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Lozinski BM, de Almeida LGN, Silva C, Dong Y, Brown D, Chopra S, Yong VW, Dufour A. Exercise rapidly alters proteomes in mice following spinal cord demyelination. Sci Rep 2021; 11:7239. [PMID: 33790323 PMCID: PMC8012633 DOI: 10.1038/s41598-021-86593-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/16/2021] [Indexed: 02/01/2023] Open
Abstract
Exercise affords broad benefits for people with multiple sclerosis (PwMS) including less fatigue, depression, and improved cognition. In animal models of multiple sclerosis (MS), exercise has been shown to improve remyelination, decrease blood-brain barrier permeability and reduce leukocyte infiltration. Despite these benefits many PwMS refrain from engaging in physical activity. This barrier to participation in exercise may be overcome by uncovering and describing the mechanisms by which exercise promotes beneficial changes in the central nervous system (CNS). Here, we show that acute bouts of exercise in mice profoundly alters the proteome in demyelinating lesions. Following lysolecithin induced demyelination of the ventral spinal cord, mice were given immediate access to a running wheel for 4 days. Lesioned spinal cords and peripheral blood serum were then subjected to tandem mass tag labeling shotgun proteomics workflow to identify alteration in protein levels. We identified 86 significantly upregulated and 85 downregulated proteins in the lesioned spinal cord as well as 14 significantly upregulated and 11 downregulated proteins in the serum following acute exercise. Altered pathways following exercise in demyelinated mice include oxidative stress response, metabolism and transmission across chemical synapses. Similar acute bout of exercise in naïve mice also changed several proteins in the serum and spinal cord, including those for metabolism and anti-oxidant responses. Improving our understanding of the mechanisms and duration of activity required to influence the injured CNS should motivate PwMS and other conditions to embrace exercise as part of their therapy to manage CNS disability.
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Affiliation(s)
- Brian Mark Lozinski
- Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
- The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada
| | - Luiz Gustavo Nogueira de Almeida
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada
- HRIC 3C64, Department of Physiology and Pharmacology, University of Calgary, 3330 Hospital Drive Calgary, Alberta, T2N 4N1, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada
| | - Claudia Silva
- Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
- The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada
| | - Yifei Dong
- Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
- The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada
| | - Dennis Brown
- Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
- The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada
| | - Sameeksha Chopra
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada
- HRIC 3C64, Department of Physiology and Pharmacology, University of Calgary, 3330 Hospital Drive Calgary, Alberta, T2N 4N1, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
- The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada
| | - Antoine Dufour
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada.
- HRIC 3C64, Department of Physiology and Pharmacology, University of Calgary, 3330 Hospital Drive Calgary, Alberta, T2N 4N1, Canada.
- The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada.
- McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada.
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2
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Kalish BT, Kim E, Finander B, Duffy EE, Kim H, Gilman CK, Yim YS, Tong L, Kaufman RJ, Griffith EC, Choi GB, Greenberg ME, Huh JR. Maternal immune activation in mice disrupts proteostasis in the fetal brain. Nat Neurosci 2021; 24:204-213. [PMID: 33361822 PMCID: PMC7854524 DOI: 10.1038/s41593-020-00762-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022]
Abstract
Maternal infection and inflammation during pregnancy are associated with neurodevelopmental disorders in offspring, but little is understood about the molecular mechanisms underlying this epidemiologic phenomenon. Here, we leveraged single-cell RNA sequencing to profile transcriptional changes in the mouse fetal brain in response to maternal immune activation (MIA) and identified perturbations in cellular pathways associated with mRNA translation, ribosome biogenesis and stress signaling. We found that MIA activates the integrated stress response (ISR) in male, but not female, MIA offspring in an interleukin-17a-dependent manner, which reduced global mRNA translation and altered nascent proteome synthesis. Moreover, blockade of ISR activation prevented the behavioral abnormalities as well as increased cortical neural activity in MIA male offspring. Our data suggest that sex-specific activation of the ISR leads to maternal inflammation-associated neurodevelopmental disorders.
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Affiliation(s)
- Brian T Kalish
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
| | - Eunha Kim
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Benjamin Finander
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Erin E Duffy
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hyunju Kim
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Casey K Gilman
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yeong Shin Yim
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lilin Tong
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Randal J Kaufman
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eric C Griffith
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gloria B Choi
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael E Greenberg
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Jun R Huh
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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3
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An H, Ordureau A, Körner M, Paulo JA, Harper JW. Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature 2020; 583:303-309. [PMID: 32612236 PMCID: PMC7351614 DOI: 10.1038/s41586-020-2446-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 02/02/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022]
Abstract
Mammalian cells reorganize their proteomes in response to nutrient stress through translational suppression and degradative mechanisms using the proteasome and autophagy systems1,2. Ribosomes are central targets of this response, as they are responsible for translation and subject to lysosomal turnover during nutrient stress3-5. The abundance of ribosomal (r)-proteins (around 6% of the proteome; 107 copies per cell)6,7 and their high arginine and lysine content has led to the hypothesis that they are selectively used as a source of basic amino acids during nutrient stress through autophagy4,7. However, the relative contributions of translational and degradative mechanisms to the control of r-protein abundance during acute stress responses is poorly understood, as is the extent to which r-proteins are used to generate amino acids when specific building blocks are limited7. Here, we integrate quantitative global translatome and degradome proteomics8 with genetically encoded Ribo-Keima5 and Ribo-Halo reporters to interrogate r-protein homeostasis with and without active autophagy. In conditions of acute nutrient stress, cells strongly suppress the translation of r-proteins, but, notably, r-protein degradation occurs largely through non-autophagic pathways. Simultaneously, the decrease in r-protein abundance is compensated for by a reduced dilution of pre-existing ribosomes and a reduction in cell volume, thereby maintaining the density of ribosomes within single cells. Withdrawal of basic or hydrophobic amino acids induces translational repression without differential induction of ribophagy, indicating that ribophagy is not used to selectively produce basic amino acids during acute nutrient stress. We present a quantitative framework that describes the contributions of biosynthetic and degradative mechanisms to r-protein abundance and proteome remodelling in conditions of nutrient stress.
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Affiliation(s)
- Heeseon An
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Körner
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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4
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Abstract
Manipulation of individual molecules with optical tweezers provides a powerful means of interrogating the structure and folding of proteins. Mechanical force is not only a relevant quantity in cellular protein folding and function, but also a convenient parameter for biophysical folding studies. Optical tweezers offer precise control in the force range relevant for protein folding and unfolding, from which single-molecule kinetic and thermodynamic information about these processes can be extracted. In this review, we describe both physical principles and practical aspects of optical tweezers measurements and discuss recent advances in the use of this technique for the study of protein folding. In particular, we describe the characterization of folding energy landscapes at high resolution, studies of structurally complex multidomain proteins, folding in the presence of chaperones, and the ability to investigate real-time cotranslational folding of a polypeptide.
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Affiliation(s)
- Carlos Bustamante
- Department of Molecular and Cell Biology, Department of Physics, Howard Hughes Medical Institute, and Kavli Energy NanoScience Institute, University of California, Berkeley, California 94720, USA;
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Lisa Alexander
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Kevin Maciuba
- Cell, Molecular, Developmental Biology, and Biophysics Graduate Program, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Christian M Kaiser
- Department of Biology and Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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5
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da Silva-Gomes RN, Gabriel Kuniyoshi ML, Oliveira da Silva Duran B, Thomazini Zanella BT, Paccielli Freire P, Gutierrez de Paula T, de Almeida Fantinatti BE, Simões Salomão RA, Carvalho RF, Delazari Santos L, Dal-Pai-Silva M. Prolonged fasting followed by refeeding modifies proteome profile and parvalbumin expression in the fast-twitch muscle of pacu (Piaractus mesopotamicus). PLoS One 2019; 14:e0225864. [PMID: 31856193 PMCID: PMC6922423 DOI: 10.1371/journal.pone.0225864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/22/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023] Open
Abstract
Here, we analyzed the fast-twitch muscle of juvenile Piaractus mesopotamicus (pacu) submitted to prolonged fasting (30d) and refeeding (6h, 24h, 48h and 30d). We measured the relative rate of weight and length increase (RRIlength and RRIweight), performed shotgun proteomic analysis and did Western blotting for PVALB after 30d of fasting and 30d of refeeding. We assessed the gene expression of igf-1, mafbx and pvalb after 30d of fasting and after 6h, 24h, 48h and 30d of refeeding. We performed a bioinformatic analysis to predict miRNAs that possibly control parvalbumin expression. After fasting, RRIlength, RRIweight and igf-1 expression decreased, while the mafbx expression increased, which suggest that prolonged fasting caused muscle atrophy. After 6h and 24h of refeeding, mafbx was not changed and igf-1 was downregulated, while after 48h of refeeding mafbx was downregulated and igf-1 was not changed. After 30d of refeeding, RRIlength and RRIweight were increased and igf-1 and mafbx expression were not changed. Proteomic analysis identified 99 proteins after 30d of fasting and 71 proteins after 30d of refeeding, of which 23 and 17, respectively, were differentially expressed. Most of these differentially expressed proteins were related to cytoskeleton, muscle contraction, and metabolism. Among these, parvalbumin (PVALB) was selected for further validation. The analysis showed that pvalb mRNA was downregulated after 6h and 24h of refeeding, but was not changed after 30d of fasting or 48h and 30d of refeeding. The Western blotting confirmed that PVALB protein was downregulated after 30d of fasting and 30d of refeeding. The downregulation of the protein and the unchanged expression of the mRNA after 30d of fasting and 30d of refeeding suggest a post-transcriptional regulation of PVALB. Our miRNA analysis predicted 444 unique miRNAs that may target pvalb. In conclusion, muscle atrophy and partial compensatory growth caused by prolonged fasting followed by refeeding affected the muscle proteome and PVALB expression.
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Affiliation(s)
- Rafaela Nunes da Silva-Gomes
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Maria Laura Gabriel Kuniyoshi
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Bruno Oliveira da Silva Duran
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Bruna Tereza Thomazini Zanella
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Paula Paccielli Freire
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Tassiana Gutierrez de Paula
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | | | - Robson Francisco Carvalho
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Lucilene Delazari Santos
- Center for the Studies of Venoms and Venomous Animals (CEVAP)/ Graduate Program in Tropical Diseases (FMB), São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Maeli Dal-Pai-Silva
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- * E-mail:
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6
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Gomez-Lopez N, Romero R, Hassan SS, Bhatti G, Berry SM, Kusanovic JP, Pacora P, Tarca AL. The Cellular Transcriptome in the Maternal Circulation During Normal Pregnancy: A Longitudinal Study. Front Immunol 2019; 10:2863. [PMID: 31921132 PMCID: PMC6928201 DOI: 10.3389/fimmu.2019.02863] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022] Open
Abstract
Pregnancy represents a unique immunological state in which the mother adapts to tolerate the semi-allogenic conceptus; yet, the cellular dynamics in the maternal circulation are poorly understood. Using exon-level expression profiling of up to six longitudinal whole blood samples from 49 pregnant women, we undertook a systems biology analysis of the cellular transcriptome dynamics and its correlation with the plasma proteome. We found that: (1) chromosome 14 was the most enriched in transcripts differentially expressed throughout normal pregnancy; (2) the strongest expression changes followed three distinct longitudinal patterns, with genes related to host immune response (e.g., MMP8, DEFA1B, DEFA4, and LTF) showing a steady increase in expression from 10 to 40 weeks of gestation; (3) multiple biological processes and pathways related to immunity and inflammation were modulated during gestation; (4) genes changing with gestation were among those specific to T cells, B cells, CD71+ erythroid cells, natural killer cells, and endothelial cells, as defined based on the GNF Gene Expression Atlas; (5) the average expression of mRNA signatures of T cells, B cells, and erythroid cells followed unique patterns during gestation; (6) the correlation between mRNA and protein abundance was higher for mRNAs that were differentially expressed throughout gestation than for those that were not, and significant mRNA-protein correlations were observed for genes part of the T-cell signature. In summary, unique changes in immune-related genes were discovered by longitudinally assessing the cellular transcriptome in the maternal circulation throughout normal pregnancy, and positive correlations were noted between the cellular transcriptome and plasma proteome for specific genes/proteins. These findings provide insights into the immunobiology of normal pregnancy.
