1
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Gomez JM, Nolte H, Vogelsang E, Dey B, Takeda M, Giudice G, Faxel M, Haunold T, Cepraga A, Zinzen RP, Krüger M, Petsalaki E, Wang YC, Leptin M. Differential regulation of the proteome and phosphoproteome along the dorso-ventral axis of the early Drosophila embryo. eLife 2024; 13:e99263. [PMID: 39221782 PMCID: PMC11466282 DOI: 10.7554/elife.99263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024] Open
Abstract
The initially homogeneous epithelium of the early Drosophila embryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso-ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3398 and 3433 were differentially regulated, respectively. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail, and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway, Toll10B and serpin27aex do this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo.
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Affiliation(s)
- Juan Manuel Gomez
- Directors's Research and Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
- Institute of Genetics, University of CologneCologneGermany
| | - Hendrik Nolte
- Institute of Genetics, CECAD Research CenterCologneGermany
| | - Elisabeth Vogelsang
- Institute of Genetics, University of CologneCologneGermany
- Molecular Cell Biology, Anatomy, University Hospital Cologne, University of CologneCologneGermany
| | - Bipasha Dey
- RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | | | - Girolamo Giudice
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusHinxtonUnited Kingdom
| | - Miriam Faxel
- Max Delbrück Center for Molecular MedicineBerlinGermany
| | - Theresa Haunold
- Directors's Research and Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Alina Cepraga
- Directors's Research and Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Marcus Krüger
- Institute of Genetics, CECAD Research CenterCologneGermany
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusHinxtonUnited Kingdom
| | - Yu-Chiun Wang
- RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Maria Leptin
- Directors's Research and Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
- Institute of Genetics, University of CologneCologneGermany
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2
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Frey N, Sönmez UM, Minden J, LeDuc P. Microfluidics for understanding model organisms. Nat Commun 2022; 13:3195. [PMID: 35680898 PMCID: PMC9184607 DOI: 10.1038/s41467-022-30814-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
New microfluidic systems for whole organism analysis and experimentation are catalyzing biological breakthroughs across many fields, from human health to fundamental biology principles. This perspective discusses recent microfluidic tools to study intact model organisms to demonstrate the tremendous potential for these integrated approaches now and into the future. We describe these microsystems' technical features and highlight the unique advantages for precise manipulation in areas including immobilization, automated alignment, sorting, sensory, mechanical and chemical stimulation, and genetic and thermal perturbation. Our aim is to familiarize technologically focused researchers with microfluidics applications in biology research, while providing biologists an entrée to advanced microengineering techniques for model organisms.
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Affiliation(s)
- Nolan Frey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Utku M Sönmez
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonathan Minden
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Philip LeDuc
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
- Department of Computation Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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3
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Mishra N, Heisenberg CP. Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics. Annu Rev Genet 2021; 55:209-233. [PMID: 34460295 DOI: 10.1146/annurev-genet-071819-103748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Nikhil Mishra
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria; ,
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4
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Islam M, Diwan A, Mani K. Come Together: Protein Assemblies, Aggregates and the Sarcostat at the Heart of Cardiac Myocyte Homeostasis. Front Physiol 2020; 11:586. [PMID: 32581848 PMCID: PMC7287178 DOI: 10.3389/fphys.2020.00586] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022] Open
Abstract
Homeostasis in vertebrate systems is contingent on normal cardiac function. This, in turn, depends on intricate protein-based cellular machinery, both for contractile function, as well as, durability of cardiac myocytes. The cardiac small heat shock protein (csHsp) chaperone system, highlighted by αB-crystallin (CRYAB), a small heat shock protein (sHsp) that forms ∼3–5% of total cardiac mass, plays critical roles in maintaining proteostatic function via formation of self-assembled multimeric chaperones. In this work, we review these ancient proteins, from the evolutionarily preserved role of homologs in protists, fungi and invertebrate systems, as well as, the role of sHsps and chaperones in maintaining cardiac myocyte structure and function. We propose the concept of the “sarcostat” as a protein quality control mechanism in the sarcomere. The roles of the proteasomal and lysosomal proteostatic network, as well as, the roles of the aggresome, self-assembling protein complexes and protein aggregation are discussed in the context of cardiac myocyte homeostasis. Finally, we will review the potential for targeting the csHsp system as a novel therapeutic approach to prevent and treat cardiomyopathy and heart failure.
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Affiliation(s)
- Moydul Islam
- Division of Cardiology, Washington University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Washington University School of Medicine, St. Louis, MO, United States.,Department of Chemistry, Washington University in St. Louis, St. Louis, MO, United States
| | - Abhinav Diwan
- Division of Cardiology, Washington University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Washington University School of Medicine, St. Louis, MO, United States.,John Cochran Veterans Affairs Medical Center, St. Louis, MO, United States
| | - Kartik Mani
- Division of Cardiology, Washington University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Washington University School of Medicine, St. Louis, MO, United States.,John Cochran Veterans Affairs Medical Center, St. Louis, MO, United States
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5
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Prat‐Rojo C, Pouille P, Buceta J, Martin‐Blanco E. Mechanical coordination is sufficient to promote tissue replacement during metamorphosis in Drosophila. EMBO J 2020; 39:e103594. [PMID: 31858605 PMCID: PMC6996571 DOI: 10.15252/embj.2019103594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/30/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022] Open
Abstract
During development, cells coordinate to organize in coherent structures. Although it is now well established that physical forces are essential for implementing this coordination, the instructive roles of mechanical inputs are not clear. Here, we show that the replacement of the larval epithelia by the adult one in Drosophila demands the coordinated exchange of mechanical signals between two cell types, the histoblasts (adult precursors) organized in nests and the surrounding larval epidermal cells (LECs). An increasing stress gradient develops from the center of the nests toward the LECs as a result of the forces generated by histoblasts as they proliferate and by the LECs as they delaminate (push/pull coordination). This asymmetric radial coordination of expansive and contractile activities contributes to epithelial replacement. Our analyses support a model in which cell-cell mechanical communication is sufficient for the rearrangements that implement epithelial morphogenesis.
