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Lee B, Tachon S, Eigenheer RA, Phinney BS, Marco ML. Lactobacillus casei Low-Temperature, Dairy-Associated Proteome Promotes Persistence in the Mammalian Digestive Tract. J Proteome Res 2015; 14:3136-47. [DOI: 10.1021/acs.jproteome.5b00387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bokyung Lee
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Sybille Tachon
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Richard A. Eigenheer
- Proteomics
Core Facility, Genome Center, University of California, 451 East
Health Sciences Drive, Davis, California 95616, United States
| | - Brett S. Phinney
- Proteomics
Core Facility, Genome Center, University of California, 451 East
Health Sciences Drive, Davis, California 95616, United States
| | - Maria L. Marco
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, California 95616, United States
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2
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Strasser B, Mlitz V, Hermann M, Rice RH, Eigenheer RA, Alibardi L, Tschachler E, Eckhart L. Evolutionary origin and diversification of epidermal barrier proteins in amniotes. Mol Biol Evol 2014; 31:3194-205. [PMID: 25169930 PMCID: PMC4245816 DOI: 10.1093/molbev/msu251] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The evolution of amniotes has involved major molecular innovations in the epidermis. In particular, distinct structural proteins that undergo covalent cross-linking during cornification of keratinocytes facilitate the formation of mechanically resilient superficial cell layers and help to limit water loss to the environment. Special modes of cornification generate amniote-specific skin appendages such as claws, feathers, and hair. In mammals, many protein substrates of cornification are encoded by a cluster of genes, termed the epidermal differentiation complex (EDC). To provide a basis for hypotheses about the evolution of cornification proteins, we screened for homologs of the EDC in non-mammalian vertebrates. By comparative genomics, de novo gene prediction and gene expression analyses, we show that, in contrast to fish and amphibians, the chicken and the green anole lizard have EDC homologs comprising genes that are specifically expressed in the epidermis and in skin appendages. Our data suggest that an important component of the cornified protein envelope of mammalian keratinocytes, that is, loricrin, has originated in a common ancestor of modern amniotes, perhaps during the acquisition of a fully terrestrial lifestyle. Moreover, we provide evidence that the sauropsid-specific beta-keratins have evolved as a subclass of EDC genes. Based on the comprehensive characterization of the arrangement, exon-intron structures and conserved sequence elements of EDC genes, we propose new scenarios for the evolutionary origin of epidermal barrier proteins via fusion of neighboring S100A and peptidoglycan recognition protein genes, subsequent loss of exons and highly divergent sequence evolution.
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Affiliation(s)
- Bettina Strasser
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Marcela Hermann
- Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Robert H Rice
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California-Davis
| | | | - Lorenzo Alibardi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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3
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Strasser B, Mlitz V, Hermann M, Rice RH, Eigenheer RA, Alibardi L, Tschachler E, Eckhart L. Evolutionary origin and diversification of epidermal barrier proteins in amniotes. Mol Biol Evol 2014. [PMID: 25169930 DOI: 10.1093/molbev/msu251.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The evolution of amniotes has involved major molecular innovations in the epidermis. In particular, distinct structural proteins that undergo covalent cross-linking during cornification of keratinocytes facilitate the formation of mechanically resilient superficial cell layers and help to limit water loss to the environment. Special modes of cornification generate amniote-specific skin appendages such as claws, feathers, and hair. In mammals, many protein substrates of cornification are encoded by a cluster of genes, termed the epidermal differentiation complex (EDC). To provide a basis for hypotheses about the evolution of cornification proteins, we screened for homologs of the EDC in non-mammalian vertebrates. By comparative genomics, de novo gene prediction and gene expression analyses, we show that, in contrast to fish and amphibians, the chicken and the green anole lizard have EDC homologs comprising genes that are specifically expressed in the epidermis and in skin appendages. Our data suggest that an important component of the cornified protein envelope of mammalian keratinocytes, that is, loricrin, has originated in a common ancestor of modern amniotes, perhaps during the acquisition of a fully terrestrial lifestyle. Moreover, we provide evidence that the sauropsid-specific beta-keratins have evolved as a subclass of EDC genes. Based on the comprehensive characterization of the arrangement, exon-intron structures and conserved sequence elements of EDC genes, we propose new scenarios for the evolutionary origin of epidermal barrier proteins via fusion of neighboring S100A and peptidoglycan recognition protein genes, subsequent loss of exons and highly divergent sequence evolution.