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Affiliation(s)
- Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD and Detroit, MI, United States
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD and Detroit, MI, United States
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, United States
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
- Detroit Medical Center, Detroit, MI, United States
- Department of Obstetrics & Gynecology, Florida International University, Miami, FL, United States
| | - Sonia S. Hassan
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Gaurav Bhatti
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD and Detroit, MI, United States
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Stanley M. Berry
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD and Detroit, MI, United States
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Juan Pedro Kusanovic
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD and Detroit, MI, United States
- Division of Obstetrics and Gynecology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Research and Innovation in Maternal-Fetal Medicine (CIMAF), Department of Obstetrics and Gynecology, Sótero del Río Hospital, Santiago, Chile
| | - Percy Pacora
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD and Detroit, MI, United States
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Adi L. Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD and Detroit, MI, United States
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, United States
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7
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Koçillari L, Fariselli P, Trovato A, Seno F, Maritan A. Signature of Pareto optimization in the Escherichia coli proteome. Sci Rep 2018; 8:9141. [PMID: 29904084 PMCID: PMC6002381 DOI: 10.1038/s41598-018-27287-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/15/2018] [Indexed: 01/20/2023] Open
Abstract
Proteins have coevolved with cellular environments to improve or preserve their functions, maintaining at the same time the degree of hydrophobicity necessary to fold correctly and enough solubility to perform their biological roles. Here, we study the Escherichia coli proteome using a Pareto front analysis in the solubility-hydrophobicity space. The results indicate the existence of a Pareto optimal front, a triangle whose vertices correspond to archetypal proteins specialized in distinct tasks, such as regulatory processes, membrane transport, outer-membrane pore formation, catalysis, and binding. The vertices are further enriched with proteins that occupy different subcellular compartments, namely, cytoplasmic, inner membrane, outer membrane, and outer membrane bounded periplasmic space. The combination of various enriching features offers an interpretation of how bacteria use the physico-chemical properties of proteins, both to drive them into their final destination in the cell and to have their tasks accomplished.
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Affiliation(s)
- Loren Koçillari
- INFN and Dipartimento di Fisica e Astronomia 'G. Galilei', Università di Padova, Via Marzolo 8, Padova, 35131, IT, Italy
| | - Piero Fariselli
- Dipartimento di Biomedicina Comparata e Alimentazione, Università di Padova, Viale dell' Università 16, Legnaro, 35020, IT, Italy
| | - Antonio Trovato
- INFN and Dipartimento di Fisica e Astronomia 'G. Galilei', Università di Padova, Via Marzolo 8, Padova, 35131, IT, Italy
| | - Flavio Seno
- INFN and Dipartimento di Fisica e Astronomia 'G. Galilei', Università di Padova, Via Marzolo 8, Padova, 35131, IT, Italy
| | - Amos Maritan
- INFN and Dipartimento di Fisica e Astronomia 'G. Galilei', Università di Padova, Via Marzolo 8, Padova, 35131, IT, Italy.
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8
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Rockenbach MF, Corrêa CCG, Heringer AS, Freitas ILJ, Santa-Catarina C, do Amaral-Júnior AT, Silveira V. Differentially abundant proteins associated with heterosis in the primary roots of popcorn. PLoS One 2018; 13:e0197114. [PMID: 29758068 PMCID: PMC5951555 DOI: 10.1371/journal.pone.0197114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 11/06/2017] [Accepted: 04/26/2018] [Indexed: 12/21/2022] Open
Abstract
Although heterosis has significantly contributed to increases in worldwide crop production, the molecular mechanisms regulating this phenomenon are still unknown. In the present study, we used a comparative proteomic approach to explore hybrid vigor via the proteome of both the popcorn L54 ♀ and P8 ♂ genotypes and the resultant UENF/UEM01 hybrid cross. To analyze the differentially abundant proteins involved in heterosis, we used the primary roots of these genotypes to analyze growth parameters and extract proteins. The results of the growth parameter analysis showed that the mid- and best-parent heterosis were positive for root length and root dry matter but negative for root fresh matter, seedling fresh matter, and protein content. The comparative proteomic analysis identified 1343 proteins in the primary roots of hybrid UENF/UEM01 and its parental lines; 220 proteins were differentially regulated in terms of protein abundance. The mass spectrometry proteomic data are available via ProteomeXchange with identifier “PXD009436”. A total of 62 regulated proteins were classified as nonadditive, of which 53.2% were classified as high parent abundance (+), 17.8% as above-high parent abundance (+ +), 16.1% as below-low parent abundance (− −), and 12.9% as low parent abundance (-). A total of 22 biological processes were associated with nonadditive proteins; processes involving translation, ribosome biogenesis, and energy-related metabolism represented 45.2% of the nonadditive proteins. Our results suggest that heterosis in the popcorn hybrid UENF/UEM01 at an early stage of plant development is associated with an up-regulation of proteins related to synthesis and energy metabolism.
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Affiliation(s)
- Mathias F. Rockenbach
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Caio C. G. Corrêa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Angelo S. Heringer
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Ismael L. J. Freitas
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), UENF, Campos dos Goytacazes, RJ, Brazil
| | | | - Antônio T. do Amaral-Júnior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), UENF, Campos dos Goytacazes, RJ, Brazil
- * E-mail: (VS); (ATAJ)
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
- * E-mail: (VS); (ATAJ)
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9
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Salamanca D, Gómez-Chaparro JL, Hidalgo A, Labella F. Differential expression of proteome in aqueous humor in patients with and without glaucoma. Arch Soc Esp Oftalmol (Engl Ed) 2018; 93:160-168. [PMID: 29439810 DOI: 10.1016/j.oftal.2017.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 06/28/2017] [Revised: 11/20/2017] [Accepted: 12/06/2017] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To determine quantitative and qualitative differences of aqueous humor proteome in patients with and without glaucoma. METHOD Observational, descriptive and cross-sectional study of 12 patients (8 men; 4 women) with and without glaucoma. There are 3 groups of minority proteins with serum equimolar contribution of each of the patients. Specimens were obtained during cataract surgery from patients without glaucoma (performed with retrobulbar anaesthesia [cataract retrobulbar patient -CRP-;n=4] or topical [cataract topical patient -CTP-; n=4]), or from patients with glaucoma (performed with retrobulbar anaesthesia [glaucoma retrobulbar patient -GRP-; n=4]). The humor proteome samples were frozen at -80°C until processing by trypsin digestion to obtain tryptic peptides, and then performing liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) to obtain the proteome and its differential expression between groups. Statistical analysis was performed using the SPSS v.17 program. RESULTS The study included 12 patients, aged (mean±standard deviation) 74.50±9.53 years. Concentrations obtained: 0.48±0.25μg/μl for CRP, 0.28±0.04μg/μl for CTP, and 0.35±0.16μg/μl for GRP. A total of 309 proteins were identified, of which 205, 210, and 182 were in CRP, CTP, and GRP, respectively. A total of 114 proteins were common to all three groups, 50 were exclusive to CRP, 58 to CTP, and 27 to GRP. CONCLUSIONS In this pilot study, a quantitative difference was found in the protein expression of humor among patients with glaucoma, there being 27 proteins unique to patients with glaucomatous disease.
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Affiliation(s)
- D Salamanca
- Universidad de Córdoba (UCO), Córdoba, España.
| | - J L Gómez-Chaparro
- Distrito Córdoba-Guadalquivir (SAS), Córdoba, España; Instituto de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, España
| | - A Hidalgo
- Departamento de Neuro-Oftalmología, Uveítis, Inmunología y Glaucoma, Hospital La Arruzafa, Córdoba, España
| | - F Labella
- Universidad de Córdoba (UCO), Córdoba, España
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10
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Roy J, Wycislo KL, Pondenis H, Fan TM, Das A. Comparative proteomic investigation of metastatic and non-metastatic osteosarcoma cells of human and canine origin. PLoS One 2017; 12:e0183930. [PMID: 28910304 PMCID: PMC5598957 DOI: 10.1371/journal.pone.0183930] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 01/20/2017] [Accepted: 08/14/2017] [Indexed: 12/17/2022] Open
Abstract
Osteosarcoma is the most common bone cancer in dogs and people. In order to improve clinical outcomes, it is necessary to identify proteins that are differentially expressed by metastatic cells. Membrane bound proteins are responsible for multiple pro-metastatic functions. Therefore characterizing the differential expression of membranous proteins between metastatic and non-metastatic clonal variants will allow the discovery of druggable targets and consequently improve treatment methodology. The objective of this investigation was to systemically identify the membrane-associated proteomics of metastatic and non-metastatic variants of human and canine origin. Two clonal variants of divergent in vivo metastatic potential from human and canine origins were used. The plasma membranes were isolated and peptide fingerprinting was used to identify differentially expressed proteins. Selected proteins were further validated using western blotting, flow cytometry, confocal microscopy and immunohistochemistry. Over 500 proteins were identified for each cell line with nearly 40% of the proteins differentially regulated. Conserved between both species, metastatic variants demonstrated significant differences in expression of membrane proteins that are responsible for pro-metastatic functions. Additionally, CD147, CD44 and vimentin were validated using various biochemical techniques. Taken together, through a comparative proteomic approach we have identified several differentially expressed cell membrane proteins that will help in the development of future therapeutics.
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Affiliation(s)
- Jahnabi Roy
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana, Illinois, United States of America
| | - Kathryn L. Wycislo
- Department of Pathobiology, University of Illinois Urbana–Champaign, Urbana, Illinois, United States of America
| | - Holly Pondenis
- Department of Veterinary Clinical Medicine, University of Illinois Urbana–Champaign, Urbana, Illinois, United States of America
| | - Timothy M. Fan
- Department of Veterinary Clinical Medicine, University of Illinois Urbana–Champaign, Urbana, Illinois, United States of America
- * E-mail: (AD); (TMF)
| | - Aditi Das
- Department of Comparative Biosciences, Department of Biochemistry, Beckman Institute for Advanced Science, Division of Nutritional Sciences, Neuroscience Program and Department of Bioengineering, University of Illinois Urbana–Champaign, Urbana, Illinois, United States of America
- * E-mail: (AD); (TMF)
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11
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Pan L, Yang Z, Wang J, Wang P, Ma X, Zhou M, Li J, Gang N, Feng G, Zhao J, Zhang X. Comparative proteomic analyses reveal the proteome response to short-term drought in Italian ryegrass (Lolium multiflorum). PLoS One 2017; 12:e0184289. [PMID: 28910323 PMCID: PMC5598972 DOI: 10.1371/journal.pone.0184289] [Citation(s) in RCA: 12] [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: 03/24/2017] [Accepted: 08/20/2017] [Indexed: 11/25/2022] Open
Abstract
Drought is a major abiotic stress that impairs growth and productivity of Italian ryegrass. Comparative analysis of drought responsive proteins will provide insight into molecular mechanism in Lolium multiflorum drought tolerance. Using the iTRAQ-based approach, proteomic changes in tolerant and susceptible lines were examined in response to drought condition. A total of 950 differentially accumulated proteins was found to be involved in carbohydrate metabolism, amino acid metabolism, biosynthesis of secondary metabolites, and signal transduction pathway, such as β-D-xylosidase, β-D-glucan glucohydrolase, glycerate dehydrogenase, Cobalamin-independent methionine synthase, glutamine synthetase 1a, Farnesyl pyrophosphate synthase, diacylglycerol, and inositol 1, 4, 5-trisphosphate, which might contributed to enhance drought tolerance or adaption in Lolium multiflorum. Interestingly, the two specific metabolic pathways, arachidonic acid and inositol phosphate metabolism including differentially accumulated proteins, were observed only in the tolerant lines. Cysteine protease cathepsin B, Cysteine proteinase, lipid transfer protein and Aquaporin were observed as drought-regulated proteins participating in hydrolysis and transmembrane transport. The activities of phospholipid hydroperoxide glutathione peroxidase, peroxiredoxin, dehydroascorbate reductase, peroxisomal ascorbate peroxidase and monodehydroascorbate reductase associated with alleviating the accumulation of reactive oxygen species in stress inducing environments. Our results showed that drought-responsive proteins were closely related to metabolic processes including signal transduction, antioxidant defenses, hydrolysis, and transmembrane transport.
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Affiliation(s)
- Ling Pan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongfu Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States of America
| | - Pengxi Wang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meiliang Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ji Li
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Nie Gang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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12
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Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Impact of Alternative Splicing on the Human Proteome. Cell Rep 2017; 20:1229-1241. [PMID: 28768205 PMCID: PMC5554779 DOI: 10.1016/j.celrep.2017.07.025] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/02/2017] [Accepted: 07/12/2017] [Indexed: 02/02/2023] Open
Abstract
Alternative splicing is a critical determinant of genome complexity and, by implication, is assumed to engender proteomic diversity. This notion has not been experimentally tested in a targeted, quantitative manner. Here, we have developed an integrative approach to ask whether perturbations in mRNA splicing patterns alter the composition of the proteome. We integrate RNA sequencing (RNA-seq) (to comprehensively report intron retention, differential transcript usage, and gene expression) with a data-independent acquisition (DIA) method, SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry), to capture an unbiased, quantitative snapshot of the impact of constitutive and alternative splicing events on the proteome. Whereas intron retention is accompanied by decreased protein abundance, alterations in differential transcript usage and gene expression alter protein abundance proportionate to transcript levels. Our findings illustrate how RNA splicing links isoform expression in the human transcriptome with proteomic diversity and provides a foundation for studying perturbations associated with human diseases.