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Affiliation(s)
- Carla Prat‐Rojo
- Instituto de Biología Molecular de BarcelonaConsejo Superior de Investigaciones CientíficasParc Científic de BarcelonaBarcelonaSpain
- Present address:
Nikon Instruments Europe BVAmsterdamThe Netherlands
| | - Philippe‐Alexandre Pouille
- Instituto de Biología Molecular de BarcelonaConsejo Superior de Investigaciones CientíficasParc Científic de BarcelonaBarcelonaSpain
| | - Javier Buceta
- Department of Bioengineering and Department of Chemical and Biomolecular EngineeringLehigh UniversityBethlehemPAUSA
| | - Enrique Martin‐Blanco
- Instituto de Biología Molecular de BarcelonaConsejo Superior de Investigaciones CientíficasParc Científic de BarcelonaBarcelonaSpain
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6
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Mutant huntingtin disrupts mitochondrial proteostasis by interacting with TIM23. Proc Natl Acad Sci U S A 2019; 116:16593-16602. [PMID: 31346086 DOI: 10.1073/pnas.1904101116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutant huntingtin (mHTT), the causative protein in Huntington's disease (HD), associates with the translocase of mitochondrial inner membrane 23 (TIM23) complex, resulting in inhibition of synaptic mitochondrial protein import first detected in presymptomatic HD mice. The early timing of this event suggests that it is a relevant and direct pathophysiologic consequence of mHTT expression. We show that, of the 4 TIM23 complex proteins, mHTT specifically binds to the TIM23 subunit and that full-length wild-type huntingtin (wtHTT) and mHTT reside in the mitochondrial intermembrane space. We investigated differences in mitochondrial proteome between wtHTT and mHTT cells and found numerous proteomic disparities between mHTT and wtHTT mitochondria. We validated these data by quantitative immunoblotting in striatal cell lines and human HD brain tissue. The level of soluble matrix mitochondrial proteins imported through the TIM23 complex is lower in mHTT-expressing cell lines and brain tissues of HD patients compared with controls. In mHTT-expressing cell lines, membrane-bound TIM23-imported proteins have lower intramitochondrial levels, whereas inner membrane multispan proteins that are imported via the TIM22 pathway and proteins integrated into the outer membrane generally remain unchanged. In summary, we show that, in mitochondria, huntingtin is located in the intermembrane space, that mHTT binds with high-affinity to TIM23, and that mitochondria from mHTT-expressing cells and brain tissues of HD patients have reduced levels of nuclearly encoded proteins imported through TIM23. These data demonstrate the mechanism and biological significance of mHTT-mediated inhibition of mitochondrial protein import, a mechanism likely broadly relevant to other neurodegenerative diseases.
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7
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Blundon M, Ganesan V, Redler B, Van PT, Minden JS. Two-Dimensional Difference Gel Electrophoresis. Methods Mol Biol 2019; 1855:229-247. [PMID: 30426421 DOI: 10.1007/978-1-4939-8793-1_20] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Two-dimensional difference gel electrophoresis (2D DIGE) is a modified form of 2D electrophoresis (2D E) that allows one to compare two or three protein samples simultaneously on the same gel. The proteins in each sample are covalently tagged with different color fluorescent dyes that are designed to have no effect on the relative migration of proteins during electrophoresis. Proteins that are common to the samples appear as "spots" with a fixed ratio of fluorescent signals, whereas proteins that differ between the samples have different fluorescence ratios. With conventional imaging systems, DIGE is capable of reliably detecting as little as 0.2 fmol of protein, and protein differences down to ± 15%, over a ~10,000-fold protein concentration range. DIGE combined with digital image analysis therefore greatly improves the statistical assessment of proteome variation. Here we describe a protocol for conducting DIGE experiments, which takes 2-3 days to complete. We have further improved upon 2D DIGE by introducing in-gel equilibration to improve protein retention during transfer between the first and second dimensions of electrophoresis and by developing a fluorescent gel imaging system with a millionfold dynamic range.
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Affiliation(s)
- Malachi Blundon
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Vinitha Ganesan
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Brendan Redler
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Phu T Van
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonathan S Minden
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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8
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Lockwood BL, Julick CR, Montooth KL. Maternal loading of a small heat shock protein increases embryo thermal tolerance in Drosophila melanogaster. J Exp Biol 2017; 220:4492-4501. [PMID: 29097593 PMCID: PMC5769566 DOI: 10.1242/jeb.164848] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
Abstract
Maternal investment is likely to have direct effects on offspring survival. In oviparous animals whose embryos are exposed to the external environment, maternal provisioning of molecular factors like mRNAs and proteins may help embryos cope with sudden changes in the environment. Here, we sought to modify the maternal mRNA contribution to offspring embryos and test for maternal effects on acute thermal tolerance in early embryos of Drosophila melanogaster We drove in vivo overexpression of a small heat shock protein gene (Hsp23) in female ovaries and measured the effects of acute thermal stress on offspring embryonic survival and larval development. We report that overexpression of the Hsp23 gene in female ovaries produced offspring embryos with increased thermal tolerance. We also found that brief heat stress in the early embryonic stage (0-1 h old) caused decreased larval performance later in life (5-10 days old), as indexed by pupation height. Maternal overexpression of Hsp23 protected embryos against this heat-induced defect in larval performance. Our data demonstrate that transient products of single genes have large and lasting effects on whole-organism environmental tolerance. Further, our results suggest that maternal effects have a profound impact on offspring survival in the context of thermal variability.