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Affiliation(s)
- Bettina Strasser
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Marcela Hermann
- Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Robert H Rice
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California-Davis
| | | | - Lorenzo Alibardi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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4
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Laatsch CN, Durbin-Johnson BP, Rocke DM, Mukwana S, Newland AB, Flagler MJ, Davis MG, Eigenheer RA, Phinney BS, Rice RH. Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis. PeerJ 2014; 2:e506. [PMID: 25165623 PMCID: PMC4137660 DOI: 10.7717/peerj.506] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/18/2014] [Indexed: 12/22/2022] Open
Abstract
Hair from different individuals can be distinguished by physical properties. Although some data exist on other species, examination of the individual molecular differences within the human hair shaft has not been thoroughly investigated. Shotgun proteomic analysis revealed considerable variation in profile among samples from Caucasian, African–American, Kenyan and Korean subjects. Within these ethnic groups, prominent keratin proteins served to distinguish individual profiles. Differences between ethnic groups, less marked, relied to a large extent on levels of keratin associated proteins. In samples from Caucasian subjects, hair shafts from axillary, beard, pubic and scalp regions exhibited distinguishable profiles, with the last being most different from the others. Finally, the profile of isolated hair cuticle cells was distinguished from that of total hair shaft by levels of more than 20 proteins, the majority of which were prominent keratins. The cuticle also exhibited relatively high levels of epidermal transglutaminase (TGM3), accounting for its observed low degree of protein extraction by denaturants. In addition to providing insight into hair structure, present findings may lead to improvements in differentiating hair from various ethnic origins and offer an approach to extending use of hair in crime scene evidence for distinguishing among individuals.
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Affiliation(s)
- Chelsea N Laatsch
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California , Davis, CA , USA
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California , Davis, CA , USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California , Davis, CA , USA
| | | | - Abby B Newland
- Procter & Gamble, Mason Business Center , Mason, OH , USA
| | | | | | | | - Brett S Phinney
- Proteomics Core Facility, University of California , Davis, CA , USA
| | - Robert H Rice
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California , Davis, CA , USA
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5
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Pha K, Wright ME, Barr TM, Eigenheer RA, Navarro L. Regulation of Yersinia protein kinase A (YpkA) kinase activity by multisite autophosphorylation and identification of an N-terminal substrate-binding domain in YpkA. J Biol Chem 2014; 289:26167-26177. [PMID: 25086045 DOI: 10.1074/jbc.m114.601153] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The serine/threonine protein kinase YpkA is an essential virulence factor produced by pathogenic Yersinia species. YpkA is delivered into host mammalian cells via a type III secretion system and localizes to the inner side of the plasma membrane. We have previously shown that YpkA binds to and phosphorylates the α subunit of the heterotrimeric G protein complex, Gαq, resulting in inhibition of Gαq signaling. To identify residues in YpkA involved in substrate binding activity we generated GFP-YpkA N-terminal deletion mutants and performed coimmunoprecipitation experiments. We located a substrate-binding domain on amino acids 40-49 of YpkA, which lies within the previously identified membrane localization domain on YpkA. Deletion of amino acids 40-49 on YpkA interfered with substrate binding, substrate phosphorylation and substrate inhibition. Autophosphorylation regulates the kinase activity of YpkA. To dissect the mechanism by which YpkA transmits signals, we performed nano liquid chromatography coupled to tandem mass spectrometry to map in vivo phosphorylation sites. Multiple serine phosphorylation sites were identified in the secretion/translocation region, kinase domain, and C-terminal region of YpkA. Using site-directed mutagenesis we generated multiple YpkA constructs harboring specific serine to alanine point mutations. Our results demonstrate that multiple autophosphorylation sites within the N terminus regulate YpkA kinase activation, whereas mutation of serine to alanine within the C terminus of YpkA had no effect on kinase activity. YpkA autophosphorylation on multiple sites may be a strategy used by pathogenic Yersinia to prevent inactivation of this important virulence protein by host proteins.
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Affiliation(s)
- Khavong Pha
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616 and
| | - Matthew E Wright
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616 and
| | - Tasha M Barr
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616 and
| | - Richard A Eigenheer
- Proteomics Core Facility, Genome Center, University of California-Davis, Davis, California 95616
| | - Lorena Navarro
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616 and.