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Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Mar Gonzàlez-Porta
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Sergio Santos
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - John C Marioni
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| | - Ashok R Venkitaraman
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK.
| | - Vihandha O Wickramasinghe
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.
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13
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Mohr T, Haudek-Prinz V, Slany A, Grillari J, Micksche M, Gerner C. Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis. PLoS One 2017; 12:e0179065. [PMID: 28617818 PMCID: PMC5472280 DOI: 10.1371/journal.pone.0179065] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [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: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 12/20/2022] Open
Abstract
Endothelial cells represent major effectors in inflammation and angiogenesis, processes that drive a multitude of pathological states such as atherosclerosis and cancer. Both inflammation and angiogenesis are interconnected with each other in the sense that many pro-inflammatory proteins possess proangiogenic properties and vice versa. To elucidate this interplay further, we present a comparative proteome study of inflammatory and angiogenic activated endothelial cells. HUVEC were stimulated with interleukin 1-β and VEGF, respectively. Cultured primary cells were fractionated into secreted, cytoplasmic and nuclear protein fractions and processed for subsequent LC-MS/MS analysis. Obtained protein profiles were filtered for fraction-specific proteins to address potential cross fractional contamination, subjected to comparative computational biology analysis (GO-Term enrichment analysis, weighted gene co-expression analysis) and compared to published mRNA profiles of IL-1β respectively VEGF stimulated HUVEC. GO Term enrichment analysis and comparative pathway analysis revealed features such as NOD and NfkB signaling for inflammatory activated HUVEC and VEGF and ErB signaling for VEGF-activated HUVEC with potential crosstalk via map kinases MAP2K2. Weighted protein co-expression network analysis revealed several potential hub genes so far not associated with driver function in inflammation or angiogenesis such as HSPG2, ANXA3, and GPI. "Classical" inflammation or angiogenesis markers such as IL6, CXCL8 or CST1 were found in a less central position within the co-expression networks. In conclusion, this study reports a framework for the computational biology based analysis of proteomics data applied to cytoplasmic, nucleic and extracellular fractions of quiescent, inflammatory and angiogenic activated HUVEC. Novel potential hub genes relevant for these processes were successfully identified.
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Affiliation(s)
- Thomas Mohr
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- ScienceConsult – DI Thomas Mohr KG, Guntramsdorf, Austria
| | - Verena Haudek-Prinz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Astrid Slany
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Johannes Grillari
- Christian Doppler Laboratory on Biotechnology of Skin Aging, Department of Biotechnology, BOKU – University of Life Sciences, Vienna, Austria
- Evercyte GmbH, Vienna, Austria
| | - Michael Micksche
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
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14
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Udvari EB, Völgyi K, Gulyássy P, Dimén D, Kis V, Barna J, Szabó ÉR, Lubec G, Juhász G, Kékesi KA, Dobolyi Á. Synaptic proteome changes in the hypothalamus of mother rats. J Proteomics 2017; 159:54-66. [PMID: 28286321 DOI: 10.1016/j.jprot.2017.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 11/15/2016] [Revised: 02/01/2017] [Accepted: 03/07/2017] [Indexed: 12/16/2022]
Abstract
To establish synaptic proteome changes associated with motherhood, we isolated synaptosome fractions from the hypothalamus of mother rats and non-maternal control females at the 11th postpartum day. Proteomic analysis by two-dimensional differential gel electrophoresis combined with mass spectrometric protein identification established 26 significant proteins, 7 increasing and 19 decreasing protein levels in the dams. The altered proteins are mainly involved in energy homeostasis, protein folding, and metabolic processes suggesting the involvement of these cellular processes in maternal adaptations. The decrease in a significantly altered protein, complement component 1q subcomponent-binding protein (C1qbp) was validated with Western blotting. Furthermore, immunohistochemistry showed its presence in hypothalamic fibers and terminals in agreement with its presence in synaptosomes. We also found the expression of C1qbp in different hypothalamic nuclei including the preoptic area and the paraventricular hypothalamic nucleus at the protein and at the mRNA level using immunohistochemistry and in situ hybridization histochemistry, respectively. Bioinformatical network analysis revealed that cytokines, growth factors, and protein kinases are common regulators, which indicates a complex regulation of the proteome change in mothers. The results suggest that maternal responsiveness is associated with synaptic proteins level changes in the hypothalamus, and that growth factors and cytokines may govern these alterations. BIOLOGICAL SIGNIFICANCE The period of motherhood is accompanied with several behavioral, neuroendocrine, emotional and metabolic adaptations in the brain. Although it is established that various hypothalamic networks participate in the maternal adaptations of the rodent brain, our knowledge on the molecular background of these alterations remains seriously limited. In the present study, we first determined that the functional alterations of the maternal brain can be detected at the level of the synaptic proteome in the hypothalamus. Independent confirmation of synaptic localization, and also the established decrease in the level of C1qbp protein suggest the validity of the data. Common regulators of altered proteins belonging to the growth factor and cytokine family suggest that the synaptic adaptation is governed by these extracellular signals and future studies should focus on their specific roles. Our study was also the first to describe the expression pattern of C1qbp in the hypothalamus, a protein potentially involved in mitochondrial and neuroimmunological regulations of synaptic plasticity. Its presence in the preoptic area responsible for maternal behaviors and also in the paraventricular hypothalamic and arcuate nuclei regulating hormonal levels suggests that the same proteins may be involved in different aspects of maternal adaptations. The conclusions of the present work contribute to establishing the molecular alterations that determine different maternal adaptations in the brain. Since maternal changes are models of neuronal plasticity in all social interactions, the reported results can affect a wide field of molecular and behavioral neuroscience.
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Affiliation(s)
- Edina Brigitta Udvari
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary; Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Katalin Völgyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary
| | - Péter Gulyássy
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary; Department of Pharmaceutical Chemistry, University of Vienna, Vienna A-1090, Austria; MTA-TTK NAP MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Diána Dimén
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary; Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Viktor Kis
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary; Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - János Barna
- Laboratory of Neuromorphology, Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1094, Hungary
| | - Éva Rebeka Szabó
- Laboratory of Neuromorphology, Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1094, Hungary
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna A-1090, Austria
| | - Gábor Juhász
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary; MTA-TTK NAP MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Katalin Adrienna Kékesi
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary; Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Árpád Dobolyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary; MTA-ELTE Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary.
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15
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Dong Z, Ba H, Zhang W, Coates D, Li C. iTRAQ-Based Quantitative Proteomic Analysis of the Potentiated and Dormant Antler Stem Cells. Int J Mol Sci 2016; 17:ijms17111778. [PMID: 27792145 PMCID: PMC5133779 DOI: 10.3390/ijms17111778] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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] [Received: 08/09/2016] [Revised: 10/08/2016] [Accepted: 10/16/2016] [Indexed: 01/13/2023] Open
Abstract
As the only known organ that can completely regenerate in mammals, deer antler is of real significance in the field of regenerative medicine. Recent studies have shown that the regenerative capacity of the antlers comes from the pedicle periosteum and the cells resident in the periosteum possess the attributes of stem cells. Currently, the molecular mechanism of antler regeneration remains unclear. In the present study, we compared the potentiated and dormant antler stem cells using isobaric tags for the relative and absolute quantification (iTRAQ) labeling of the peptides, coupled with two-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) to compare the proteome profiles. Proteins were identified by searching against the NCBI nr database and our own Cervine transcriptome database, and bioinformatics analysis was conducted to identify the differentially expressed proteins. Based on this searching strategy, we identified 169 differentially expressed proteins in total, consisting of 70 up- and 99 down-regulated in the potentiated vs. dormant antler stem cells. Reliability of the iTRAQ was confirmed via quantitative real-time polymerase chain reaction (qRT-PCR) to measure the expression of selected genes. We identified transduction pathways through the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, such as HIF-1 and PI3K-AKT signaling pathways that play important roles in regulating the regeneration of antlers. In summary, the initiation stage of antler regeneration, a process from dormant to potentiated states in antler stem cells, is regulated by multiple proteins and complicated signal networks.
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Affiliation(s)
- Zhen Dong
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun 130112, China.
| | - Hengxing Ba
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun 130112, China.
| | - Wei Zhang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun 130112, China.
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 647, Dunedin 9054, New Zealand.
| | - Chunyi Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun 130112, China.
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16
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de Mello CS, Van Dijk JP, Voorhuijzen M, Kok EJ, Arisi ACM. Tuber proteome comparison of five potato varieties by principal component analysis. J Sci Food Agric 2016; 96:3928-3936. [PMID: 26799786 DOI: 10.1002/jsfa.7635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/02/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Data analysis of omics data should be performed by multivariate analysis such as principal component analysis (PCA). The way data are clustered in PCA is of major importance to develop some classification systems based on multivariate analysis, such as soft independent modeling of class analogy (SIMCA). In a previous study a one-class classifier based on SIMCA was built using microarray data from a set of potatoes. The PCA grouped the transcriptomic data according to varieties. The present work aimed to use PCA to verify the clustering of the proteomic profiles for the same potato varieties. RESULTS Proteomic profiles of five potato varieties (Biogold, Fontane, Innovator, Lady Rosetta and Maris Piper) were evaluated by two-dimensional gel electrophoresis (2-DE) performed on two immobilized pH gradient (IPG) strip lengths, 13 and 24 cm, both under pH range 4-7. For each strip length, two gels were prepared from each variety; in total there were ten gels per analysis. For 13 cm strips, 199-320 spots were detected per gel, and for 24 cm strips, 365-684 spots. CONCLUSION All four PCAs performed with these datasets presented clear grouping of samples according to the varieties. The data presented here showed that PCA was applicable for proteomic analysis of potato and was able to separate the samples by varieties. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Carla Souza de Mello
- Food Science and Technology Department, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-001, Florianópolis, SC, Brazil
| | - Jeroen P Van Dijk
- RIKILT, Wageningen University and Research Centre, PO Box 230, NL-6700, AE, Wageningen, The Netherlands
| | - Marleen Voorhuijzen
- RIKILT, Wageningen University and Research Centre, PO Box 230, NL-6700, AE, Wageningen, The Netherlands
| | - Esther J Kok
- RIKILT, Wageningen University and Research Centre, PO Box 230, NL-6700, AE, Wageningen, The Netherlands
| | - Ana Carolina Maisonnave Arisi
- Food Science and Technology Department, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-001, Florianópolis, SC, Brazil
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17
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Abstract
The mitochondrial matrix is unique in that it must integrate the folding and assembly of proteins derived from the nuclear and mitochondrial genomes. In Caenorhabditis elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis. While misfolded mitochondrial-matrix-localized ornithine transcarbamylase induces chaperonin expression, our understanding of mammalian UPRmt is rudimentary, reflecting a lack of acute triggers for UPRmt activation. This limitation has prevented analysis of the cellular responses to matrix protein misfolding and the effects of UPRmt on mitochondrial translation to control protein folding loads. Here we combine pharmacological inhibitors of matrix-localized HSP90/TRAP1 (ref. 8) or LON protease, which promote chaperonin expression, with global transcriptional and proteomic analysis to reveal an extensive and acute response of human cells to UPRmt. This response encompasses widespread induction of nuclear genes, including matrix-localized proteins involved in folding, pre-RNA processing and translation. Functional studies revealed rapid but reversible translation inhibition in mitochondria occurring concurrently with defects in pre-RNA processing caused by transcriptional repression and LON-dependent turnover of the mitochondrial pre-RNA processing nuclease MRPP3 (ref. 10). This study reveals that acute mitochondrial protein folding stress activates both increased chaperone availability within the matrix and reduced matrix-localized protein synthesis through translational inhibition, and provides a framework for further dissection of mammalian UPRmt.