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Affiliation(s)
- Brent L Lockwood
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Cole R Julick
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
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9
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Di G, Kong X, Miao X, Zhang Y, Huang M, Gu Y, You W, Zhang J, Ke C. Proteomic analysis of trochophore and veliger larvae development in the small abalone Haliotis diversicolor. BMC Genomics 2017; 18:809. [PMID: 29058591 PMCID: PMC5651566 DOI: 10.1186/s12864-017-4203-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/08/2017] [Indexed: 12/19/2022] Open
Abstract
Background Haliotis diversicolor is commercially important species. The trochophore and veliger are distinct larval stages in gastropod development. Their development involves complex morphological and physiological changes. We studied protein changes during the embryonic development of H. diversicolor using two dimensional electrophoresis (2-DE) and label-free methods, tandem mass spectrometry (MS/ MS), and Mascot for protein identification. Results A total of 150 2-DE gel spots were identified. Protein spots showed upregulation of 15 proteins and downregulation of 28 proteins as H. diversicolor developed from trochophore to veliger larvae. Trochophore and veliger larvae were compared using a label-free quantitative proteomic approach. A total of 526 proteins were identified from both samples, and 104 proteins were differentially expressed (> 1.5 fold). Compared with trochophore larvae, veliger larvae had 55 proteins upregulated and 49 proteins downregulated. These differentially expressed proteins were involved in shell formation, energy metabolism, cellular and stress response processes, protein synthesis and folding, cell cycle, and cell fate determination. Compared with the 5 protein (fructose-bisphosphate aldolase, 14–3-3ε, profilin, actin-depolymerizing factor (ADF)/cofilin) and calreticulin) expression patterns, the mRNA expression exhibited similar patterns except gene of fructose-bisphosphate aldolase. Conclusion Our results provide insight into novel aspects of protein function in shell formation, torsion, and nervous system development, and muscle system differentiation in H. diversicolor larvae. “Quality control” proteins were identified to be involved in abalone larval development. Electronic supplementary material The online version of this article (10.1186/s12864-017-4203-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guilan Di
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China.,State Key Laboratory of Marine Environmental Science, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian Province, 361005, People's Republic of China
| | - Xianghui Kong
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xiulian Miao
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - Yifang Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian Province, 361005, People's Republic of China
| | - Miaoqin Huang
- State Key Laboratory of Marine Environmental Science, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian Province, 361005, People's Republic of China
| | - Yuting Gu
- State Key Laboratory of Marine Environmental Science, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian Province, 361005, People's Republic of China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian Province, 361005, People's Republic of China.
| | - Jianxin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian Province, 361005, People's Republic of China.
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10
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Blundon MA, Schlesinger DR, Parthasarathy A, Smith SL, Kolev HM, Vinson DA, Kunttas-Tatli E, McCartney BM, Minden JS. Proteomic analysis reveals APC-dependent post-translational modifications and identifies a novel regulator of β-catenin. Development 2016; 143:2629-40. [PMID: 27287809 DOI: 10.1242/dev.130567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 05/31/2016] [Indexed: 01/02/2023]
Abstract
Wnt signaling generates patterns in all embryos, from flies to humans, and controls cell fate, proliferation and metabolic homeostasis. Inappropriate Wnt pathway activation results in diseases, including colorectal cancer. The adenomatous polyposis coli (APC) tumor suppressor gene encodes a multifunctional protein that is an essential regulator of Wnt signaling and cytoskeletal organization. Although progress has been made in defining the role of APC in a normal cellular context, there are still significant gaps in our understanding of APC-dependent cellular function and dysfunction. We expanded the APC-associated protein network using a combination of genetics and a proteomic technique called two-dimensional difference gel electrophoresis (2D-DIGE). We show that loss of Drosophila Apc2 causes protein isoform changes reflecting misregulation of post-translational modifications (PTMs), which are not dependent on β-catenin transcriptional activity. Mass spectrometry revealed that proteins involved in metabolic and biosynthetic pathways, protein synthesis and degradation, and cell signaling are affected by Apc2 loss. We demonstrate that changes in phosphorylation partially account for the altered PTMs in APC mutants, suggesting that APC mutants affect other types of PTM. Finally, through this approach Aminopeptidase P was identified as a new regulator of β-catenin abundance in Drosophila embryos. This study provides new perspectives on the cellular effects of APC that might lead to a deeper understanding of its role in development.
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Affiliation(s)
- Malachi A Blundon
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Danielle R Schlesinger
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Amritha Parthasarathy
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Samantha L Smith
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Hannah M Kolev
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - David A Vinson
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ezgi Kunttas-Tatli
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Brooke M McCartney
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jonathan S Minden
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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11
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Baron MN, Klinger CM, Rachubinski RA, Simmonds AJ. A Systematic Cell-Based Analysis of Localization of PredictedDrosophilaPeroxisomal Proteins. Traffic 2016; 17:536-53. [DOI: 10.1111/tra.12384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Matthew N. Baron
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Christen M. Klinger
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Richard A. Rachubinski
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Andrew J. Simmonds
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
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12
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Drosophila Small Heat Shock Proteins: An Update on Their Features and Functions. HEAT SHOCK PROTEINS 2015. [DOI: 10.1007/978-3-319-16077-1_25] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Van PT, Ganesan V, Bass V, Parthasarathy A, Schlesinger D, Minden JS. In-gel equilibration for improved protein retention in 2DE-based proteomic workflows. Electrophoresis 2014; 35:3012-7. [PMID: 25042010 DOI: 10.1002/elps.201400256] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/26/2014] [Accepted: 07/08/2014] [Indexed: 11/09/2022]
Abstract
The 2DE is a powerful proteomic technique, with excellent protein separation capabilities where intact proteins are spatially separated by pI and molecular weight. 2DE is commonly used in conjunction with MS to identify proteins of interest. Current 2DE workflow requires several manual processing steps that can lead to experimental variability and sample loss. One such step is the transition between first dimension IEF and second-dimension SDS-PAGE, which requires exchanging denaturants and the reduction and alkylation of proteins. This in-solution-based equilibration step has been shown to be rather inefficient, losing up to 30% of the original starting material through diffusion effects. We have developed a refinement of this equilibration step using agarose stacking gels poured on top of the second-dimension SDS-PAGE gel, referred to as in-gel equilibration. We show that in-gel equilibration is effective at reduction and alkylation in SDS-PAGE gels. Quantification of whole-cell extracts separated on 2DE gels shows that in-gel equilibration increases protein retention, decreased intergel variability, and simplifies 2DE workflow.
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Affiliation(s)
- Phu T Van
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
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14
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Van PT, Bass V, Shiwarski D, Lanni F, Minden J. High dynamic range proteome imaging with the structured illumination gel imager. Electrophoresis 2014; 35:2642-55. [PMID: 24935033 DOI: 10.1002/elps.201400126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/14/2014] [Accepted: 06/10/2014] [Indexed: 11/08/2022]
Abstract
A current challenge for proteomics is detecting proteins over the large concentration ranges found in complex biological samples such as whole-cell extracts. Currently, no unbiased, whole-proteome analysis scheme is capable of detecting the full range of cellular proteins. This is due in part to the limited dynamic range of the detectors used to sense proteins or peptides. We present a new technology, structured illumination (SI) gel imager, which detects fluorescently labeled proteins in electrophoretic gels over a 1 000 000-fold concentration range. SI uses computer-generated masks to attenuate the illumination of highly abundant proteins, allowing for long exposures of low-abundance proteins, thus avoiding detector saturation. A series of progressively masked gel images are assembled into a single, very high dynamic range image. We demonstrate that the SI imager can detect proteins over a concentration range of approximately 1 000 000-fold, making it a useful tool for comprehensive, unbiased proteome-wide surveys.