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6
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Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Schmuth M, Gruber R. Distinguishing ichthyoses by protein profiling. PLoS One 2013; 8:e75355. [PMID: 24130705 PMCID: PMC3793978 DOI: 10.1371/journal.pone.0075355] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/13/2013] [Indexed: 12/22/2022] Open
Abstract
To explore the usefulness of protein profiling for characterization of ichthyoses, we here determined the profile of human epidermal stratum corneum by shotgun proteomics. Samples were analyzed after collection on tape circles from six anatomic sites (forearm, palm, lower leg, forehead, abdomen, upper back), demonstrating site-specific differences in profiles. Additional samples were collected from the forearms of subjects with ichthyosis vulgaris (filaggrin (FLG) deficiency), recessive X-linked ichthyosis (steroid sulfatase (STS) deficiency) and autosomal recessive congenital ichthyosis type lamellar ichthyosis (transglutaminase 1 (TGM1) deficiency). The ichthyosis protein expression patterns were readily distinguishable from each other and from phenotypically normal epidermis. In general, the degree of departure from normal was lower from ichthyosis vulgaris than from lamellar ichthyosis, parallel to the severity of the phenotype. Analysis of samples from families with ichthyosis vulgaris and concomitant modifying gene mutations (STS deficiency, GJB2 deficiency) permitted correlation of alterations in protein profile with more complex genetic constellations.
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Affiliation(s)
- Robert H. Rice
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, United States of America
| | - Katie M. Bradshaw
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, United States of America
| | - Blythe P. Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California Davis, Davis, California, United States of America
| | - David M. Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core and Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | - Richard A. Eigenheer
- Proteomics Core Facility, University of California Davis, Davis, California, United States of America
| | - Brett S. Phinney
- Proteomics Core Facility, University of California Davis, Davis, California, United States of America
| | - Matthias Schmuth
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck, Austria
| | - Robert Gruber
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck, Austria
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7
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Hu Q, Rice RH, Qin Q, Phinney BS, Eigenheer RA, Bao W, Zhao B. Proteomic analysis of human keratinocyte response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure. J Proteome Res 2013; 12:5340-7. [PMID: 23991859 DOI: 10.1021/pr4006266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chronic exposure to 2,3,7,8-tetrachlorodibeno-p-dioxin (TCDD) and related polyhalogenated organic pollutants occurs as a consequence of modern life. Exploring the cellular basis for their action is anticipated to help understand the risk they pose and improve the foundation for their regulation. A basis for the striking change in human keratinocyte colony morphology due to TCDD exposure has been investigated by shotgun proteomics. Concentrating on changes in protein levels among three cell strains has revealed significant decreases in the differentiation markers filaggrin, keratin 1, and keratin 10. EGF treatment in concert with TCDD enhanced the changes in these markers and several other proteins while reducing the levels of certain other proteins. The only protein stimulated by TCDD in all three strains and reversed by EGF in them was vimentin, not previously observed to be in the aryl hydrocarbon receptor response domain. Although TCDD is often proposed to enhance keratinocyte differentiation, proteomic analysis reveals it uncouples the differentiation program and suggests that reduced levels of differentiation marker proteins contribute to the observed excessive stratification it induces.
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Affiliation(s)
- Qin Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
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Vu K, Eigenheer RA, Phinney BS, Gelli A. Cryptococcus neoformans promotes its transmigration into the central nervous system by inducing molecular and cellular changes in brain endothelial cells. Infect Immun 2013; 81:3139-47. [PMID: 23774597 PMCID: PMC3754227 DOI: 10.1128/iai.00554-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/07/2013] [Indexed: 12/31/2022] Open
Abstract
Cryptococcus spp. cause fungal meningitis, a life-threatening infection that occurs predominately in immunocompromised individuals. In order for Cryptococcus neoformans to invade the central nervous system (CNS), it must first penetrate the brain endothelium, also known as the blood-brain barrier (BBB). Despite the importance of the interrelation between C. neoformans and the brain endothelium in establishing CNS infection, very little is known about this microenvironment. Here we sought to resolve the cellular and molecular basis that defines the fungal-BBB interface during cryptococcal attachment to, and internalization by, the human brain endothelium. In order to accomplish this by a systems-wide approach, the proteomic profile of human brain endothelial cells challenged with C. neoformans was resolved using a label-free differential quantitative mass spectrometry method known as spectral counting (SC). Here, we demonstrate that as brain endothelial cells associate with, and internalize, cryptococci, they upregulate the expression of several proteins involved with cytoskeleton, metabolism, signaling, and inflammation, suggesting that they are actively signaling and undergoing cytoskeleton remodeling via annexin A2, S100A10, transgelin, and myosin. Transmission electronic microscopy (TEM) analysis demonstrates dramatic structural changes in nuclei, mitochondria, the endoplasmic reticulum (ER), and the plasma membrane that are indicative of cell stress and cell damage. The translocation of HMGB1, a marker of cell injury, the downregulation of proteins that function in transcription, energy production, protein processing, and the upregulation of cyclophilin A further support the notion that C. neoformans elicits changes in brain endothelial cells that facilitate the migration of cryptococci across the BBB and ultimately induce endothelial cell necrosis.