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Naveen V, Hsiao CD. NrdR Transcription Regulation: Global Proteome Analysis and Its Role in Escherichia coli Viability and Virulence. PLoS One 2016; 11:e0157165. [PMID: 27275780 PMCID: PMC4898720 DOI: 10.1371/journal.pone.0157165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 01/21/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Bacterial ribonucleotide reductases (RNRs) play an important role in the synthesis of dNTPs and their expression is regulated by the transcription factors, NrdR and Fur. Recent transcriptomic studies using deletion mutants have indicated a role for NrdR in bacterial chemotaxis and in the maintenance of topoisomerase levels. However, NrdR deletion alone has no effect on bacterial growth or virulence in infected flies or in human blood cells. Furthermore, transcriptomic studies are limited to the deletion strain alone, and so are inadequate for drawing biological implications when the NrdR repressor is active or abundant. Therefore, further examination is warranted of changes in the cellular proteome in response to both NrdR overexpression, as well as deletion, to better understand its functional relevance as a bacterial transcription repressor. Here, we profile bacterial fate under conditions of overexpression and deletion of NrdR in E. coli. Biochemical assays show auxiliary zinc enhances the DNA binding activity of NrdR. We also demonstrate at the physiological level that increased nrdR expression causes a significant reduction in bacterial growth and fitness even at normal temperatures, and causes lethality at elevated temperatures. Corroborating these direct effects, global proteome analysis following NrdR overexpression showed a significant decrease in global protein expression. In parallel, studies on complementary expression of downregulated essential genes polA, eno and thiL showed partial rescue of the fitness defect caused by NrdR overexpression. Deletion of downregulated non-essential genes ygfK and trxA upon NrdR overexpression resulted in diminished bacterial growth and fitness suggesting an additional role for NrdR in regulating other genes. Moreover, in comparison with NrdR deletion, E. coli cells overexpressing NrdR showed significantly diminished adherence to human epithelial cells, reflecting decreased bacterial virulence. These results suggest that elevated expression of NrdR could be a suitable means to retard bacterial growth and virulence, as its elevated expression reduces bacterial fitness and impairs host cell adhesion.
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Affiliation(s)
- Vankadari Naveen
- Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Chwan-Deng Hsiao
- Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
- * E-mail:
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Ding X, Lu J, Yu R, Wang X, Wang T, Dong F, Peng B, Wu W, Liu H, Geng Y, Zhang R, Ma H, Cheng J, Yu M, Fang S. Preliminary Proteomic Analysis of A549 Cells Infected with Avian Influenza Virus H7N9 and Influenza A Virus H1N1. PLoS One 2016; 11:e0156017. [PMID: 27223893 PMCID: PMC4880285 DOI: 10.1371/journal.pone.0156017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 01/01/2016] [Accepted: 05/09/2016] [Indexed: 11/18/2022] Open
Abstract
A newly emerged H7N9 influenza virus poses high risk to human beings. However, the pathogenic mechanism of the virus remains unclear. The temporal response of primary human alveolar adenocarcinoma epithelial cells (A549) infected with H7N9 influenza virus and H1N1 influenza A virus (H1N1, pdm09) were evaluated using the proteomics approaches (2D-DIGE combined with MALDI-TOF-MS/MS) at 24, 48 and 72 hours post of the infection (hpi). There were 11, 12 and 33 proteins with significant different expressions (P<0.05) at 24, 48 and 72hpi, especially F-actin-capping protein subunit alpha-1 (CAPZA1), Ornithine aminotransferase (OAT), Poly(rC)-binding protein 1 (PCBP1), Eukaryotic translation initiation factor 5A-1 (EIF5A) and Platelet-activating factor acetylhydrolaseⅠb subunit beta (PAFAH1B2) were validated by western-blot analysis. The functional analysis revealed that the differential proteins in A549 cells involved in regulating cytopathic effect. Among them, the down-regulation of CAPZA1, OAT, PCBP1, EIF5A are related to the death of cells infected by H7N9 influenza virus. This is the first time show that the down-regulation of PAFAH1B2 is related to the later clinical symptoms of patients infected by H7N9 influenza virus. These findings may improve our understanding of pathogenic mechanism of H7N9 influenza virus in proteomics.
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Affiliation(s)
- Xiaoman Ding
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiahai Lu
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ruoxi Yu
- Southern Medical University, Guangzhou, China
| | - Xin Wang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ting Wang
- Nanshan Center for Disease Control and Prevention, Shenzhen, China
| | - Fangyuan Dong
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Bo Peng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Weihua Wu
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hui Liu
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yijie Geng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Renli Zhang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hanwu Ma
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jinquan Cheng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Muhua Yu
- Nanshan Center for Disease Control and Prevention, Shenzhen, China
- * E-mail: (MHY); (SSF)
| | - Shisong Fang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
- * E-mail: (MHY); (SSF)
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Pasquali M, Serchi T, Cocco E, Leclercq CC, Planchon S, Guignard C, Renaut J, Hoffmann L. A Fusarium graminearum strain-comparative proteomic approach identifies regulatory changes triggered by agmatine. J Proteomics 2016; 137:107-16. [PMID: 26585460 DOI: 10.1016/j.jprot.2015.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 07/14/2015] [Revised: 10/15/2015] [Accepted: 11/10/2015] [Indexed: 11/20/2022]
Abstract
UNLABELLED Plant pathogens face different environmental clues depending on the stage of the infection cycle they are in. Fusarium graminearum infects small grain cereals producing trichothecenes type B (TB) that act as virulence factor in the interaction with the plant and have important food safety implications. This study addresses at the proteomic level the effect of an environmental stimulus (such as the presence of a polyamine like agmatine) possibly encountered by the fungus when it is already within the plant. Because biological diversity affects the proteome significantly, a multistrain (n=3) comparative approach was used to identify consistent effects caused on the fungus by the nitrogen source (agmatine or glutamic acid). Proteomics analyses were performed by the use of 2D-DIGE. Results showed that agmatine augmented TB production but not equally in all strains. The polyamine reshaped drastically the proteome of the fungus activating specific pathways linked to the translational control within the cell. Chromatin restructuring, ribosomal regulations, protein and mRNA processing enzymes were modulated by the agmatine stimulus as well as metabolic, structural and virulence-related proteins, suggesting the need to reshape specifically the fungal cell for TB production, a key step for the pathogen spread within the spike. BIOLOGICAL SIGNIFICANCE Induction of toxin synthesis by plant compounds plays a crucial role in toxin contamination of food and feed, in particular trichothecenes type B produced mainly by F. graminearum on wheat. This work describes the level of diversity of 3 strains facing 2 toxin inducing plant derived compounds. This knowledge is of use for the research community on toxigenic Fusarium strains in cereals for understanding the role of fungal diversity in toxin inducibility. This work also suggests that environmental clues that can be found within the plant during infection (like different nitrogen compounds) are crucial stimuli for reshaping the proteome profile and consequently the specialization profiling of the fungus, ultimately leading to very different toxin contamination levels in the plant.
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Affiliation(s)
- M Pasquali
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg.
| | - T Serchi
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg
| | - E Cocco
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg
| | - C C Leclercq
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg
| | - S Planchon
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg
| | - C Guignard
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg
| | - J Renaut
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg
| | - L Hoffmann
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, 41, rue du Brill, L-4422, Belvaux, Luxembourg
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21
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Shankaran M, Shearer TW, Stimpson SA, Turner SM, King C, Wong PYA, Shen Y, Turnbull PS, Kramer F, Clifton L, Russell A, Hellerstein MK, Evans WJ. Proteome-wide muscle protein fractional synthesis rates predict muscle mass gain in response to a selective androgen receptor modulator in rats. Am J Physiol Endocrinol Metab 2016; 310:E405-17. [PMID: 26714847 DOI: 10.1152/ajpendo.00257.2015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 12/23/2015] [Indexed: 12/25/2022]
Abstract
Biomarkers of muscle protein synthesis rate could provide early data demonstrating anabolic efficacy for treating muscle-wasting conditions. Androgenic therapies have been shown to increase muscle mass primarily by increasing the rate of muscle protein synthesis. We hypothesized that the synthesis rate of large numbers of individual muscle proteins could serve as early response biomarkers and potentially treatment-specific signaling for predicting the effect of anabolic treatments on muscle mass. Utilizing selective androgen receptor modulator (SARM) treatment in the ovariectomized (OVX) rat, we applied an unbiased, dynamic proteomics approach to measure the fractional synthesis rates (FSR) of 167-201 individual skeletal muscle proteins in triceps, EDL, and soleus. OVX rats treated with a SARM molecule (GSK212A at 0.1, 0.3, or 1 mg/kg) for 10 or 28 days showed significant, dose-related increases in body weight, lean body mass, and individual triceps but not EDL or soleus weights. Thirty-four out of the 94 proteins measured from the triceps of all rats exhibited a significant, dose-related increase in FSR after 10 days of SARM treatment. For several cytoplasmic proteins, including carbonic anhydrase 3, creatine kinase M-type (CK-M), pyruvate kinase, and aldolase-A, a change in 10-day FSR was strongly correlated (r(2) = 0.90-0.99) to the 28-day change in lean body mass and triceps weight gains, suggesting a noninvasive measurement of SARM effects. In summary, FSR of multiple muscle proteins measured by dynamics of moderate- to high-abundance proteins provides early biomarkers of the anabolic response of skeletal muscle to SARM.
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Affiliation(s)
| | - Todd W Shearer
- Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
| | - Stephen A Stimpson
- Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
| | | | | | | | - Ying Shen
- Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
| | - Philip S Turnbull
- Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
| | - Fritz Kramer
- Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
| | - Lisa Clifton
- Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
| | - Alan Russell
- Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
| | - Marc K Hellerstein
- KineMed, Inc., Emeryville, California; Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, California
| | - William J Evans
- KineMed, Inc., Emeryville, California; Muscle Metabolism Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, GlaxoSmithKline, Research Triangle Park, North Carolina; and
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22
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Ljunggren SA, Iggland M, Rönn M, Lind L, Lind PM, Karlsson H. Altered heart proteome in fructose-fed Fisher 344 rats exposed to bisphenol A. Toxicology 2016; 347-349:6-16. [PMID: 26930160 DOI: 10.1016/j.tox.2016.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 12/07/2015] [Revised: 02/18/2016] [Accepted: 02/25/2016] [Indexed: 01/01/2023]
Abstract
Bisphenol A (BPA), is an artificial estrogen initially produced for medical purposes but is today widely used in polycarbonate plastics and epoxy resins. Exposure-related reproductive disorders have been found, but recently it has also been suggested that BPA may be involved in obesity, diabetes, myocardial hypertrophy and myocardial infarction in humans. To mimic a modern lifestyle, female rats were fed with fructose or fructose plus BPA (0.25mg/L drinking water). The myocardial left ventricle proteome of water controls, fructose-fed and fructose-fed plus BPA supplemented rats was explored. The proteome was investigated using nano-liquid chromatography tandem mass spectrometry and two-dimensional gel electrophoresis followed by matrix assisted laser desorption/ionization mass spectrometry identification. In total, 41 proteins were significantly altered by BPA exposure compared to water or fructose controls. Principal component analysis and cellular process enrichment analysis of altered proteins suggested increased fatty acid transport and oxidation, increased ROS generation and altered structural integrity of the myocardial left ventricle in the fructose-fed BPA-exposed rats, indicating unfavorable effects on the myocardium. In conclusion, BPA exposure in the rats induces major alterations in the myocardial proteome.
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Affiliation(s)
- S A Ljunggren
- Occupational and Environmental Medicine Center, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | - M Iggland
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | - M Rönn
- Department of Medical Sciences, Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden.
| | - L Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden.
| | - P M Lind
- Department of Medical Sciences, Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden.
| | - H Karlsson
- Occupational and Environmental Medicine Center, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
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Campos A, Danielsson G, Farinha AP, Kuruvilla J, Warholm P, Cristobal S. Shotgun proteomics to unravel marine mussel (Mytilus edulis) response to long-term exposure to low salinity and propranolol in a Baltic Sea microcosm. J Proteomics 2016; 137:97-106. [PMID: 26820222 DOI: 10.1016/j.jprot.2016.01.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 10/22/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED Pharmaceuticals, among them the β-adrenoceptor blocker propranolol, are an important group of environmental contaminants reported in European waters. Laboratory exposure to pharmaceuticals on marine species has been performed without considering the input of the ecosystem flow. To unravel the ecosystem response to long-term exposure to propranolol we have performed long-term exposure to propranolol and low salinity in microcosms. We applied shotgun proteomic analysis to gills of Mytilus edulis from those Baltic Sea microcosms and identified 2071 proteins with a proteogenomic strategy. The proteome profiling patterns from the 587 highly reproductive proteins among groups define salinity as a key factor in the mussel's response to propranolol. Exposure at low salinity drives molecular mechanisms of adaptation based on a decrease in the abundance of several cytoskeletal proteins, signalling and intracellular membrane trafficking pathway combined with a response towards the maintenance of transcription and translation. The exposure to propranolol combined with low salinity modulates the expression of structural proteins including cilia functions and decreases the expression of membrane protein transporters. This study reinforces the environment concerns of the impact of low salinity in combination with anthropogenic pollutants and anticipates critical physiological conditions for the survival of the blue mussel in the northern areas. BIOLOGICAL SIGNIFICANCE Applying shotgun proteomic analysis to M. edulis gills samples from a long-term microcosm exposure to propranolol and following a proteogenomic identification strategy, we have identified 2071 proteins. The proteomic analysis unrevealed which molecular mechanisms drive the adaptation to low salinity stress and how salinity modulates the effects of exposure to propranolol. These results reinforce the idea of the impact of low salinity in combination with anthropogenic pollutants and anticipate critical physiological condition.
