to release flower- and star-like clusters which adhere to motile cilia. We also observe fibrous nets that are associated with entrapped bacteria. Examination of the structure of rhabdites ejected onto a porous surface suggests a mechanism by which their structure allows them to both bind to the porous surface and provide a smooth layer over which the animal could glide. Such sGAG-based structures might provide models for the design of artificial biomimetic replacements for tears, saliva, bio-compatible lubricants or drug-delivery vehicles.
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Affiliation(s)
- Matthew J Hayes
- EM Unit, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
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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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Goupil LS, Ivry SL, Hsieh I, Suzuki BM, Craik CS, O’Donoghue AJ, McKerrow JH. Cysteine and Aspartyl Proteases Contribute to Protein Digestion in the Gut of Freshwater Planaria. PLoS Negl Trop Dis 2016; 10:e0004893. [PMID: 27501047 PMCID: PMC4976874 DOI: 10.1371/journal.pntd.0004893] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/11/2016] [Indexed: 01/06/2023] Open
Abstract
Proteases perform numerous vital functions in flatworms, many of which are likely to be conserved throughout the phylum Platyhelminthes. Within this phylum are several parasitic worms that are often poorly characterized due to their complex life-cycles and lack of responsiveness to genetic manipulation. The flatworm Schmidtea mediterranea, or planaria, is an ideal model organism to study the complex role of protein digestion due to its simple life cycle and amenability to techniques like RNA interference (RNAi). In this study, we were interested in deconvoluting the digestive protease system that exists in the planarian gut. To do this, we developed an alcohol-induced regurgitation technique to enrich for the gut enzymes in S. mediterranea. Using a panel of fluorescent substrates, we show that this treatment produces a sharp increase in proteolytic activity. These enzymes have broad yet diverse substrate specificity profiles. Proteomic analysis of the gut contents revealed the presence of cysteine and metallo-proteases. However, treatment with class-specific inhibitors showed that aspartyl and cysteine proteases are responsible for the majority of protein digestion. Specific RNAi knockdown of the cathepsin B-like cysteine protease (SmedCB) reduced protein degradation in vivo. Immunohistochemistry and whole-mount in situ hybridization (WISH) confirmed that the full-length and active forms of SmedCB are found in secretory cells surrounding the planaria intestinal lumen. Finally, we show that the knockdown of SmedCB reduces the speed of tissue regeneration. Defining the roles of proteases in planaria can provide insight to functions of conserved proteases in parasitic flatworms, potentially uncovering drug targets in parasites.
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Affiliation(s)
- Louise S. Goupil
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Sam L. Ivry
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Ivy Hsieh
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| | - Brian M. Suzuki
- Skaggs School of Pharmacy and Pharmaceutical Chemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Chemistry, University of California, San Diego, La Jolla, California, United States of America
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Chemistry, University of California, San Diego, La Jolla, California, United States of America
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13
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Caruana NJ, Cooke IR, Faou P, Finn J, Hall NE, Norman M, Pineda SS, Strugnell JM. A combined proteomic and transcriptomic analysis of slime secreted by the southern bottletail squid, Sepiadarium austrinum (Cephalopoda). J Proteomics 2016; 148:170-82. [PMID: 27476034 DOI: 10.1016/j.jprot.2016.07.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/20/2016] [Accepted: 07/24/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED Sepiadarium austrinum, the southern bottletail squid, is a small squid that inhabits soft sediments along Australia's south-east coast. When provoked, it rapidly secretes large volumes of slime, presumably as a form of chemical defense. We analyzed the proteomic composition of this slime using tandem mass spectrometry and transcriptomics and found that it was remarkably complex with 1735 identified protein groups (FDR:0.01). To investigate the chemical defense hypothesis we performed an Artemia toxicity assay and used sequence analysis to search for toxin-like molecules. Although the slime did not appear to be toxic to Artemia we found 13 proteins in slime with the hallmarks of toxins, namely cysteine richness, short length, a signal peptide and/or homology to known toxins. These included three short (80-130AA) cysteine rich secreted proteins with no homology to proteins on the NCBI or UniProt databases. Other protein families found included, CAP, phospholipase-B, ShKT-like peptides, peptidase S10, Kunitz BPTI and DNase II. Quantitative analysis using intensity based absolute quantification (iBAQ via MaxQuant) revealed 20 highly abundant proteins, accounting for 67% of iBAQ signal, and three of these were toxin-like. No mucin homologues were found suggesting that the structure of the slime gel may be formed by an unknown mechanism. BIOLOGICAL SIGNIFICANCE This study is the first known instance of a slime secretion from a cephalopod to be analyzed by proteomics methods and is the first investigation of a member of the family Sepiadariidae using proteomic methods. 1735 proteins were identified with 13 of these fitting criteria established for the identification of putative toxins. The slime is dominated by 20 highly abundant proteins with secreted, cysteine rich proteins. The study highlights the importance of 'omics approaches in understanding novel organisms.