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Affiliation(s)
- Kiem Vu
- Department of Pharmacology, School of Medicine, University of California, Genome and Biomedical Sciences Facility, Davis, California, USA
| | - Richard A. Eigenheer
- Proteomics Core Facility, University of California, Genome Center, Davis, California, USA
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Genome Center, Davis, California, USA
| | - Angie Gelli
- Department of Pharmacology, School of Medicine, University of California, Genome and Biomedical Sciences Facility, Davis, California, USA
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Xavier MN, Winter MG, Spees AM, den Hartigh AB, Nguyen K, Roux CM, Silva TMA, Atluri VL, Kerrinnes T, Keestra AM, Monack DM, Luciw PA, Eigenheer RA, Bäumler AJ, Santos RL, Tsolis RM. PPARγ-mediated increase in glucose availability sustains chronic Brucella abortus infection in alternatively activated macrophages. Cell Host Microbe 2013; 14:159-70. [PMID: 23954155 PMCID: PMC3777723 DOI: 10.1016/j.chom.2013.07.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/17/2013] [Accepted: 06/20/2013] [Indexed: 01/16/2023]
Abstract
Eradication of persistent intracellular bacterial pathogens with antibiotic therapy is often slow or incomplete. However, strategies to augment antibiotics are hampered by our poor understanding of the nutritional environment that sustains chronic infection. Here we show that the intracellular pathogen Brucella abortus survives and replicates preferentially in alternatively activated macrophages (AAMs), which are more abundant during chronic infection. A metabolic shift induced by peroxisome proliferator-activated receptor γ (PPARγ), which increases intracellular glucose availability, is identified as a causal mechanism promoting enhanced bacterial survival in AAMs. Glucose uptake was crucial for increased replication of B. abortus in AAMs, and for chronic infection, as inactivation of the bacterial glucose transporter gluP reduced both intracellular survival in AAMs and persistence in mice. Thus, a shift in intracellular nutrient availability induced by PPARγ promotes chronic persistence of B. abortus within AAMs, and targeting this pathway may aid in eradicating chronic infection.
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Affiliation(s)
- Mariana N. Xavier
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Maria G. Winter
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Alanna M. Spees
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Andreas B. den Hartigh
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Kim Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Christelle M. Roux
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Teane M. A. Silva
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Vidya L. Atluri
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Tobias Kerrinnes
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - A. Marijke Keestra
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Denise M. Monack
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Paul A. Luciw
- Center for Comparative Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Richard A. Eigenheer
- Proteomics Core Facility, University of California at Davis Genome Center, Davis, CA, 95616, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
| | - Renato L. Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Renée M. Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, 95616, USA
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Keestra AM, Winter MG, Auburger JJ, Frässle SP, Xavier MN, Winter SE, Kim A, Poon V, Ravesloot MM, Waldenmaier JFT, Tsolis RM, Eigenheer RA, Bäumler AJ. Manipulation of small Rho GTPases is a pathogen-induced process detected by NOD1. Nature 2013; 496:233-7. [PMID: 23542589 PMCID: PMC3625479 DOI: 10.1038/nature12025] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 02/19/2013] [Indexed: 12/11/2022]
Abstract
Our innate immune system distinguishes microbes from self by detecting conserved pathogen-associated molecular patterns. However, these are produced by all microbes, regardless of their pathogenic potential. To distinguish virulent microbes from those with lower disease-causing potential the innate immune system detects conserved pathogen-induced processes, such as the presence of microbial products in the host cytosol, by mechanisms that are not fully resolved. Here we show that NOD1 senses cytosolic microbial products by monitoring the activation state of small Rho GTPases. Activation of RAC1 and CDC42 by bacterial delivery or ectopic expression of SopE, a virulence factor of the enteric pathogen Salmonella, triggered the NOD1 signalling pathway, with consequent RIP2 (also known as RIPK2)-mediated induction of NF-κB-dependent inflammatory responses. Similarly, activation of the NOD1 signalling pathway by peptidoglycan required RAC1 activity. Furthermore, constitutively active forms of RAC1, CDC42 and RHOA activated the NOD1 signalling pathway. Our data identify the activation of small Rho GTPases as a pathogen-induced process sensed through the NOD1 signalling pathway.