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Affiliation(s)
- Alexandre Campos
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Gabriela Danielsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ana Paula Farinha
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Jacob Kuruvilla
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Per Warholm
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Basque Country UPV/EHU, Bizkaia, Spain.
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Geng X, Chang C, Zang X, Sun J, Li P, Guo J, Xu C. Integrative proteomic and microRNA analysis of the priming phase during rat liver regeneration. Gene 2015; 575:224-32. [PMID: 26341052 DOI: 10.1016/j.gene.2015.08.066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/22/2015] [Accepted: 08/30/2015] [Indexed: 11/20/2022]
Abstract
The partial hepatectomy (PH) model provides an effective medium for study of liver regeneration (LR). Considering that LR is regulated by microRNAs (miRNAs), investigation of the regulatory role of miRNAs is critical for revealing how regenerative processes are initiated and controlled. Using high-throughput sequencing technology, we examined miRNA expression profiles of the regenerating rat liver after PH, and found that 23 miRNAs were related to rat LR. Among them, several miRNAs were significantly altered at 2h and 6h after PH, corresponding to the priming phase of LR. Furthermore, we examined the protein profiles in the regenerating rat liver at 2h and 6h after PH by iTRAQ coupled with LC-MS/MS, and found that 278 proteins were significantly changed. Subsequently, an integrative proteomic and microRNA analysis by Ingenuity Pathway Analysis 9.0 (IPA) software showed that miR-125a, miR-143, miR-150, miR-181c, miR-182, miR-183, miR-199a, miR-429 regulated the priming phase of rat LR by modulating the expression of proteins involved in networks critical for cell apoptosis, cell survival, cell cycle, inflammatory response, metabolism, etc. Thus, our studies provide novel evidence for a functional molecular network populated by the down-regulated targets of the up-regulated miRNAs in the priming phase of rat LR.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China
| | - Cuifang Chang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Jingyan Sun
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Pengfei Li
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Jianli Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang 453007, China; Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, China; College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.
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25
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Tiedke J, Borner J, Beeck H, Kwiatkowski M, Schmidt H, Thiel R, Fabrizius A, Burmester T. Evaluating the Hypoxia Response of Ruffe and Flounder Gills by a Combined Proteome and Transcriptome Approach. PLoS One 2015; 10:e0135911. [PMID: 26273839 PMCID: PMC4537130 DOI: 10.1371/journal.pone.0135911] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/29/2015] [Indexed: 11/24/2022] Open
Abstract
Hypoxia has gained ecological importance during the last decades, and it is the most dramatically increasing environmental factor in coastal areas and estuaries. The gills of fish are the prime target of hypoxia and other stresses. Here we have studied the impact of the exposure to hypoxia (1.5 mg O2/l for 48 h) on the protein expression of the gills of two estuarine fish species, the ruffe (Gymnocephalus cernua) and the European flounder (Platichthys flesus). First, we obtained the transcriptomes of mixed tissues (gills, heart and brain) from both species by Illumina next-generation sequencing. Then, the gill proteomes were investigated using two-dimensional gel electrophoresis and mass spectrometry. Quantification of the normalized proteome maps resulted in a total of 148 spots in the ruffe, of which 28 (18.8%) were significantly regulated (> 1.5-fold). In the flounder, 121 spots were found, of which 27 (22.3%) proteins were significantly regulated. The transcriptomes were used for the identification of these proteins, which was successful for 15 proteins of the ruffe and 14 of the flounder. The ruffe transcriptome dataset comprised 87,169,850 reads, resulting in an assembly of 72,108 contigs (N50 = 1,828 bp). 20,860 contigs (26.93%) had blastx hits with E < 1e-5 in the human sequences in the RefSeq database, representing 14,771 unique accession numbers. The flounder transcriptome with 78,943,030 reads assembled into 49,241 contigs (N50 = 2,106 bp). 20,127 contigs (40.87%) had a hit with human proteins, corresponding to 14,455 unique accession numbers. The regulation of selected genes was confirmed by quantitative real-time RT-PCR. Most of the regulated proteins that were identified by this approach function in the energy metabolism, while others are involved in the immune response, cell signalling and the cytoskeleton.
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Affiliation(s)
- Jessica Tiedke
- Institute of Zoology, University of Hamburg, Hamburg, Germany
| | - Janus Borner
- Institute of Zoology, University of Hamburg, Hamburg, Germany
| | - Hendrik Beeck
- Institute of Zoology, University of Hamburg, Hamburg, Germany
| | - Marcel Kwiatkowski
- Department of Clinical Chemistry, University Medical Centre Hamburg-Eppendorf, Campus Forschung, Hamburg, Germany
| | - Hanno Schmidt
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Ralf Thiel
- Zoological Museum, Centre of Natural History, University of Hamburg, Hamburg, Germany
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Mao PH, Lü J, Cai CL. PROTEOMIC CHANGES OF RECOMBINANT YEAST: PHARMACO-INDUSTRIAL POTENTIAL. J BIOL REG HOMEOS AG 2015; 29:569-578. [PMID: 26403395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The original yeast strain Hansenula anomala 2340 was implanted by low-energy nitrogen ion (N+) to obtain the mutant strain N6076. The mutant strain produced a red quinone compound, not synthesized by the parent strain. Two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) and mass spectrometry (MS) were utilized to analyze the protein profile of the mutant strain N6076. The proteome changes were compared to those of the original strain to assess the amount of change that the metabolic pathways underwent in the mutant strain. The results indicated the detection of 57 different expressed proteins (P<0.05) when the N6076 mutant strain was cultured in the liquid medium for 96 h as compared to that of the original strain. Of these different expressed protein spots, 27 were upregulated, and 30 were down-regulated. Also, 56 protein spots were identified with the aid of MALDI-TOF and tandem (TOF-TOF) MS. The protein score confidence interval (CI) of the protein profiling in the down-regulated protein spots 273 and 1294 were 81.371% and 12.864%, respectively, by bioinformatic analysis. This probably points to the fact that the irradiation by N+ contributed to the mutation of these two proteins.
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Affiliation(s)
- P-H Mao
- Center of Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Peoples Republic of China
| | - J Lü
- Center of Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Peoples Republic of China
| | - C-L Cai
- Research Center of Ion Beam Biotechnology and Biodiversity, Xian Technological University, Xian, Peoples Republic of China
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Abstract
The human vitreous contains primarily water, but also contains proteins which have yet to be fully characterized. To gain insight into the four vitreous substructures and their potential functions, we isolated and analyzed the vitreous protein profiles of three non-diseased human eyes. The four analyzed substructures were the anterior hyaloid, the vitreous cortex, the vitreous core, and the vitreous base. Proteins were separated by multidimensional liquid chromatography and identified by tandem mass spectrometry. Bioinformatics tools then extracted the expression profiles, signaling pathways, and interactomes unique to each tissue. From each substructure, a mean of 2,062 unique proteins were identified, with many being differentially expressed in a specific substructure: 278 proteins were unique to the anterior hyaloid, 322 to the vitreous cortex, 128 to the vitreous base, and 136 to the vitreous core. When the identified proteins were organized according to relevant functional pathways and networks, key patterns appeared. The blood coagulation pathway and extracellular matrix turnover networks were highly represented. Oxidative stress regulation and energy metabolism proteins were distributed throughout the vitreous. Immune functions were represented by high levels of immunoglobulin, the complement pathway, damage-associated molecular patterns (DAMPs), and evolutionarily conserved antimicrobial proteins. The majority of vitreous proteins detected were intracellular proteins, some of which originate from the retina, including rhodopsin (RHO), phosphodiesterase 6 (PDE6), and glial fibrillary acidic protein (GFAP). This comprehensive analysis uncovers a picture of the vitreous as a biologically active tissue, where proteins localize to distinct substructures to protect the intraocular tissues from infection, oxidative stress, and energy disequilibrium. It also reveals the retina as a potential source of inflammatory mediators. The vitreous proteome catalogues the dynamic interactions between the vitreous and surrounding tissues. It therefore could be an indirect and effective method for surveying vitreoretinal disease for specific biomarkers.
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Affiliation(s)
- Jessica M. Skeie
- Omics Laboratory, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
| | - C. Nathaniel Roybal
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
| | - Vinit B. Mahajan
- Omics Laboratory, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
- * E-mail:
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Li J, Zhao WG, Shen ZF, Yuan T, Liu SN, Liu Q, Fu Y, Sun W. Comparative proteome analysis of brown adipose tissue in obese C57BL/6J mice using iTRAQ-coupled 2D LC-MS/MS. PLoS One 2015; 10:e0119350. [PMID: 25747866 PMCID: PMC4352050 DOI: 10.1371/journal.pone.0119350] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/12/2015] [Indexed: 12/14/2022] Open
Abstract
High-fat diet (HFD) leads to the development of obesity accompanied by insulin resistance, which increases the risk of type 2 diabetes mellitus and cardiovascular disease. Brown adipose tissue (BAT) plays an essential role in energy metabolism, thus it will give us promising treatment targets through elucidating underlying mechanisms of BAT in obesity. In this study, female C57BL/6J mice were fed HFD or normal diet (ND) for 22 weeks. Hyperinsulinemic-euglycemic clamp was performed to evaluate insulin sensitivity, which was independently correlated with obesity. Using isobaric tag for relative and absolute quantification (iTRAQ) coupled with 2D LC-MS/MS, we quantitated 3048 proteins in BAT. As compared HFD with ND, we obtained 727 differentially expressed proteins. Functional analysis found that those proteins were mainly assigned to the pathway of mitochondrial function. In this pathway, carnitine O-palmitoyltransferase 2 (CPT2), uncoupling protein 1 (UCP1) and apoptosis-inducing factor 1 (AIF1) were up-regulated significantly by HFD, and they were confirmed by western blotting. The results indicated that HFD might induce the apoptosis of brown adipocytes via the up-regulated AIF1. Meanwhile, HFD also stimulated fatty acid β-oxidation and raised compensatory energy consuming through the increases of CPT2 and UCP1, respectively. However, the apoptosis of brown adipocytes might weaken the compensatory energy expenditure, and finally contribute to overweight/obesity. So, preventing the apoptosis of brown adipocytes may be the key target to treat obesity.
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Affiliation(s)
- Juan Li
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei-Gang Zhao
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- * E-mail: (WGZ); (WS)
| | - Zhu-Fang Shen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Diabetes Research Center of Chinese Academy of Medical Sciences, Beijing, China
| | - Tao Yuan
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shuai-Nan Liu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Diabetes Research Center of Chinese Academy of Medical Sciences, Beijing, China
| | - Quan Liu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Diabetes Research Center of Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Fu
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China
- * E-mail: (WGZ); (WS)
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Wilson MM, Anderson DE, Bernstein HD. Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms. PLoS One 2015; 10:e0117732. [PMID: 25658944 PMCID: PMC4319957 DOI: 10.1371/journal.pone.0117732] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [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: 10/02/2014] [Accepted: 12/31/2014] [Indexed: 01/28/2023] Open
Abstract
Bacteroides fragilis is a widely distributed member of the human gut microbiome and an opportunistic pathogen. Cell surface molecules produced by this organism likely play important roles in colonization, communication with other microbes, and pathogenicity, but the protein composition of the outer membrane (OM) and the mechanisms used to transport polypeptides into the extracellular space are poorly characterized. Here we used LC-MS/MS to analyze the OM proteome and secretome of B. fragilis NCTC 9343 grown under laboratory conditions. Of the 229 OM proteins that we identified, 108 are predicted to be lipoproteins, and 61 are predicted to be TonB-dependent transporters. Based on their proximity to genes encoding TonB-dependent transporters, many of the lipoprotein genes likely encode proteins involved in nutrient or small molecule uptake. Interestingly, protease accessibility and biotinylation experiments indicated that an unusually large fraction of the lipoproteins are cell-surface exposed. We also identified three proteins that are members of a novel family of autotransporters, multiple potential type I protein secretion systems, and proteins that appear to be components of a type VI secretion apparatus. The secretome consisted of lipoproteins and other proteins that might be substrates of the putative type I or type VI secretion systems. Our proteomic studies show that B. fragilis differs considerably from well-studied Gram-negative bacteria such as Escherichia coli in both the spectrum of OM proteins that it produces and the range of secretion strategies that it utilizes.