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Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, Vic 3086, Australia.
| | - Ira R Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, Qld 4811, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Vic 3086, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Vic 3086, Australia
| | - Julian Finn
- Sciences, Museum Victoria, Carlton, Vic 3053, Australia
| | - Nathan E Hall
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Vic 3053, Australia
| | - Mark Norman
- Sciences, Museum Victoria, Carlton, Vic 3053, Australia
| | - Sandy S Pineda
- Institute for Molecular Bioscience, The University of Queensland, QLD 4072, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, Vic 3086, Australia
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14
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Adhesive organ regeneration in Macrostomum lignano. BMC DEVELOPMENTAL BIOLOGY 2016; 16:20. [PMID: 27255153 PMCID: PMC4890501 DOI: 10.1186/s12861-016-0121-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022]
Abstract
Background Flatworms possess pluripotent stem cells that can give rise to all cell types, which allows them to restore lost body parts after injury or amputation. This makes flatworms excellent model systems for studying regeneration. In this study, we present the adhesive organs of a marine flatworm as a simple model system for organ regeneration. Macrostomum lignano has approximately 130 adhesive organs at the ventral side of its tail plate. One adhesive organ consists of three interacting cells: one adhesive gland cell, one releasing gland cell, and one modified epidermal cell, called an anchor cell. However, no specific markers for these cell types were available to study the regeneration of adhesive organs. Results We tested 15 commercially available lectins for their ability to label adhesive organs and found one lectin (peanut agglutinin) to be specific to adhesive gland cells. We visualized the morphology of regenerating adhesive organs using lectin- and antibody staining as well as transmission electron microscopy. Our findings indicate that the two gland cells differentiate earlier than the connected anchor cells. Using EdU/lectin staining of partially amputated adhesive organs, we showed that their regeneration can proceed in two ways. First, adhesive gland cell bodies are able to survive partial amputation and reconnect with newly formed anchor cells. Second, adhesive gland cell bodies are cleared away, and the entire adhesive organ is build anew. Conclusion Our results provide the first insights into adhesive organ regeneration and describe ten new markers for differentiated cells and tissues in M. lignano. The position of adhesive organ cells within the blastema and their chronological differentiation have been shown for the first time. M. lignano can regenerate adhesive organs de novo but also replace individual anchor cells in an injured organ. Our findings contribute to a better understanding of organogenesis in flatworms and enable further molecular investigations of cell-fate decisions during regeneration. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0121-1) contains supplementary material, which is available to authorized users.
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15
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Pales Espinosa E, Koller A, Allam B. Proteomic characterization of mucosal secretions in the eastern oyster, Crassostrea virginica. J Proteomics 2015; 132:63-76. [PMID: 26612663 DOI: 10.1016/j.jprot.2015.11.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/03/2015] [Accepted: 11/17/2015] [Indexed: 12/24/2022]
Abstract
The soft body surface of marine invertebrates is covered by a layer of mucus, a slippery gel secreted by mucocytes lining epithelia. The functions of this gel are diverse including locomotion, cleansing, food particles processing and defense against physicochemical injuries and infectious agents. In oysters, mucus covering pallial organs has been demonstrated to have a major importance in the processing of food particles and in the interactions with waterborne pathogens. Given the limited information available on mucus in bivalves and the apparent wide spectra of activity of bioactive molecules present in this matrix, the characterization of these mucosal secretions has become a research priority. In this study, mucus was separately collected from the mantle, gills and labial palps of the eastern oyster (Crassostrea virginica) and analyzed by liquid chromatography and tandem mass spectrometry. Results showed the presence of a wide variety of molecules involved in host-microbe interactions, including putative adhesion molecules (e.g. c-type lectins) confirming that transcripts previously identified in epithelial cells are translated into proteins secreted in mucus. Mucus composition was different among samples collected from different organs. These results generate a reference map for C. virginica pallial mucus to better characterize the various physiological functions of mucosal secretions.
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Affiliation(s)
- Emmanuelle Pales Espinosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, United States.
| | - Antonius Koller
- Proteomics Center, Stony Brook University Medical Center, Stony Brook, NY 11794-8691, United States
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, United States
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16
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Hennebert E, Leroy B, Wattiez R, Ladurner P. An integrated transcriptomic and proteomic analysis of sea star epidermal secretions identifies proteins involved in defense and adhesion. J Proteomics 2015; 128:83-91. [DOI: 10.1016/j.jprot.2015.07.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/02/2015] [Indexed: 01/04/2023]
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17
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Cochet-Escartin O, Mickolajczyk KJ, Collins EMS. Scrunching: a novel escape gait in planarians. Phys Biol 2015; 12:056010. [PMID: 26356147 DOI: 10.1088/1478-3975/12/5/056010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The ability to escape a predator or other life-threatening situations is central to animal survival. Different species have evolved unique strategies under anatomical and environmental constraints. In this study, we describe a novel musculature-driven escape gait in planarians, 'scrunching', which is quantitatively different from other planarian gaits, such as gliding and peristalsis. We show that scrunching is a conserved gait among different flatworm species, underlying its importance as an escape mechanism. We further demonstrate that it can be induced by a variety of physical stimuli, including amputation, high temperature, electric shock and low pH. We discuss the functional basis for scrunching as the preferential gait when gliding is impaired due to a disruption of mucus production. Finally, we show that the key mechanical features of scrunching are adequately captured by a simple biomechanical model that is solely based on experimental data from traction force microscopy and tissue rheology without fit parameters. Together, our results form a complete description of this novel form of planarian locomotion. Because scrunching has distinct dynamics, this gait can serve as a robust behavioral readout for studies of motor neuron and muscular functions in planarians and in particular the restoration of these functions during regeneration.