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Affiliation(s)
- A Marijke Keestra
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Avenue, Davis, California 95616, USA
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11
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Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Sundberg JP. Differentiating inbred mouse strains from each other and those with single gene mutations using hair proteomics. PLoS One 2012; 7:e51956. [PMID: 23251662 PMCID: PMC3522583 DOI: 10.1371/journal.pone.0051956] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 11/07/2012] [Indexed: 01/29/2023] Open
Abstract
Mutant laboratory mice with distinctive hair phenotypes are useful for identifying genes responsible for hair diseases. The work presented here demonstrates that shotgun proteomic profiling can distinguish hair shafts from different inbred mouse strains. For this purpose, analyzing the total hair shaft provided better discrimination than analyzing the isolated solubilized and particulate (cross-linked) fractions. Over 100 proteins exhibited significant differences among the 11 strains and 5 mutant stocks across the wide spectrum of strains surveyed. Effects on the profile of single gene mutations causing hair shaft defects were profound. Since the hair shaft provides a discrete sampling of the species proteome, with constituents serving important functions in epidermal appendages and throughout the body, this work provides a foundation for non-invasive diagnosis of genetic diseases of hair and perhaps other tissues.
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Affiliation(s)
- Robert H Rice
- Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, USA.
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12
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Hotton SK, Castro MF, Eigenheer RA, Callis J. Recovery of DDB1a (damaged DNA binding protein1a) in a screen to identify novel RUB-modified proteins in Arabidopsis thaliana. Mol Plant 2012; 5:1163-1166. [PMID: 22893627 DOI: 10.1093/mp/sss077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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13
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Katz E, Boo KH, Kim HY, Eigenheer RA, Phinney BS, Shulaev V, Negre-Zakharov F, Sadka A, Blumwald E. Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development. J Exp Bot 2011; 62:5367-84. [PMID: 21841177 PMCID: PMC3223037 DOI: 10.1093/jxb/err197] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/17/2011] [Accepted: 05/20/2011] [Indexed: 05/18/2023]
Abstract
Label-free LC-MS/MS-based shot-gun proteomics was used to quantify the differential protein synthesis and metabolite profiling in order to assess metabolic changes during the development of citrus fruits. Our results suggested the occurrence of a metabolic change during citrus fruit maturation, where the organic acid and amino acid accumulation seen during the early stages of development shifted into sugar synthesis during the later stage of citrus fruit development. The expression of invertases remained unchanged, while an invertase inhibitor was up-regulated towards maturation. The increased expression of sucrose-phosphate synthase and sucrose-6-phosphate phosphatase and the rapid sugar accumulation suggest that sucrose is also being synthesized in citrus juice sac cells during the later stage of fruit development.