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Affiliation(s)
- Phu T Van
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
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15
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Fernandez-Gomez FJ, Jumeau F, Derisbourg M, Burnouf S, Tran H, Eddarkaoui S, Obriot H, Dutoit-Lefevre V, Deramecourt V, Mitchell V, Lefranc D, Hamdane M, Blum D, Buée L, Buée-Scherrer V, Sergeant N. Consensus brain-derived protein, extraction protocol for the study of human and murine brain proteome using both 2D-DIGE and mini 2DE immunoblotting. J Vis Exp 2014. [PMID: 24747743 DOI: 10.3791/51339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Two-dimensional gel electrophoresis (2DE) is a powerful tool to uncover proteome modifications potentially related to different physiological or pathological conditions. Basically, this technique is based on the separation of proteins according to their isoelectric point in a first step, and secondly according to their molecular weights by SDS polyacrylamide gel electrophoresis (SDS-PAGE). In this report an optimized sample preparation protocol for little amount of human post-mortem and mouse brain tissue is described. This method enables to perform both two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mini 2DE immunoblotting. The combination of these approaches allows one to not only find new proteins and/or protein modifications in their expression thanks to its compatibility with mass spectrometry detection, but also a new insight into markers validation. Thus, mini-2DE coupled to western blotting permits to identify and validate post-translational modifications, proteins catabolism and provides a qualitative comparison among different conditions and/or treatments. Herein, we provide a method to study components of protein aggregates found in AD and Lewy body dementia such as the amyloid-beta peptide and the alpha-synuclein. Our method can thus be adapted for the analysis of the proteome and insoluble proteins extract from human brain tissue and mice models too. In parallel, it may provide useful information for the study of molecular and cellular pathways involved in neurodegenerative diseases as well as potential novel biomarkers and therapeutic targets.
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Affiliation(s)
| | - Fanny Jumeau
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837; EA 4308-Department of Reproductive Biology-Spermiology-CECOS, CHRU-Lille
| | - Maxime Derisbourg
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Sylvie Burnouf
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Hélène Tran
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Sabiha Eddarkaoui
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Hélène Obriot
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | | | | | - Valérie Mitchell
- EA 4308-Department of Reproductive Biology-Spermiology-CECOS, CHRU-Lille
| | - Didier Lefranc
- EA2686-Laboratorie d'Immunologie, Faculté de Médecine - Pôle Recherche
| | - Malika Hamdane
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - David Blum
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Luc Buée
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | | | - Nicolas Sergeant
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837;
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16
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Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics 2014; 1:401-9. [PMID: 15966837 DOI: 10.1586/14789450.1.4.401] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
2D polyacrylamide gel electrophoresis has been the traditional workhorse of proteomics, allowing for the resolution of several thousand proteins in a single gel. Difference gel electrophoresis is an emerging technology that allows for accurate quantification with statistical confidence while controlling for nonbiologic variation, and also increases the dynamic range and sensitivity of traditional 2D polyacrylamide gel electrophoresis. With inclusion of an internal standard formed from equal amounts of every sample in an experiment, difference gel electrophoresis technology also allows for repetitive measurements and multivariable analyses to be quantitatively analyzed in one co-ordinated experiment, yielding statistically-significant changes in protein expression related to many disease states. This technique promises to be an important tool in clinical proteomics and the study of the mechanism of disease, investigating diagnostic biomarkers and pinpointing novel therapeutic targets.
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Affiliation(s)
- Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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17
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Ratnaparkhi A. Signaling by Folded gastrulation is modulated by mitochondrial fusion and fission. J Cell Sci 2013; 126:5369-76. [PMID: 24101729 DOI: 10.1242/jcs.127985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondria are increasingly being identified as integrators and regulators of cell signaling pathways. Folded gastrulation (Fog) is a secreted signaling molecule best known for its role in regulating cell shape change at the ventral furrow during gastrulation in Drosophila. Fog is thought to signal, through a G-protein-coupled receptor, to effect downstream cytoskeletal changes necessary for cell shape change. However, the mechanisms regulating Fog signaling that lead to change in cell morphology are poorly understood. This study describes the identification of proteins involved in mitochondrial fusion and fission as regulators of Fog signaling. Pro-fission factors were found to function as enhancers of signaling, whereas pro-fusion factors were found to have the opposite effect. Consistent with this, activation of Fog signaling resulted in mitochondrial fragmentation, and inhibiting this process could attenuate Fog signaling. The findings presented here show that mitochondria, through regulation of fusion and fission, function as downstream effectors and modulators of Fog signaling and Fog-dependent cell shape change.
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Affiliation(s)
- Anuradha Ratnaparkhi
- Agharkar Research Institute, Animal Sciences Division, Zoology Group, G.G. Agarkar Road, Pune 411 004, India
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18
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Lourenço AP, Guidugli-Lazzarini KR, Freitas FCP, Bitondi MMG, Simões ZLP. Bacterial infection activates the immune system response and dysregulates microRNA expression in honey bees. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:474-482. [PMID: 23499934 DOI: 10.1016/j.ibmb.2013.03.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/16/2013] [Accepted: 03/04/2013] [Indexed: 06/01/2023]
Abstract
In insects, a rapid and massive synthesis of antimicrobial peptides (AMPs) is activated through signaling pathways (Toll and Imd) to combat invading microbial pathogens. However, it is still unclear whether different types of bacteria provoke specific responses. Immune response mechanisms and the activation of specific genes were investigated by challenging Apis mellifera workers with the Gram-negative bacterium Serratia marcescens or the Gram-positive bacterium Micrococcus luteus. The immune system responded by activating most genes of the Toll and Imd pathways, particularly AMP genes. However, genes specifically regulated by M. luteus or S. marcescens were not detected, suggesting an interaction between the signaling pathways that lead to immune effectors synthesis. Despite this finding, kappaB motifs in the 5'-UTRs of selected genes suggest a pathway-specific control of AMP and transferrin-1 gene expression. Regulation by miRNAs was also investigated and revealed a number of candidates for the post-transcriptional regulation of immune genes in bees.