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Affiliation(s)
- Marlena M. Wilson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - D. Eric Anderson
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Harris D. Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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Lee JJ, Kim YH, Kwak YS, An JY, Kim PJ, Lee BH, Kumar V, Park KW, Chang ES, Jeong JC, Lee HS, Kwak SS. A comparative study of proteomic differences between pencil and storage roots of sweetpotato (Ipomoea batatas (L.) Lam.). Plant Physiol Biochem 2015; 87:92-101. [PMID: 25562766 DOI: 10.1016/j.plaphy.2014.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 09/18/2014] [Accepted: 12/13/2014] [Indexed: 05/25/2023]
Abstract
Fibrous roots of sweetpotato (Ipomoea batatas (L.) Lam.) usually develop into both pencil and storage roots. To understand protein function in root development, a proteomic analysis was conducted on the pencil and storage roots of the light orange-fleshed sweetpotato cultivar, Yulmi. Two-dimensional gel electrophoresis showed that expression of 30 protein spots differed between pencil and storage roots: 15 proteins were up-regulated or expressed in pencil roots and 15 in storage roots. Differentially expressed proteins spots were investigated using matrix-assisted laser desorption/ionization time of flight mass spectrometry, and 10 proteins from pencil roots were identified as binding protein isoform A, catechol oxidase, peroxidases, ascorbate peroxidase, endochitinase, flavanone 3-hydroxylase and unknown proteins. Of the proteins up-regulated in, or restricted to, storage roots, 13 proteins were identified as protein disulfide isomerase, anionic peroxidase, putative ripening protein, sporamin B, sporamin A and sporamin A precursor. An analysis of enzyme activity revealed that catechol oxidase and peroxidase as the first and last enzymes of the lignin biosynthesis pathway, and ascorbate peroxidase had higher activities in pencil than in storage roots. The total concentration of phenolic compounds was also far higher in pencil than in storage roots, and lignin accumulated only in pencil roots. These results provide important insight into sweetpotato proteomics, and imply that lignin biosynthesis and stress-related proteins are up-regulated or uniquely expressed in pencil roots. The results indicate that the reduction of carbon flow toward phenylpropanoid biosynthesis and its delivery to carbohydrate metabolism is a major event in storage root formation.
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Affiliation(s)
- Jeung Joo Lee
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, College of Education, IALS, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Youn-Sig Kwak
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jae Young An
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Pil Joo Kim
- Division of Applied Life Science (BK21 Program), IALS, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Byung Hyun Lee
- Division of Applied Life Science (BK21 Program), IALS, PMBBRC, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Vikranth Kumar
- Division of Applied Life Science (BK21 Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Kee Woong Park
- Department of Crop Science, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Eun Sil Chang
- Gyeongsangnam-do Agricultural Research & Extension Services, Jinju 660-985, Republic of Korea
| | - Jae Cheol Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Haeng-Soon Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea.
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Abstract
The site-specific incorporation of bioorthogonal groups via genetic code expansion provides a powerful general strategy for site-specifically labeling proteins with any probe. Here we describe the genetic encoding of dienophile-bearing unnatural amino acids into proteins expressed in Escherichia coli and mammalian cells using the pyrrolysyl-tRNA synthetase/tRNACUA pair and its variants. We describe the rapid fluorogenic labeling of proteins containing these unnatural amino acids in vitro, in E. coli, and in live mammalian cells with tetrazine-fluorophore conjugates in a bioorthogonal Diels-Alder reaction with inverse electron demand. These approaches have been extended to site-specific protein labeling in animals, and we anticipate that they will have a broad impact on the labeling and imaging field.
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Affiliation(s)
- Kathrin Lang
- Faculty of Chemistry, Technische Universität München, Institute for Advanced Study, Lichtenbergstr. 4, Garching, 85748, Germany,
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Prokopec SD, Watson JD, Pohjanvirta R, Boutros PC. Identification of reference proteins for Western blot analyses in mouse model systems of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity. PLoS One 2014; 9:e110730. [PMID: 25329058 PMCID: PMC4201576 DOI: 10.1371/journal.pone.0110730] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 01/16/2014] [Accepted: 09/24/2014] [Indexed: 01/15/2023] Open
Abstract
Western blotting is a well-established, inexpensive and accurate way of measuring protein content. Because of technical variation between wells, normalization is required for valid interpretation of results across multiple samples. Typically this involves the use of one or more endogenous controls to adjust the measured levels of experimental molecules. Although some endogenous controls are widely used, validation is required for each experimental system. This is critical when studying transcriptional-modulators, such as toxicants like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).To address this issue, we examined hepatic tissue from 192 mice representing 47 unique combinations of strain, sex, Ahr-genotype, TCDD dose and treatment time. We examined 7 candidate reference proteins in each animal and assessed consistency of protein abundance through: 1) TCDD-induced fold-difference in protein content from basal levels, 2) inter- and intra- animal stability, and 3) the ability of each candidate to reduce instability of the other candidates. Univariate analyses identified HPRT as the most stable protein. Multivariate analysis indicated that stability generally increased with the number of proteins used, but gains from using >3 proteins were small. Lastly, by comparing these new data to our previous studies of mRNA controls on the same animals, we were able to show that the ideal mRNA and protein control-genes are distinct, and use of only 2–3 proteins provides strong stability, unlike in mRNA studies in the same cohort, where larger control-gene batteries were needed.
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Affiliation(s)
- Stephenie D. Prokopec
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John D. Watson
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Raimo Pohjanvirta
- Laboratory of Toxicology, National Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Paul C. Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Gutiérrez-Praena D, Campos A, Azevedo J, Neves J, Freitas M, Guzmán-Guillén R, Cameán AM, Renaut J, Vasconcelos V. Exposure of Lycopersicon esculentum to microcystin-LR: effects in the leaf proteome and toxin translocation from water to leaves and fruits. Toxins (Basel) 2014; 6:1837-54. [PMID: 24921194 PMCID: PMC4073132 DOI: 10.3390/toxins6061837] [Citation(s) in RCA: 44] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/30/2014] [Accepted: 06/03/2014] [Indexed: 11/21/2022] Open
Abstract
Natural toxins such as those produced by freshwater cyanobacteria have been regarded as an emergent environmental threat. However, the impact of these water contaminants in agriculture is not yet fully understood. The aim of this work was to investigate microcystin-LR (MC-LR) toxicity in Lycopersicon esculentum and the toxin accumulation in this horticultural crop. Adult plants (2 month-old) grown in a greenhouse environment were exposed for 2 weeks to either pure MC-LR (100 μg/L) or Microcystis aeruginosa crude extracts containing 100 μg/L MC-LR. Chlorophyll fluorescence was measured, leaf proteome investigated with two-dimensional gel electrophoresis and Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF)/TOF, and toxin bioaccumulation assessed by liquid chromatography-mass spectrometry (LC-MS)/MS. Variations in several protein markers (ATP synthase subunits, Cytochrome b6-f complex iron-sulfur, oxygen-evolving enhancer proteins) highlight the decrease of the capacity of plants to synthesize ATP and to perform photosynthesis, whereas variations in other proteins (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and ribose-5-phosphate isomerase) suggest an increase of carbon fixation and decrease of carbohydrate metabolism reactions in plants exposed to pure MC-LR and cyanobacterial extracts, respectively. MC-LR was found in roots (1635.21 μg/kg fw), green tomatoes (5.15–5.41 μg/kg fw), mature tomatoes (10.52–10.83 μg/kg fw), and leaves (12,298.18 μg/kg fw). The results raise concerns relative to food safety and point to the necessity of monitoring the bioaccumulation of water toxins in agricultural systems affected by cyanotoxin contamination.
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Affiliation(s)
| | - Alexandre Campos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), Porto 4050-123, Portugal.
| | - Joana Azevedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), Porto 4050-123, Portugal.
| | - Joana Neves
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), Porto 4050-123, Portugal.
| | - Marisa Freitas
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), Porto 4050-123, Portugal.
| | | | - Ana María Cameán
- Area of Toxicology, Faculty of Pharmacy, University of Seville, Seville 41012, Spain.
| | - Jenny Renaut
- Department of Environment and Agro-biotechnologies (EVA), Centre de Recherche Public-Gabriel Lippmann, Belvaux L-4422, Luxembourg.
| | - Vitor Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), Porto 4050-123, Portugal.
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Cho IK, Chang CL, Li QX. Diet-induced over-expression of flightless-I protein and its relation to flightlessness in Mediterranean fruit fly, Ceratitis capitata. PLoS One 2013; 8:e81099. [PMID: 24312525 PMCID: PMC3849048 DOI: 10.1371/journal.pone.0081099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 04/26/2013] [Accepted: 10/12/2013] [Indexed: 11/22/2022] Open
Abstract
The Mediterranean fruit fly (medfly), Ceratitis capitata is among the most economically important pests worldwide. Understanding nutritional requirement helps rearing healthy medfly for biocontrol of its population in fields. Flight ability is a high priority criterion. Two groups of medfly larvae were reared with two identical component diets except one with fatty acids (diet A) and another without it (diet B). Adults from larvae reared on diet B demonstrated 20±8% of normal flight ability, whereas those from larvae reared on diet A displayed full flight ability of 97±1%. Proteomes were profiled to compare two groups of medfly pupae using shotgun proteomics to study dietary effects on flight ability. When proteins detected in pupae A were compared with those in pupae B, 233 and 239 proteins were, respectively, under- and over-expressed in pupae B, while 167 proteins were overlapped in both pupae A and B. Differential protein profiles indicate that nutritional deficiency induced over-expression of flightless-I protein (fli-I) in medfly. All proteins were subjected to Ingenuity Pathway Analysis (IPA) to create 13 biological networks and 17 pathways of interacting protein clusters in human ortholog. Fli-I, leucine-rich repeat (LRR)-containing G protein-coupled receptor 2, LRR protein soc-2 and protein wings apart-like were over-expressed in pupae B. Inositol-1,4,5-trisphosphate receptor, protocadherin-like wing polarity protein stan and several Wnt pathway proteins were under-expressed in pupae B. These results suggest down-regulation of the Wnt/wingless signaling pathway, which consequently may result in flightlessness in pupae B. The fli-I gene is known to be located within the Smith-Magenis syndrome (SMS) region on chromosome 17, and thus, we speculate that nutritional deficiency might induce over-expression of fli-I (or fli-I gene) and be associated with human SMS. However, more evidence would be needed to confirm our speculation.
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Affiliation(s)
- Il Kyu Cho
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Chiou Ling Chang
- U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii, United States of America
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii, United States of America
- * E-mail:
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Aradská J, Šmidák R, Turkovičová L, Turňa J, Lubec G. Proteomic differences between tellurite-sensitive and tellurite-resistant E.coli. PLoS One 2013; 8:e78010. [PMID: 24244285 PMCID: PMC3823874 DOI: 10.1371/journal.pone.0078010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/11/2013] [Indexed: 01/20/2023] Open
Abstract
Tellurite containing compounds are in use for industrial processes and increasing delivery into the environment generates specific pollution that may well result in contamination and subsequent potential adverse effects on public health. It was the aim of the current study to reveal mechanism of toxicity in tellurite-sensitive and tellurite-resistant E. coli at the protein level. In this work an approach using gel-based mass spectrometrical analysis to identify a differential protein profile related to tellurite toxicity was used and the mechanism of ter operon-mediated tellurite resistance was addressed. E. coli BL21 was genetically manipulated for tellurite-resistance by the introduction of the resistance-conferring ter genes on the pLK18 plasmid. Potassium tellurite was added to cultures in order to obtain a final 3.9 micromolar concentration. Proteins from tellurite-sensitive and tellurite-resistant E. coli were run on 2-D gel electrophoresis, spots of interest were picked, in-gel digested and subsequently analysed by nano-LC-MS/MS (ion trap). In addition, Western blotting and measurement of enzymatic activity were performed to verify the expression of certain candidate proteins. Following exposure to tellurite, in contrast to tellurite-resistant bacteria, sensitive cells exhibited increased levels of antioxidant enzymes superoxide dismutases, catalase and oxidoreductase YqhD. Cysteine desulfurase, known to be related to tellurite toxicity as well as proteins involved in protein folding: GroEL, DnaK and EF-Tu were upregulated in sensitive cells. In resistant bacteria, several isoforms of four essential Ter proteins were observed and following tellurite treatment the abovementioned protein levels did not show any significant proteome changes as compared to the sensitive control. The absence of general defense mechanisms against tellurite toxicity in resistant bacteria thus provides further evidence that the four proteins of the ter operon function by a specific mode of action in the mechanism of tellurite resistance probably involving protein cascades from antioxidant and protein folding pathways.