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Affiliation(s)
- Ehud Katz
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Kyung Hwan Boo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Ho Youn Kim
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Richard A. Eigenheer
- Genome Center, Proteomics Core Facility, University of California, Davis, CA 95616, USA
| | - Brett S. Phinney
- Genome Center, Proteomics Core Facility, University of California, Davis, CA 95616, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, TX 76203-5017, USA
| | | | - Avi Sadka
- Department of Fruit Tree Species, ARO, The Volcani Center, 50250 Bet Dagan, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- To whom correspondence should be addressed. E-mail:
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Hotton SK, Eigenheer RA, Castro MF, Bostick M, Callis J. AXR1-ECR1 and AXL1-ECR1 heterodimeric RUB-activating enzymes diverge in function in Arabidopsis thaliana. Plant Mol Biol 2011; 75:515-26. [PMID: 21311953 PMCID: PMC3044220 DOI: 10.1007/s11103-011-9750-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 01/27/2011] [Indexed: 05/08/2023]
Abstract
RELATED TO UBIQUITIN (RUB) modification of CULLIN (CUL) subunits of the CUL-RING ubiquitin E3 ligase (CRL) superfamily regulates CRL ubiquitylation activity. RUB modification requires E1 and E2 enzymes that are analogous to, but distinct from, those activities required for UBIQUITIN (UBQ) attachment. Gene duplications are widespread in angiosperms, and in line with this observation, components of the RUB conjugation pathway are found in multiples in Arabidopsis. To further examine the extent of redundancy within the RUB pathway, we undertook biochemical and genetic characterizations of one such duplication event- the duplication of the genes encoding a subunit of the RUB E1 into AUXIN RESISTANT1 (AXR1) and AXR1-LIKE1 (AXL1). In vitro, the two proteins have similar abilities to function with E1 C-TERMINAL-RELATED1 (ECR1) in catalyzing RUB1 activation and RUB1-ECR1 thioester formation. Using mass spectrometry, endogenous AXR1 and AXL1 proteins were found in complex with 3HA-RUB1, suggesting that AXR1 and AXL1 exist in parallel RUB E1 complexes in Arabidopsis. In contrast, AXR1 and AXL1 differ in ability to correct phenotypic defects in axr1-30, a severe loss-of-function AXR1 mutant, when the respective coding sequences are expressed from the same promoter, suggesting differential in vivo functions. These results suggest that while both proteins function in the RUB pathway and are biochemically similar in RUB-ECR1 thioester formation, they are not functionally equivalent.
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Affiliation(s)
- Sara K. Hotton
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA 95616 USA
| | - Richard A. Eigenheer
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616 USA
| | - Meliza F. Castro
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA 95616 USA
| | - Magnolia Bostick
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA 95616 USA
- Present Address: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Judy Callis
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA 95616 USA
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Katz E, Fon M, Eigenheer RA, Phinney BS, Fass JN, Lin D, Sadka A, Blumwald E. A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development. Proteome Sci 2010; 8:68. [PMID: 21162737 PMCID: PMC3017515 DOI: 10.1186/1477-5956-8-68] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 12/16/2010] [Indexed: 01/03/2023] Open
Abstract
Background Citrus is one of the most important and widely grown commodity fruit crops. In this study a label-free LC-MS/MS based shot-gun proteomics approach was taken to explore three main stages of citrus fruit development. These approaches were used to identify and evaluate changes occurring in juice sac cells in various metabolic pathways affecting citrus fruit development and quality. Results Protein changes in citrus juice sac cells were identified and quantified using label-free shotgun methodologies. Two alternative methods, differential mass-spectrometry (dMS) and spectral counting (SC) were used to analyze protein changes occurring during earlier and late stages of fruit development. Both methods were compared in order to develop a proteomics workflow that could be used in a non-model plant lacking a sequenced genome. In order to resolve the bioinformatics limitations of EST databases from species that lack a full sequenced genome, we established iCitrus. iCitrus is a comprehensive sequence database created by merging three major sources of sequences (HarvEST:citrus, NCBI/citrus/unigenes, NCBI/citrus/proteins) and improving the annotation of existing unigenes. iCitrus provided a useful bioinformatics tool for the high-throughput identification of citrus proteins. We have identified approximately 1500 citrus proteins expressed in fruit juice sac cells and quantified the changes of their expression during fruit development. Our results showed that both dMS and SC provided significant information on protein changes, with dMS providing a higher accuracy. Conclusion Our data supports the notion of the complementary use of dMS and SC for label-free comparative proteomics, broadening the identification spectrum and strengthening the identification of trends in protein expression changes during the particular processes being compared.
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Affiliation(s)
- Ehud Katz
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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Kundu S, Brinkmeyer MK, Eigenheer RA, David SS. Ser 524 is a phosphorylation site in MUTYH and Ser 524 mutations alter 8-oxoguanine (OG): a mismatch recognition. DNA Repair (Amst) 2010; 9:1026-37. [PMID: 20724227 DOI: 10.1016/j.dnarep.2010.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 06/22/2010] [Accepted: 07/02/2010] [Indexed: 12/17/2022]
Abstract
MUTYH-associated polyposis (MAP) is a colorectal cancer predisposition syndrome that is caused by inherited biallelic mutations in the base excision repair (BER) gene, MUTYH. MUTYH is a DNA glycosylase that removes adenine (A) misinserted opposite 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG). In this work, wild type (WT) MUTYH overexpressed using a baculovirus-driven insect cell expression system (BEVS) provided significantly higher levels of enzyme compared to bacterial overexpression. The isolated MUTYH enzyme was analyzed for potential post-translational modifications using mass spectrometry. An in vivo phosphorylation site was validated at Serine 524, which is located in the C-terminal OG recognition domain within the proliferating cell nuclear antigen (PCNA) binding region. Characterization of the phosphomimetic (S524D) and phosphoablating (S524A) mutants together with the observation that Ser 524 can be phosphorylated suggest that this residue may play an important regulatory role in vivo by altering stability and OG:A mismatch affinity.