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Affiliation(s)
- Anete P Lourenço
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900 Ribeirão Preto, São Paulo, Brazil.
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19
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Veraksa A. Regulation of developmental processes: insights from mass spectrometry-based proteomics. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:723-34. [PMID: 24014456 DOI: 10.1002/wdev.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass spectrometry (MS)-based proteomics has become an indispensable tool for protein identification and quantification. In this paper, common MS workflows are described, with an emphasis on applications of MS-based proteomics in developmental biology. Progress has been made in the analysis of proteome changes during tissue differentiation and in various genetic perturbations. MS-based proteomics has been particularly useful for identifying novel protein interactions by affinity purification-mass spectrometry (AP-MS), many of which have been subsequently functionally validated and led to the discovery of previously unknown modes of developmental regulation. Quantitative proteomics approaches can be used to study posttranslational modifications (PTMs) of proteins such as phosphorylation, to reveal the dynamics of intracellular signal transduction. Integrative approaches combine quantitative MS-based proteomics with other high-throughput methods, with the promise of a systems level understanding of developmental regulation.
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Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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20
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Krajcovic MM, Minden JS. Assessing the critical period for Rho kinase activity during Drosophila ventral furrow formation. Dev Dyn 2012; 241:1729-43. [PMID: 22972587 DOI: 10.1002/dvdy.23859] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Drosophila ventral furrow formation (VFF), which is the first morphogenetic event during embryo development, serves as a model for epithelial sheet folding. VFF can be subdivided into five cell shape changes: apical membrane flattening, apicobasal nuclear migration, apicobasal cell shortening, random apical constriction, and concerted apical constriction. These processes are generally believed to be driven by Rho kinase (Rok) activation of myosin II to stimulate the constriction of the apical actomyosin network. To test the role of Rok and its downstream target myosin II in VFF, timed injections of the Rok inhibitor, Y-27632, were performed. RESULTS Embryos injected with Y-27632 before the concerted apical constriction phase of VFF were able to execute apicobasal nuclear migration and random apical constriction, but were unable to enter the concerted apical constriction phase. Embryos injected with Y-27632 during concerted apical constriction reverted to the transition point between random apical constriction and concerted apical constriction. Finally, embryos injected with Y-27632 upon the initiation of furrow ingression were able to complete VFF. CONCLUSIONS Together these results suggest a critical period for Rok activity and presumably myosin II activation during the initiation of the concerted apical constriction phase of VFF.
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Affiliation(s)
- Melissa M Krajcovic
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, PA 15213, USA
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21
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Hernández G, Han H, Gandin V, Fabian L, Ferreira T, Zuberek J, Sonenberg N, Brill JA, Lasko P. Eukaryotic initiation factor 4E-3 is essential for meiotic chromosome segregation, cytokinesis and male fertility in Drosophila. Development 2012; 139:3211-20. [PMID: 22833128 DOI: 10.1242/dev.073122] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gene expression is translationally regulated during many cellular and developmental processes. Translation can be modulated by affecting the recruitment of mRNAs to the ribosome, which involves recognition of the 5' cap structure by the cap-binding protein eIF4E. Drosophila has several genes encoding eIF4E-related proteins, but the biological role of most of them remains unknown. Here, we report that Drosophila eIF4E-3 is required specifically during spermatogenesis. Males lacking eIF4E-3 are sterile, showing defects in meiotic chromosome segregation, cytokinesis, nuclear shaping and individualization. We show that eIF4E-3 physically interacts with both eIF4G and eIF4G-2, the latter being a factor crucial for spermatocyte meiosis. In eIF4E-3 mutant testes, many proteins are present at different levels than in wild type, suggesting widespread effects on translation. Our results imply that eIF4E-3 forms specific eIF4F complexes that are essential for spermatogenesis.
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Affiliation(s)
- Greco Hernández
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, Québec, H3G 0B1, Canada
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22
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Tettweiler G, Kowanda M, Lasko P, Sonenberg N, Hernández G. The Distribution of eIF4E-Family Members across Insecta. Comp Funct Genomics 2012; 2012:960420. [PMID: 22745595 PMCID: PMC3382400 DOI: 10.1155/2012/960420] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 03/14/2012] [Indexed: 11/20/2022] Open
Abstract
Insects are part of the earliest faunas that invaded terrestrial environments and are the first organisms that evolved controlled flight. Nowadays, insects are the most diverse animal group on the planet and comprise the majority of extant animal species described. Moreover, they have a huge impact in the biosphere as well as in all aspects of human life and economy; therefore understanding all aspects of insect biology is of great importance. In insects, as in all cells, translation is a fundamental process for gene expression. However, translation in insects has been mostly studied only in the model organism Drosophila melanogaster. We used all publicly available genomic sequences to investigate in insects the distribution of the genes encoding the cap-binding protein eIF4E, a protein that plays a crucial role in eukaryotic translation. We found that there is a diversity of multiple ortholog genes encoding eIF4E isoforms within the genus Drosophila. In striking contrast, insects outside this genus contain only a single eIF4E gene, related to D. melanogaster eIF4E-1. We also found that all insect species here analyzed contain only one Class II gene, termed 4E-HP. We discuss the possible evolutionary causes originating the multiplicity of eIF4E genes within the genus Drosophila.
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Affiliation(s)
- Gritta Tettweiler
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada H3A 1A3
| | - Michelle Kowanda
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
| | - Paul Lasko
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada H3A 1A3
| | - Greco Hernández
- Division of Basic Research, National Institute for Cancer (INCan), Avenida San Fernando No. 22, Tlalpan, 14080 Mexico City, DF, Mexico
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23
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24
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Abstract
Two-dimensional difference gel electrophoresis (2D DIGE) is a modified form of 2D electrophoresis (2DE) that allows one to compare two or three protein samples simultaneously on the same gel. The proteins in each sample are covalently tagged with different color fluorescent dyes that are designed to have no effect on the relative migration of proteins during electrophoresis. Proteins that are common to the samples appear as "spots" with a fixed ratio of fluorescent signals, whereas proteins that differ between the samples have different fluorescence ratios. With the appropriate imaging system, difference gel electrophoresis (DIGE) is capable of reliably detecting as little as 0.2 fmol of protein, and protein differences down to ±15%, over a ∼20,000-fold protein concentration range. DIGE combined with digital image analysis therefore greatly improves the statistical assessment of proteome variation. Here we describe a protocol for conducting DIGE experiments, which takes 2-3 days to complete.