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Affiliation(s)
- Jana Aradská
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovakia
| | - Roman Šmidák
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovakia
| | - Lenka Turkovičová
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovakia
| | - Ján Turňa
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovakia
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Abstract
The maturation of an oocyte into an egg is a key step in preparation for fertilization. In Xenopus, oocyte maturation is independent of transcription, being regulated at the level of translation and post-translational modifications of proteins. To identify factors involved in the maturation process we used two-dimensional differential gel electrophoresis to compare the proteome of oocytes and eggs. Protein abundance changes were observed in multiple cellular pathways during oocyte maturation. Most prominent was a general reduction in abundance of enzymes in the glycolytic pathway. Injection into oocytes of the glycolytic intermediates glyceraldehyde-3-phosphate, phosphoenolpyruvate and glucose-6-phosphate prevented oocyte maturation. Instead, these metabolites stimulated ROS production and subsequent apoptosis of the oocyte. In contrast, all other metabolites tested had no effect on oocyte maturation and did not induce apoptosis. These data suggest that a subset of glycolytic metabolites have the capacity to regulate oocyte viability.
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Affiliation(s)
- Lloyd Berger
- The Department of Molecular Genetics and the Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Wilde
- The Department of Molecular Genetics and the Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Liu C, Sheng W, Fu R, Wang H, Li L, Liu H, Shao Z. Differential expression of the proteome of myeloid dendritic cells in severe aplastic anemia. Cell Immunol 2013; 285:141-8. [PMID: 24185280 DOI: 10.1016/j.cellimm.2013.09.007] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/25/2013] [Accepted: 09/30/2013] [Indexed: 12/23/2022]
Abstract
Severe aplastic anemia (SAA) is a syndrome of severe bone marrow failure with high mortality. Our previous studies have demonstrated that both immature and activated DC1 increased in the bone marrow of SAA patients, and the balance of DC1 subsets shifted the stable form to active one, which might promote Th0 cells to polarize to Th1 cells and cause the over-function of T lymphocytes and hematopoiesis failure in SAA. So we assumed myeloid dendritic cells (mDCs) may be the key immune cells that cause destruction of hematopoietic cells in SAA, but the mechanism of activation of mDCs is unclear. Here, we investigated the proteome of mDCs in SAA patients to further explore the pathogenesis of SAA and the possible antigen that leads to immune activation in SAA. mDCs from 12 SAA patients, 12 remission patients and 12 controls were sorted by flow cytometry and examined by two-dimensional gel electrophoresis and mass spectrometry. Intensity changes of 41 spots were detected with statistical significance. Nine of the 41 spots were identified by MALDI-TOF/TOF tandem mass spectrometry. Changes in protein expression levels were found in the SAA group. These changes reveal that abnormal expression of cofilin, glucose-6-phosphate dehydrogenase and pyruvate kinase enzyme M2 in mDCs from SAA patients may be the reason for mDC hyperfunction.
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Affiliation(s)
- Chunyan Liu
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China
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38
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Hou D, Chen Y, Liu J, Xu L, Zhang Z, Zhang J, Wang H, Wang X, Chen J, Zhao R, Hu A, Hakonarson H, Zhang L, Shen Y. Proteomics screen to reveal molecular changes mediated by C722G missense mutation in CHRM2 gene. J Proteomics 2013; 89:39-50. [PMID: 23743182 DOI: 10.1016/j.jprot.2013.05.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 01/09/2013] [Revised: 05/15/2013] [Accepted: 05/24/2013] [Indexed: 11/19/2022]
Abstract
UNLABELLED Previously, we reported a missense mutation (C722G) in the M2-muscarinic acetylcholine receptor (CHRM2) gene associated with familial dilated cardiomyopathy. However, the exact molecular mechanisms by the related protein changes of CHRM2-C722G mutation induced are still unclear. CHRM2 and CHRM2-C722G lentiviral vector was infected to CHO cells. Proteomic analysis by label-free shotgun strategy and the STRING 9.0 software were performed. A total of 102 proteins with at least 2-fold change in the CHRM2-C722G group were identified, 42 proteins were up-regulated, whereas 57 were down-regulated. These altered proteins belong to three broad functional categories: (i) metabolic (e.g. Cytosolic acyl coenzyme A thioester hydrolase, Malate dehydrogenase); (ii) cytoskeletal (e.g. Actin-related protein, Myosin light polypeptide 6 and Alpha-actinin-1) and (iii) stress response (e.g. heat shock protein 70, Ras-related protein Rab-10). Interestingly, the marked differences in the expression of selected eight proteins (change >4.0-fold), were connected with many proteins related to apoptosis and immune/inflammatory response such as: FOS, BAX, MYC, TP53 and IL6. This novel study demonstrated for the first time a full-scale screening of the proteomics research by CHRM2-C722G mutation and profiled 102 changed proteins, of which, eight might be critical in cardiac dysfunction for future mapping. SIGNIFICANCE It was a full-scale screening of the proteomics research by CHRM2-C722G mutation. These proteins might serve as valuable biomarkers that could predict the presence of a precursor field. These proteins might serve to further explore the pathophysiological mechanisms in familial DCM patients with C176W mutation.
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Affiliation(s)
- Dongyan Hou
- Heart Failure Center, Department of Cardiology, Capital Medical University, Chao-Yang Hospital, Beijing, China
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Abstract
The past century had witnessed vast advances in biomedical research, particularly in the fields of genomics and proteomics, yet the translation of these discoveries into clinical practice has been hindered by gaps in mechanistic understanding of variability governing disease susceptibility and pathogenesis. Among the greatest challenges are the dynamic nature of the proteome and the imperfect methodologies currently available to study it. Here, we review key recently developed proteomic techniques that have allowed for dynamic characterization of protein quality, as well as quantity, and discuss their potential applications in understanding aging and metabolic disorders including diabetes. These methodologies revealed that senescence is characterized, in part, by decreased rates of de novo protein synthesis and potentially also degradation, in addition to concomitantly increased levels of oxidative stress, ultimately resulting in excessive accumulation of damaged and dysfunctional proteins. Insulin may be a key mediator in these pathologies, as hyperinsulinemia has been shown to hinder protein degradation while transient insulin deficiency may accelerate oxidative damage. We also discuss two interventions that have been proposed to delay, and possibly reverse, senescence by augmenting protein degradation: chronic caloric restriction and aerobic exercise.
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Affiliation(s)
- Rozalina G McCoy
- Department of Internal Medicine, Division of Endocrinology, Endocrinology Research Unit, Mayo Clinic College of Medicine, Rochester, MN, USA
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40
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Jiang SS, Liang XN, Li X, Wang SL, Lv DW, Ma CY, Li XH, Ma WJ, Yan YM. Wheat drought-responsive grain proteome analysis by linear and nonlinear 2-DE and MALDI-TOF mass spectrometry. Int J Mol Sci 2012; 13:16065-83. [PMID: 23443111 PMCID: PMC3546679 DOI: 10.3390/ijms131216065] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [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] [Received: 10/15/2012] [Revised: 11/13/2012] [Accepted: 11/14/2012] [Indexed: 02/03/2023] Open
Abstract
A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the nonlinear 2-DE had much higher resolution than the linear 2-DE. A total of 153 differentially expressed protein spots were detected by both 2-DE maps, of which 122 protein spots were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified differential proteins were mainly involved in carbohydrate metabolism (26%), detoxification and defense (23%), and storage proteins (17%). Some key proteins demonstrated significantly different expression patterns between the two varieties. In particular, catalase isozyme 1, WD40 repeat protein, LEA and alpha-amylase inhibitors displayed an upregulated expression pattern in Kauz, whereas they were downregulated or unchanged in Janz. Small and large subunit ADP glucose pyrophosphorylase, ascorbate peroxidase and G beta-like protein were all downregulated under drought stress in Janz, but had no expression changes in Kauz. Sucrose synthase and triticin precursor showed an upregulated expression pattern under water deficits in both varieties, but their upregulation levels were much higher in Kauz than in Janz. These differentially expressed proteins could be related to the biochemical pathways for stronger drought resistance of Kauz.
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Affiliation(s)
- Shan-Shan Jiang
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
| | - Xiao-Na Liang
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
| | - Xin Li
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
| | - Shun-Li Wang
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
| | - Dong-Wen Lv
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
| | - Chao-Ying Ma
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
| | - Xiao-Hui Li
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
| | - Wu-Jun Ma
- State Agriculture Biotechnology Centre, Western Australian Department of Agriculture and Food, Perth, WA 6150, Australia
| | - Yue-Ming Yan
- College of Life Science, Capital Normal University, Beijing 100048, China; E-Mails: (S.-S.J.); (X.-N.L.); (X.L.); (S.-L.W.); (D.-W.L.); (C.-Y.M.); (X.-H.L.)
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Boatti L, Robotti E, Marengo E, Viarengo A, Marsano F. Effects of nickel, chlorpyrifos and their mixture on the Dictyostelium discoideum proteome. Int J Mol Sci 2012; 13:15679-705. [PMID: 23443088 PMCID: PMC3546656 DOI: 10.3390/ijms131215679] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 11/13/2012] [Accepted: 11/15/2012] [Indexed: 11/16/2022] Open
Abstract
Mixtures of chemicals can have additive, synergistic or antagonistic interactions. We investigated the effects of the exposure to nickel, the organophosphate insecticide chlorpyrifos at effect concentrations (EC) of 25% and 50% and their binary mixture (Ec25 + EC25) on Dictyostelium discoideum amoebae based on lysosomal membrane stability (LMS). We treated D. discoideum with these compounds under controlled laboratory conditions and evaluated the changes in protein levels using a two-dimensional gel electrophoresis (2DE) proteomic approach. Nickel treatment at EC25 induced changes in 14 protein spots, 12 of which were down-regulated. Treatment with nickel at EC50 resulted in changes in 15 spots, 10 of which were down-regulated. Treatment with chlorpyrifos at EC25 induced changes in six spots, all of which were down-regulated; treatment with chlorpyrifos at EC50 induced changes in 13 spots, five of which were down-regulated. The mixture corresponding to EC25 of each compound induced changes in 19 spots, 13 of which were down-regulated. The data together reveal that a different protein expression signature exists for each treatment, and that only a few proteins are modulated in multiple different treatments. For a simple binary mixture, the proteomic response does not allow for the identification of each toxicant. The protein spots that showed significant differences were identified by mass spectrometry, which revealed modulations of proteins involved in metal detoxification, stress adaptation, the oxidative stress response and other cellular processes.
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Affiliation(s)
- Lara Boatti
- Department of Science & Technological Innovation (DiSIT), The University of Eastern Piedmont Amedeo Avogadro, Alessandria, Novara, Vercelli, Viale Teresa Michel, 11-15121 Alessandria, Italy.
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Tananova ON, Arianova EA, Gmoshinskiĭ IV, Aksenov IV, Zgoda VG, Khotimchenko SA. [Effect of titanium dioxide nanoparticles on protein expression profiles in rat liver microsomes]. Vopr Pitan 2012; 81:18-22. [PMID: 22774473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
There was studied an influence of intragastric administration of titanium dioxide (anatase form) nanoparticles (NP) on protein expression profiles in rat's liver microsomes by methods of proteomics. Animals received water suspension of NP in doses from 0,1 to 10 mg per kg body weight intragastrically daily during 28 days. Microsomes were isolated from liver by means of preparative ultracentrifugation. Proteins composition was studied by 2D-electrophoresis in acrylamide gel. Protein spots were identified by MALDI-TOF analysis. The results demonstrated appearance of 53 new protein spots and disappearance of 19 spots in animals subjected to NP irrespective of their dose. In addition 25 new spots appeared and 3 disappeared in higher doses of NP when compared to low dose group and control animals. Mass-spectrum analysis showed presence of few polypeptides registered in international database among proteins expressed under influence of NP. One of this dominant expressed proteins corresponded to enzyme glutathione transpherase Mu 2 isoform (M=41,55 kD, pI=8,0). The conclusion was made of well advances of proteomic analysis in artificial NP influences on biosynthetic processes estimation.
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43
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Dash S, Chandramouli KH, Zhang Y, Qian PY. Effects of poly-ether B on proteome and phosphoproteome expression in biofouling Balanus amphitrite cyprids. Biofouling 2012; 28:405-415. [PMID: 22519465 DOI: 10.1080/08927014.2012.679731] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biofouling is ubiquitous in marine environments, and the barnacle Balanus amphitrite is one of the most recalcitrant and aggressive biofoulers in tropical waters. Several natural antifoulants that were claimed to be non-toxic have been isolated in recent years, although the mechanism by which they inhibit fouling is yet to be investigated. Poly-ether B has shown promise in the non-toxic inhibition of larval barnacle attachment. Hence, in this study, multiplex two-dimensional electrophoresis (2-DE) was applied in conjunction with mass spectrometry to investigate the effects of poly-ether B on barnacle larvae at the molecular level. The cyprid proteome response to poly-ether B treatment was analyzed at the total proteome and phosphoproteome levels, with 65 protein and 19 phosphoprotein spots found to be up- or down-regulated. The proteins were found to be related to energy-metabolism, oxidative stress, and molecular chaperones, thus indicating that poly-ether B may interfere with the redox-regulatory mechanisms governing the settlement of barnacle larvae. The results of this study demonstrate the usefulness of the proteomic technique in revealing the working mechanisms of antifouling compounds.