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Affiliation(s)
- Sucharita Kundu
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
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Smilowitz JT, Argov N, Eigenheer RA, Lemay DG, German JB. Metabolic Phenotyping to Assess Personalized Nutrition: Use of the Response‐to‐Challenge Model. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.542.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Nurit Argov
- The Hebrew University of JerusalemTel‐AvivIsrael
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Todorović V, Desai BV, Eigenheer RA, Yin T, Amargo EV, Mrksich M, Green KJ, Patterson MJS. Detection of differentially expressed basal cell proteins by mass spectrometry. Mol Cell Proteomics 2009; 9:351-61. [PMID: 19955077 DOI: 10.1074/mcp.m900358-mcp200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The ability of cells to modulate interactions with each other and the substrate is essential for epithelial tissue remodeling during processes such as wound healing and tumor progression. However, despite strides made in the field of proteomics, proteins involved in adhesion have been difficult to study. Here, we report a method for the enrichment and analysis of proteins associated with the basal surface of the cell and its underlying matrix. The enrichment involves deroofing the cells with 20 mM ammonium hydroxide and the removal of cytosolic and organellar proteins by stringent water wash. Proteomic profiling was achieved by LC-FTMS, which allowed comparison of differentially expressed or shared proteins under different cell states. First, we analyzed and compared the basal cell components of mouse keratinocytes lacking the cell-cell junction molecule plakoglobin with their control counterparts. Changes in the molecules involved in motility and invasion were detected in plakoglobin-deficient cells, including decreased detection of fibronectin, integrin beta(4), and FAT tumor suppressor. Second, we assessed the differences in basal cell components between two human oral squamous cell carcinoma lines originating from different sites in the oral cavity (CAL33 and UM-SCC-1). The data show differences between the two lines in the type and abundance of proteins specific to cell adhesion, migration, and angiogenesis. Therefore, the method described here has the potential to serve as a platform to assess proteomic changes in basal cell components including extracellular and adhesion-specific proteins involved in wound healing, cancer, and chronic and acquired adhesion-related disorders.
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Affiliation(s)
- Viktor Todorović
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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Eigenheer RA, Jin Lee Y, Blumwald E, Phinney BS, Gelli A. Extracellular glycosylphosphatidylinositol-anchored mannoproteins and proteases of Cryptococcus neoformans. FEMS Yeast Res 2007; 7:499-510. [PMID: 17233760 DOI: 10.1111/j.1567-1364.2006.00198.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Extracellular proteins of Cryptococcus neoformans are involved in the pathogenesis of cryptococcosis, and some are immunoreactive antigens that may potentially serve as candidates for vaccine development. To further study the extracellular proteome of the human fungal pathogen Cry. neoformans, we conducted a proteomic analysis of secreted and cell wall-bound proteins with an acapsular strain of Cry. neoformans. Proteins were identified from both intact cells and cell walls. In both cases, extracellular proteins were removed with trypsin or beta-glucanase, and then all proteins/peptides were purified by solid-phase extraction, spin dialysis, and HPLC, and identified by liquid chromatography-mass spectrometry. This study identified 29 extracellular proteins with a predicted N-terminal signal sequence and also a predicted glycosylphosphatidylinositol anchor motif in more than half. Among the novel proteins identified were five glycosylphosphatidylinositol-anchored proteins with extensive Ser/Thr-rich regions but no apparent functional domains, a glycosylphosphatidylinositol-anchored aspartic protease, and a metalloprotease with structural similarity to an elastinolytic metalloprotease of Aspergillus fumigatus. This study suggests that Cry. neoformans has the machinery required to target glycosylphosphatidylinositol-anchored proteins to the cell wall, and it confirms the extracellular proteolytic ability of Cry. neoformans.