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25
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Crow T, Xue-Bian JJ. Proteomic analysis of short- and intermediate-term memory in Hermissenda. Neuroscience 2011; 192:102-11. [PMID: 21736919 DOI: 10.1016/j.neuroscience.2011.06.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 12/20/2022]
Abstract
Changes in cellular and synaptic plasticity related to learning and memory are accompanied by both upregulation and downregulation of the expression levels of proteins. Both de novo protein synthesis and post-translational modification of existing proteins have been proposed to support the induction and maintenance of memory underlying learning. However, little is known regarding the identity of proteins regulated by learning that are associated with the early stages supporting the formation of memory over time. In this study we have examined changes in protein abundance at two different times following one-trial in vitro conditioning of Hermissenda using two-dimensional difference gel electrophoresis (2D-DIGE), quantification of differences in protein abundance between conditioned and unpaired controls, and protein identification with tandem mass spectrometry. Significant regulation of protein abundance following one-trial in vitro conditioning was detected 30 min and 3 h post-conditioning. Proteins were identified that exhibited statistically significant increased or decreased abundance at both 30 min and 3 h post-conditioning. Proteins were also identified that exhibited a significant increase in abundance only at 30 min, or only at 3 h post-conditioning. A few proteins were identified that expressed a significant decrease in abundance detected at both 30 min and 3 h post-conditioning, or a significant decrease in abundance only at 3 h post-conditioning. The proteomic analysis indicates that proteins involved in diverse cellular functions such as translational regulation, cell signaling, cytoskeletal regulation, metabolic activity, and protein degradation contribute to the formation of memory produced by one-trial in vitro conditioning. These findings support the view that changes in protein abundance over time following one-trial in vitro conditioning involve dynamic and complex interactions of the proteome.
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Affiliation(s)
- T Crow
- Department of Neurobiology and Anatomy, University of Texas Medical School, 6431 Fannin Street, Houston, TX 77030, USA.
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26
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Li J, Fang Y, Zhang L, Begna D. Honeybee (Apis mellifera ligustica) drone embryo proteomes. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:372-384. [PMID: 21172355 DOI: 10.1016/j.jinsphys.2010.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/09/2010] [Accepted: 12/10/2010] [Indexed: 05/30/2023]
Abstract
Little attention has been paid to the drone honeybee (Apis mellifera ligustica) which is a haploid individual carrying only the set of alleles that it inherits from its mother. Molecular mechanisms underlying drone embryogenesis are poorly understood. This study evaluated protein expression profiles of drone embryogenesis at embryonic ages of 24, 48 and 72h. More than 100 reproducible proteins were analyzed by mass spectrometry on 2D electrophoresis gels. Sixty-two proteins were significantly changed at the selected three experimental age points. Expression of the metabolic energy requirement-related protein peaked at the embryonic age of 48h, whereas development and metabolizing amino acid-related proteins expressed optimally at 72h. Cytoskeleton, protein folding and antioxidant-related proteins were highly expressed at 48 and 72h. Protein networks of the identified proteins were constructed and protein expressions were validated at the transcription level. This first proteomic study of drone embryogenesis in the honeybee may provide geneticists an exact timetable and candidate protein outline for further manipulations of drone stem cells.
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Affiliation(s)
- Jianke Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Science/Key Laboratory of Pollinating Insect Biology, 1# Beigou, Xiangshan, Haidian District, Beijing, China.
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27
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Veraksa A. When peptides fly: advances in Drosophila proteomics. J Proteomics 2010; 73:2158-70. [PMID: 20580952 DOI: 10.1016/j.jprot.2010.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/11/2010] [Indexed: 10/25/2022]
Abstract
In the past decade, improvements in genome annotation, protein fractionation methods and mass spectrometry instrumentation resulted in rapid growth of Drosophila proteomics. This review presents the current status of proteomics research in the fly. Areas that have seen major advances in recent years include efforts to map and catalog the Drosophila proteome and high-throughput as well as targeted studies to analyze protein-protein interactions and post-translational modifications. Stable isotope labeling of flies and other applications of quantitative proteomics have opened up new possibilities for functional analyses. It is clear that proteomics is becoming an indispensable tool in Drosophila systems biology research that adds a unique dimension to studying gene function.
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Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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28
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Sun J, Zhang Y, Thiyagarajan V, Qian PY, Qiu JW. Protein expression during the embryonic development of a gastropod. Proteomics 2010; 10:2701-11. [DOI: 10.1002/pmic.200900846] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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29
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Monzo K, Dowd SR, Minden JS, Sisson JC. Proteomic analysis reveals CCT is a target of Fragile X mental retardation protein regulation in Drosophila. Dev Biol 2010; 340:408-18. [PMID: 20122915 DOI: 10.1016/j.ydbio.2010.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/21/2010] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
Abstract
Fragile X mental retardation protein (FMRP) is an RNA-binding protein that is required for the translational regulation of specific target mRNAs. Loss of FMRP causes Fragile X syndrome (FXS), the most common form of inherited mental retardation in humans. Understanding the basis for FXS has been limited because few in vivo targets of FMRP have been identified and mechanisms for how FMRP regulates physiological targets are unclear. We have previously demonstrated that Drosophila FMRP (dFMRP) is required in early embryos for cleavage furrow formation. In an effort to identify new targets of dFMRP-dependent regulation and new effectors of cleavage furrow formation, we used two-dimensional difference gel electrophoresis and mass spectrometry to identify proteins that are misexpressed in dfmr1 mutant embryos. Of the 28 proteins identified, we have identified three subunits of the Chaperonin containing TCP-1 (CCT) complex as new direct targets of dFMRP-dependent regulation. Furthermore, we found that the septin Peanut, a known effector of cleavage, is a likely conserved substrate of fly CCT and is mislocalized in both cct and in dfmr1 mutant embryos. Based on these results we propose that dFMRP-dependent regulation of CCT subunits is required for cleavage furrow formation and that at least one of its substrates is affected in dfmr1- embryos suggesting that dFMRP-dependent regulation of CCT contributes to the cleavage furrow formation phenotype.