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Affiliation(s)
- Swagatika Dash
- KAUST Global Collaborative Research, Division of Life Science, Hong Kong University of Science and Technology, HKSAR, China
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Francischetti IMB, Anderson JM, Manoukis N, Pham VM, Ribeiro JMC. An insight into the sialotranscriptome and proteome of the coarse bontlegged tick, Hyalomma marginatum rufipes. J Proteomics 2011; 74:2892-908. [PMID: 21851864 PMCID: PMC3215792 DOI: 10.1016/j.jprot.2011.07.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 07/11/2011] [Accepted: 07/13/2011] [Indexed: 01/28/2023]
Abstract
Ticks are mites specialized in acquiring blood from vertebrates as their sole source of food and are important disease vectors to humans and animals. Among the specializations required for this peculiar diet, ticks evolved a sophisticated salivary potion that can disarm their host's hemostasis, inflammation, and immune reactions. Previous transcriptome analysis of tick salivary proteins has revealed many new protein families indicative of fast evolution, possibly due to host immune pressure. The hard ticks (family Ixodidae) are further divided into two basal groups, of which the Metastriata have 11 genera. While salivary transcriptomes and proteomes have been described for some of these genera, no tick of the genus Hyalomma has been studied so far. The analysis of 2084 expressed sequence tags (EST) from a salivary gland cDNA library allowed an exploration of the proteome of this tick species by matching peptide ions derived from MS/MS experiments to this data set. We additionally compared these MS/MS derived peptide sequences against the proteins from the bovine host, finding many host proteins in the salivary glands of this tick. This annotated data set can assist the discovery of new targets for anti-tick vaccines as well as help to identify pharmacologically active proteins.
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Affiliation(s)
- Ivo MB Francischetti
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD 20852, USA
| | - Jennifer M Anderson
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD 20852, USA
| | - Nicholas Manoukis
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD 20852, USA
| | - Van M Pham
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD 20852, USA
| | - José MC Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD 20852, USA
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Lee JY, Kim BJ, Sim G, Kim GT, Kang D, Jung JH, Hwa JS, Kwak YJ, Choi YJ, Park YS, Han J, Lee CS, Kang KR. Spinal cord injury markedly altered protein expression patterns in the affected rat urinary bladder during healing stages. J Korean Med Sci 2011; 26:814-23. [PMID: 21655070 PMCID: PMC3102878 DOI: 10.3346/jkms.2011.26.6.814] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 04/05/2011] [Indexed: 01/01/2023] Open
Abstract
The influence of spinal cord injury (SCI) on protein expression in the rat urinary bladder was assessed by proteomic analysis at different time intervals post-injury. After contusion SCI between T9 and T10, bladder tissues were processed by 2-DE and MALDI-TOF/MS at 6 hr to 28 days after SCI to identify proteins involved in the healing process of SCI-induced neurogenic bladder. Approximately 1,000 spots from the bladder of SCI and sham groups were visualized and identified. At one day after SCI, the expression levels of three protein were increased, and seven spots were down-regulated, including heat shock protein 27 (Hsp27) and heat shock protein 20 (Hsp20). Fifteen spots such as S100-A11 were differentially expressed seven days post-injury, and seven proteins including transgelin had altered expression patterns 28 days after injury. Of the proteins with altered expression levels, transgelin, S100-A11, Hsp27 and Hsp20 were continuously and variably expressed throughout the entire post-SCI recovery of the bladder. The identified proteins at each time point belong to eight functional categories. The altered expression patterns identified by 2-DE of transgelin and S100-A11 were verified by Western blot. Transgelin and protein S100-A11 may be candidates for protein biomarkers in the bladder healing process after SCI.
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Affiliation(s)
- Ji-Young Lee
- MRCND and Department of Biochemistry, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Bong Jo Kim
- MRCND and Department of Psychiatry, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Gyujin Sim
- MRCND and Department of Biochemistry, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Gyu-Tae Kim
- MRCND and Department of Physiology, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Dawon Kang
- MRCND and Department of Physiology, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Jae Hun Jung
- MRCND and Department of Urology, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Jeong Seok Hwa
- MRCND and Department of Urology, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Yeon Ju Kwak
- MRCND and Department of Biochemistry, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Yeon Jin Choi
- MRCND and Department of Biochemistry, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Young Sook Park
- Department of Physical Medicine and Rehabilitation, Changwon Samsung Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Jaehee Han
- MRCND and Department of Physiology, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Cheol Soon Lee
- MRCND and Department of Psychiatry, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
| | - Kee Ryeon Kang
- MRCND and Department of Biochemistry, BK21 Program for Biomedical Sciences, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Korea
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46
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Herath K, Bhat G, Miller PL, Wang SP, Kulick A, Andrews-Kelly G, Johnson C, Rohm RJ, Lassman ME, Previs SF, Johns DG, Hubbard BK, Roddy TP. Equilibration of (2)H labeling between body water and free amino acids: enabling studies of proteome synthesis. Anal Biochem 2011; 415:197-9. [PMID: 21596013 DOI: 10.1016/j.ab.2011.04.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [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: 12/04/2010] [Revised: 04/02/2011] [Accepted: 04/19/2011] [Indexed: 11/19/2022]
Abstract
Protein synthesis can be estimated by measuring the incorporation of a labeled amino acid into a proteolytic peptide. Although prelabeled amino acids are typically administered, recent studies have tested (2)H(2)O; the assumption is that there is rapid equilibration of (2)H (in body water) with the carbon-bound hydrogens of amino acids before those amino acids are incorporated into a protein(s). We have determined the temporal changes in (2)H labeling of body water and amino acids which should build confidence in (2)H(2)O-based studies of protein synthesis when one aims to measure the (2)H labeling of proteolytic peptides.
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Affiliation(s)
- Kithsiri Herath
- Atherosclerosis, Merck Research Laboratories, Rahway, NJ 07065, USA
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Cruz-Topete D, List EO, Okada S, Kelder B, Kopchick JJ. Proteomic changes in the heart of diet-induced pre-diabetic mice. J Proteomics 2011; 74:716-27. [PMID: 21354350 DOI: 10.1016/j.jprot.2011.02.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [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: 12/20/2010] [Revised: 02/10/2011] [Accepted: 02/15/2011] [Indexed: 01/18/2023]
Abstract
The development of type 2 diabetes (T2D) is strongly associated with obesity. In humans, T2D increases the risk for end organ complications. Among these, heart disease has been ranked as the leading cause of death. We used a proteomic methodology to test the hypothesis that a pre-diabetic state generated by high-fat diet leads to changes in proteins related to heart function and structure. Over 300 protein spots were resolved by two-dimensional gel electrophoresis (2-DE). Fifteen protein spots were found to be altered (7 decreased and 8 increased) in pre-diabetic hearts. The protein spots were then identified by mass spectrometry and immunoblots. Among the decreased proteins, 3 are involved in heart structure (one isoform of desmin, troponin T2 and α-cardiac actin), 3 are involved in energy metabolism (mitochondrial ATP synthase β subunit, adenylate kinase and creatine kinase) and one is a component of the citric acid cycle (isocitrate dehydrogenase 3). In contrast, proteins involved in fatty acid oxidation (two isoforms of peroxisomal enoyl-CoA hydratase) and the citric acid cycle (three isoforms of malate dehydrogenase) were increased in pre-diabetic hearts. The results suggest that changes in the levels of several heart proteins may have implications in the development of the cardiac phenotype associated to T2D.
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Affiliation(s)
- Diana Cruz-Topete
- Edison Biotechnology Institute and Dept. of Biomedical Sciences, Ohio University, 1 Water Tower Drive, The Ridges, Athens, OH 45701, USA
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Camerino GM, Pellegrino MA, Brocca L, Digennaro C, Camerino DC, Pierno S, Bottinelli R. Statin or fibrate chronic treatment modifies the proteomic profile of rat skeletal muscle. Biochem Pharmacol 2011; 81:1054-64. [PMID: 21300028 DOI: 10.1016/j.bcp.2011.01.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [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: 11/15/2010] [Revised: 01/27/2011] [Accepted: 01/31/2011] [Indexed: 11/18/2022]
Abstract
Statins and fibrates can cause myopathy. To further understand the causes of the damage we performed a proteome analysis in fast-twitch skeletal muscle of rats chronically treated with different hypolipidemic drugs. The proteomic maps were obtained from extensor digitorum longus (EDL) muscles of rats treated for 2-months with 10mg/kg atorvastatin, 20 mg/kg fluvastatin, 60 mg/kg fenofibrate and control rats. The proteins differentially expressed were identified by mass spectrometry and further analyzed by immunoblot analysis. We found a significant modification in 40 out of 417 total spots analyzed in atorvastatin treated rats, 15 out of 436 total spots in fluvastatin treated rats and 21 out of 439 total spots in fenofibrate treated rats in comparison to controls. All treatments induced a general tendency to a down-regulation of protein expression; in particular, atorvastatin affected the protein pattern more extensively with respect to the other treatments. Energy production systems, both oxidative and glycolytic enzymes and creatine kinase, were down-regulated following atorvastatin administration, whereas fenofibrate determined mostly alterations in glycolytic enzymes and creatine kinase, oxidative enzymes being relatively spared. Additionally, all treatments resulted in some modifications of proteins involved in cellular defenses against oxidative stress, such as heat shock proteins, and of myofibrillar proteins. These results were confirmed by immunoblot analysis. In conclusions, the proteomic analysis showed that either statin or fibrate administration can modify the expression of proteins essential for skeletal muscle function suggesting potential mechanisms for statin myopathy.
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MESH Headings
- Animals
- Dose-Response Relationship, Drug
- Down-Regulation
- Electrophoresis, Gel, Two-Dimensional
- Fibric Acids/administration & dosage
- Fibric Acids/adverse effects
- Hydroxymethylglutaryl-CoA Reductase Inhibitors/administration & dosage
- Hydroxymethylglutaryl-CoA Reductase Inhibitors/adverse effects
- Immunoblotting
- Isoelectric Focusing
- Male
- Muscle Fibers, Fast-Twitch/drug effects
- Muscle Fibers, Fast-Twitch/metabolism
- Muscle Proteins/biosynthesis
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- Muscular Diseases/chemically induced
- Muscular Diseases/metabolism
- Oxidative Stress/drug effects
- Proteome/biosynthesis
- Rats
- Rats, Wistar
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Giulia Maria Camerino
- Department of Pharmacobiology, Section of Pharmacology, Faculty of Pharmacy, University of Bari "Aldo Moro", Via Orabona 4, 70124 Bari, Italy
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Abstract
Systematic study of proteins requires the availability of thousands of proteins in functional format. However, traditional recombinant protein expression and purification methods have many drawbacks for such study at the proteome level. We have developed an innovative in situ protein expression and capture system, namely NAPPA (nucleic acid programmable protein array), where C-terminal tagged proteins are expressed using an in vitro expression system and efficiently captured/purified by antitag antibodies coprinted at each spot. The NAPPA technology presented in this chapter enable researchers to produce and display fresh proteins just in time in a multiplexed high-throughput fashion and utilize them for various downstream biochemical researches of interest. This platform could revolutionize the field of functional proteomics with it ability to produce thousands of spatially separated proteins in high density with narrow dynamic rand of protein concentrations, reproducibly and functionally.
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Affiliation(s)
- Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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50
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Krasnov GS, Khankin SL, Bukurova IA, Zatsepina OG, Oparina NI, Garbuz DG, Ershov AN, Mashkova TD, Karpov VL, Beresten' SF. [Proteomic expression analysis of human colorectal cancer: of soluble overexpressed proteins]. Mol Biol (Mosk) 2009; 43:610-615. [PMID: 19807022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Colon cancer is one of the leading causes of cancer deaths in developed countries due to the absence of tumor specific markers for early diagnosis of the disease, providing adequate sensitivity. Search for diagnostic markers of various types of cancer by proteomic approaches has been limited by large differences in protein centration. We used preliminary extraction of major cellular proteins by 0.2 M sodium chloride in presence of nonionic detergent NP-40 in order to raise the sensitivity of the 2D PAGE detection of low-abundant soluble proteins, some of which may penetrate in blood circulation during carcinogenesis. Application of this procedure prior to 2D comparative analysis of proteomes of normal tissues and matched colon cancer specimens led to selection of ten proteins, which are frequently overexpressed in colon adenocarcinomas. Mass-spectrometric identification of selected proteins led to discovery of two novel protein markers of colon tumors--TAF9 and CISH. Low level of CISH expression in various tissues suggests that it is a novel prospective marker for diagnosis of colon cancer.
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