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Affiliation(s)
- Richard A Eigenheer
- Department of Medical Pharmacology and Toxicology Genome and Biomedical Sciences Facility, University of California, California 95616, USA
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Abstract
We isolated from head extracts of Tenebrio molitor a peptide that inhibits fluid secretion by the Malpighian tubules of this insect. This second antidiuretic factor, ADFb, like the previously published ADFa, works through cyclic GMP as a second messenger. It has primary structure Tyr-Asp-Asp-Gly-Ser-Tyr-Lys-Pro-His-Ile-Tyr-Gly-Phe-OH with an EC(50) of approximately 240 pM in a fluid secretion assay. This peptide is now the second sequenced endogenous insect ADF which inhibits Malpighian tubule fluid secretion. Immunohistochemical techniques show that the peptide is localized in the brain; it appears to be produced mainly in two pairs of bilaterally symmetrical cells in the protocerebrum.
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Affiliation(s)
- Richard A Eigenheer
- Department of Biochemistry, 160 Howard Medical Science, University of Nevada, Mail Stop 330, Reno, NV 89557-0014, USA
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Wiehart UIM, Nicolson SW, Eigenheer RA, Schooley DA. Antagonistic control of fluid secretion by the Malpighian tubules ofTenebrio molitor: effects of diuretic and antidiuretic peptides and their second messengers. J Exp Biol 2002; 205:493-501. [PMID: 11893763 DOI: 10.1242/jeb.205.4.493] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARYFluid secretion by insect Malpighian tubules is controlled by haemolymph-borne factors. The mealworm Tenebrio molitor provides the first known example of antagonistic interactions between endogenous neuropeptides acting on Malpighian tubules. The two corticotropin-releasing-factor (CRF)-related diuretic peptides previously isolated from Tenebrio molitor, Tenmo-DH37 and Tenmo-DH47, were found to stimulate Tenebrio molitor tubules in vitro in a dose-dependent manner with EC50 values of 0.12 nmol l–1 and 26 nmol l–1 respectively. However, no synergistic or additive effect was observed when these two peptides were tested simultaneously. We then investigated antagonism between second messengers: dose–response curves were constructed for stimulation of Tenebrio molitor tubules by cyclic AMP and their inhibition by cyclic GMP. When both cyclic nucleotides were included in the bathing Ringer, the stimulatory effect of cyclic AMP was neutralised by cyclic GMP. Similarly, the stimulatory effect of Tenmo-DH37 was reversed on addition of an antidiuretic peptide (Tenmo-ADF), which was recently isolated from Tenebrio molitor and acts via cyclic GMP. The cardioacceleratory peptide CAP2b, originally isolated from Manduca sexta, also increases intracellular cyclic GMP levels and inhibited fluid secretion by Tenebrio molitor tubules, with an EC50 value of 85 nmol l–1. This inhibitory effect was reversed by Tenmo-DH37. Endogenous diuretic and antidiuretic peptides, effective at low concentrations and acting via antagonistic second messengers, have the potential for fine control of secretion rates in the Malpighian tubules of Tenebrio molitor.
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Affiliation(s)
- U I M Wiehart
- Department of Zoology, University of Cape Town, Rondebosch 7701, South Africa
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Eigenheer RA, Nicolson SW, Schegg KM, Hull JJ, Schooley DA. Identification of a potent antidiuretic factor acting on beetle Malpighian tubules. Proc Natl Acad Sci U S A 2002; 99:84-9. [PMID: 11756661 PMCID: PMC117518 DOI: 10.1073/pnas.012436199] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2001] [Indexed: 11/18/2022] Open
Abstract
Beetles, like other insects, depend on diuretic and antidiuretic hormones to control water balance. We have isolated, using head extracts from the beetle Tenebrio molitor, a peptide that strongly inhibits fluid secretion by the Malpighian tubules of this insect. This antidiuretic factor (ADF) appears to elicit its effect via cGMP as a second messenger but does not stimulate NO production. It has primary structure: Val-Val-Asn-Thr-Pro-Gly-His-Ala-Val-Ser-Tyr-His-Val-Tyr-OH. The ADF inhibits tubule secretion with high potency: the EC(50) is around 10 fM. It bears no significant resemblance to other biologically active neuropeptides. To our knowledge this is the only endogenous insect ADF acting on Malpighian tubules to be sequenced, and the first coleopteran (beetle) antidiuretic factor fully characterized to date.
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