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Affiliation(s)
- Kate Monzo
- Institute of Cellular and Molecular Biology and Section of Molecular Cell and Developmental Biology, University of Texas at Austin, 2400 Speedway Ave, Patterson Labs 216, Austin, TX 78712, USA.
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30
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Cheng KW, Wong CC, Wang M, He QY, Chen F. Identification and characterization of molecular targets of natural products by mass spectrometry. MASS SPECTROMETRY REVIEWS 2010; 29:126-155. [PMID: 19319922 DOI: 10.1002/mas.20235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Natural products, and their derivatives and mimics, have contributed to the development of important therapeutics to combat diseases such as infections and cancers over the past decades. The value of natural products to modern drug discovery is still considerable. However, its development is hampered by a lack of a mechanistic understanding of their molecular action, as opposed to the emerging molecule-targeted therapeutics that are tailored to a specific protein target(s). Recent advances in the mass spectrometry-based proteomic approaches have the potential to offer unprecedented insights into the molecular action of natural products. Chemical proteomics is established as an invaluable tool for the identification of protein targets of natural products. Small-molecule affinity selection combined with mass spectrometry is a successful strategy to "fish" cellular targets from the entire proteome. Mass spectrometry-based profiling of protein expression is also routinely employed to elucidate molecular pathways involved in the therapeutic and possible toxicological responses upon treatment with natural products. In addition, mass spectrometry is increasingly utilized to probe structural aspects of natural products-protein interactions. Limited proteolysis, photoaffinity labeling, and hydrogen/deuterium exchange in conjunction with mass spectrometry are sensitive and high-throughput strategies that provide low-resolution structural information of non-covalent natural product-protein complexes. In this review, we provide an overview on the applications of mass spectrometry-based techniques in the identification and characterization of natural product-protein interactions, and we describe how these applications might revolutionize natural product-based drug discovery.
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Affiliation(s)
- Ka-Wing Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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31
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Li JY, Chen X, Hosseini Moghaddam SH, Chen M, Wei H, Zhong BX. Shotgun proteomics approach to characterizing the embryonic proteome of the silkworm, Bombyx mori, at labrum appearance stage. INSECT MOLECULAR BIOLOGY 2009; 18:649-660. [PMID: 19754742 DOI: 10.1111/j.1365-2583.2009.00903.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The shotgun approach has gained considerable acknowledgement in recent years as a dominant strategy in proteomics. We observed a dramatic increase of specific protein spots in two-dimensional electrophoresis (2-DE) gels of the silkworm (Bombyx mori) embryo at labrum appearance, a characteristic stage during embryonic development of silkworm which is involved with temperature increase by silkworm raiser. We employed shotgun liquid chromatography tandem mass spectrometry (LC-MS/MS) technology to analyse the proteome of B. mori embryos at this stage. A total of 2168 proteins were identified with an in-house database. Approximately 47% of them had isoelectric point (pI) values distributed theoretically in the range pI 5-7 and approximately 60% of them had molecular weights of 15-45 kDa. Furthermore, 111 proteins had an pI greater than 10 and were difficult to separate by 2-DE. Many important functional proteins related to embryonic development, stress response, DNA transcription/translation, cell growth, proliferation and differentiation, organogenesis and reproduction were identified. Among them proteins related to nervous system development were noticeable. All known heat shock proteins (HSPs) were detected in this developmental stage of B. mori embryo. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed energetic metabolism at this stage. These results were expected to provide more information for proteomic monitoring of the insect embryo and better understanding of the spatiotemporal expression of genes during embryonic developmental processes.
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Affiliation(s)
- J-Y Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310029, P. R. China
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32
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Minden JS, Dowd SR, Meyer HE, Stühler K. Difference gel electrophoresis. Electrophoresis 2009; 30 Suppl 1:S156-61. [DOI: 10.1002/elps.200900098] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Gouw JW, Pinkse MWH, Vos HR, Moshkin Y, Verrijzer CP, Heck AJR, Krijgsveld J. In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition. Mol Cell Proteomics 2009; 8:1566-78. [PMID: 19321433 DOI: 10.1074/mcp.m900114-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
An important hallmark in embryonic development is characterized by the maternal-to-zygotic transition (MZT) where zygotic transcription is activated by a maternally controlled environment. Post-transcriptional and translational regulation is critical for this transition and has been investigated in considerable detail at the gene level. We used a proteomics approach using metabolic labeling of Drosophila to quantitatively assess changes in protein expression levels before and after the MZT. By combining stable isotope labeling of fruit flies in vivo with high accuracy quantitative mass spectrometry we could quantify 2,232 proteins of which about half changed in abundance during this process. We show that approximately 500 proteins increased in abundance, providing direct evidence of the identity of proteins as a product of embryonic translation. The group of down-regulated proteins is dominated by maternal factors involved in translational control of maternal and zygotic transcripts. Surprisingly a direct comparison of transcript and protein levels showed that the mRNA levels of down-regulated proteins remained relatively constant, indicating a translational control mechanism specifically targeting these proteins. In addition, we found evidence for post-translational processing of cysteine proteinase-1 (Cathepsin L), which became activated during the MZT as evidenced by the loss of its N-terminal propeptide. Poly(A)-binding protein was shown to be processed at its C-terminal tail, thereby losing one of its protein-interacting domains. Altogether this quantitative proteomics study provides a dynamic profile of known and novel proteins of maternal as well as embryonic origin. This provides insight into the production, stability, and modification of individual proteins, whereas discrepancies between transcriptional profiles and protein dynamics indicate novel control mechanisms in genome activation during early fly development.