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Affiliation(s)
- Olivier Cochet-Escartin
- Physics Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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18
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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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19
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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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20
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Pawar H, Renuse S, Khobragade SN, Chavan S, Sathe G, Kumar P, Mahale KN, Gore K, Kulkarni A, Dixit T, Raju R, Prasad TSK, Harsha HC, Patole MS, Pandey A. Neglected Tropical Diseases and Omics Science: Proteogenomics Analysis of the Promastigote Stage ofLeishmania majorParasite. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:499-512. [DOI: 10.1089/omi.2013.0159] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Rajiv Gandhi University of Health Sciences, Bangalore, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | | | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | | | | | - Tanwi Dixit
- National Centre for Cell Sciences, Pune, India
| | - Rajesh Raju
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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21
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Innate immune system and tissue regeneration in planarians: an area ripe for exploration. Semin Immunol 2014; 26:295-302. [PMID: 25082737 DOI: 10.1016/j.smim.2014.06.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 06/24/2014] [Indexed: 01/11/2023]
Abstract
The immune system has been implicated as an important modulator of tissue regeneration. However, the mechanisms driving injury-induced immune response and tissue repair remain poorly understood. For over 200 years, planarians have been a classical model for studies on tissue regeneration, but the planarian immune system and its potential role in repair is largely unknown. We found through comparative genomic analysis and data mining that planarians contain many potential homologs of the innate immune system that are activated during injury and repair of adult tissues. These findings support the notion that the relationship between adult tissue repair and the immune system is an ancient feature of basal Bilateria. Further analysis of the planarian immune system during regeneration could potentially add to our understanding of how the innate immune system and inflammatory responses interplay with regenerative signals to induce scar-less tissue repair in the context of the adult organism.
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22
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Nirujogi RS, Pawar H, Renuse S, Kumar P, Chavan S, Sathe G, Sharma J, Khobragade S, Pande J, Modak B, Prasad TSK, Harsha HC, Patole MS, Pandey A. Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. J Proteomics 2014; 97:48-61. [PMID: 23665000 PMCID: PMC4710096 DOI: 10.1016/j.jprot.2013.04.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 04/02/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-based identification based on related Leishmania species (L. infantum, L. major and L. braziliensis) whose genomes have been sequenced. Recently, the genome of L. donovani was fully sequenced and the data became publicly available. We took advantage of the availability of its genomic sequence to carry out a more accurate proteogenomic analysis of L. donovani proteome using our previously generated dataset. This resulted in identification of 17,504 unique peptides upon database-dependent search against the annotated proteins in L. donovani. These peptides were assigned to 3999 unique proteins in L. donovani. 2296 proteins were identified in both the life stages of L. donovani, while 613 and 1090 proteins were identified only from amastigote and promastigote stages, respectively. The proteomic data was also searched against six-frame translated L. donovani genome, which led to 255 genome search-specific peptides (GSSPs) resulting in identification of 20 novel genes and correction of 40 existing gene models in L. donovani. BIOLOGICAL SIGNIFICANCE Leishmania donovani genome sequencing was recently completed, which permitted us to use a proteogenomic approach to map its proteome and to carry out annotation of it genome. This resulted in mapping of 50% (3999 proteins) of L. donovani proteome. Our study identified 20 novel genes previously not predicted from the L. donovani genome in addition to correcting annotations of 40 existing gene models. The identified proteins may help in better understanding of stage-specific protein expression profiles in L. donovani and to identify novel stage-specific drug targets in L. donovani which could be used in the treatment of leishmaniasis. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | | | | | - Bhakti Modak
- National Centre for Cell Sciences, Pune 411007, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605014, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | | | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA.
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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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Armengaud J, Christie-Oleza JA, Clair G, Malard V, Duport C. Exoproteomics: exploring the world around biological systems. Expert Rev Proteomics 2013. [PMID: 23194272 DOI: 10.1586/epr.12.52] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The term 'exoproteome' describes the protein content that can be found in the extracellular proximity of a given biological system. These proteins arise from cellular secretion, other protein export mechanisms or cell lysis, but only the most stable proteins in this environment will remain in abundance. It has been shown that these proteins reflect the physiological state of the cells in a given condition and are indicators of how living systems interact with their environments. High-throughput proteomic approaches based on a shotgun strategy, and high-resolution mass spectrometers, have modified the authors' view of exoproteomes. In the present review, the authors describe how these new approaches should be exploited to obtain the maximum useful information from a sample, whatever its origin. The methodologies used for studying secretion from model cell lines derived from eukaryotic, multicellular organisms, virulence determinants of pathogens and environmental bacteria and their relationships with their habitats are illustrated with several examples. The implication of such data, in terms of proteogenomics and the discovery of novel protein functions, is discussed.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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