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Affiliation(s)
- Joost W Gouw
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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34
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Ettensohn CA. Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity and morphogenesis. Development 2009; 136:11-21. [PMID: 19060330 DOI: 10.1242/dev.023564] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Significant new insights have emerged from the analysis of a gene regulatory network (GRN) that underlies the development of the endoskeleton of the sea urchin embryo. Comparative studies have revealed ways in which this GRN has been modified (and conserved) during echinoderm evolution, and point to mechanisms associated with the evolution of a new cell lineage. The skeletogenic GRN has also recently been used to study the long-standing problem of developmental plasticity. Other recent findings have linked this transcriptional GRN to morphoregulatory proteins that control skeletal anatomy. These new studies highlight powerful new ways in which GRNs can be used to dissect development and the evolution of morphogenesis.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
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35
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Witzberger MM, Fitzpatrick JAJ, Crowley JC, Minden JS. End-on imaging: a new perspective on dorsoventral development in Drosophila embryos. Dev Dyn 2009; 237:3252-9. [PMID: 18855896 DOI: 10.1002/dvdy.21752] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Drosophila ventral furrow formation has frequently been used as a model to study developmentally-regulated cell-shape changes. However, a technique to follow all cellular changes during this process within a single living embryo has been lacking. We describe a novel technique, called "end-on imaging", to collect time-lapse images of transversely mounted living embryos. End-on imaging revealed several new features of dorsoventral development. First, we observed a wave of syncytial nuclear divisions predicting the location of the ventral furrow. Second, we determined that there is a 5-min gap between the end of cellularization and the start of ventral furrow formation, suggesting that the two processes may share the same pool of cytoskeletal components. Lastly, we show that apical-membrane flattening, the first step in ventral furrow formation, is due to the ventral cells pushing against the vitelline membrane, rather than flattening the dome-shaped, apical surfaces of these cells by a pulling or constriction motion.
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Affiliation(s)
- Melissa M Witzberger
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania 15213, USA
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36
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Abstract
Two-dimensional difference in-gel electrophoresis (2D-DIGE) is a modified 2D electrophoresis (2DE) technique that enables comparison of two (or three) proteomes simultaneously on the same gel. The different protein samples to be compared are covalently tagged with spectrally different fluorescent dyes that are designed to have no effect on the relative migration of proteins during isoelectric focusing or molecular mass separation during electrophoresis. The "spot maps" generated from the dye scans for each of the dyes are then superimposed to discern the expression pattern of the proteome samples being compared. Proteins that do not change in expression are seen as spots with a fixed ratio of fluorescent signals, whereas proteins that differ between the samples have different fluorescence ratios. The fluorescent dyes used in DIGE are cyanine flours and matched in respect of molecular weight. Two different dye chemistries are available enabling fluorescent tagging of as low as 5 mu g of proteins to get the analysis of the regulation of the proteome. Furthermore, DIGE is a sensitive technique, capable of detecting as little as 0.5 fmol of protein, and this detection system is linear over a >10,000-fold concentration range.
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Affiliation(s)
- Rajat Sapra
- Biosystems Research Department, Sandia National Laboratories, Livermore, CA, USA
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37
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Nomura M, Nakajima A, Inaba K. Proteomic profiles of embryonic development in the ascidian Ciona intestinalis. Dev Biol 2009; 325:468-81. [DOI: 10.1016/j.ydbio.2008.10.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Revised: 10/24/2008] [Accepted: 10/28/2008] [Indexed: 12/24/2022]
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38
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39
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Reintsch WE, Mandato CA. Deciphering animal development through proteomics: requirements and prospects. Proteome Sci 2008; 6:21. [PMID: 18652672 PMCID: PMC2516511 DOI: 10.1186/1477-5956-6-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 07/24/2008] [Indexed: 12/28/2022] Open
Abstract
In recent years proteomic techniques have started to become very useful tools in a variety of model systems of developmental biology. Applications cover many different aspects of development, including the characterization of changes in the proteome during early embryonic stages. During early animal development the embryo becomes patterned through the temporally and spatially controlled activation of distinct sets of genes. Patterning information is then translated, from gastrulation onwards, into regional specific morphogenetic cell and tissue movements that give the embryo its characteristic shape. On the molecular level, patterning is the outcome of intercellular communication via signaling molecules and the local activation or repression of transcription factors. Genetic approaches have been used very successfully to elucidate the processes behind these events. Morphogenetic movements, on the other hand, have to be orchestrated through regional changes in the mechanical properties of cells. The molecular mechanisms that govern these changes have remained much more elusive, at least in part due to the fact that they are more under translational/posttranslational control than patterning events. However, recent studies indicate that proteomic approaches can provide the means to finally unravel the mechanisms that link patterning to the generation of embryonic form. To intensify research in this direction will require close collaboration between proteome scientists and developmental researchers. It is with this aim in mind that we first give an outline of the classical questions of patterning and morphogenesis. We then summarize the proteomic approaches that have been applied in developmental model systems and describe the pioneering studies that have been done to study morphogenesis. Finally we discuss current and future strategies that will allow characterizing the changes in the embryonic proteome and ultimately lead to a deeper understanding of the cellular mechanisms that govern the generation of embryonic form.
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Affiliation(s)
- Wolfgang E Reintsch
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
| | - Craig A Mandato
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
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40
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Minden J. Comparative proteomics and difference gel electrophoresis. Biotechniques 2008; 43:739, 741, 743 passim. [PMID: 18251249 DOI: 10.2144/000112653] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The goal of comparative proteomics is to analyze proteome changes in response to development, disease, or environment. This is a two-step process in which proteins within cellular extracts are first fractionated to reduce sample complexity, and then the proteins are identified by mass spectrometry. Two-dimensional electrophoresis (2DE) is the long-time standard for protein separation, but it has suffered from poor reproducibility and limited sensitivity. Difference gel electrophoresis (DIGE), in which two protein samples are separately labeled with different fluorescent dyes and then co-electrophoresed on the same 2DE gel, was developed to overcome the reproducibility and sensitivity limitations. In this essay, I discuss the principles of comparative proteomics and the development of DIGE.
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Affiliation(s)
- Jonathan Minden
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
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41
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Kim BY, Lee KS, Choo YM, Kim I, Je YH, Woo SD, Lee SM, Park HC, Sohn HD, Jin BR. Insect transferrin functions as an antioxidant protein in a beetle larva. Comp Biochem Physiol B Biochem Mol Biol 2008; 150:161-9. [PMID: 18400534 DOI: 10.1016/j.cbpb.2008.02.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 02/19/2008] [Accepted: 02/21/2008] [Indexed: 10/22/2022]
Abstract
In insects transferrin is known as an iron transporter, an antibiotic agent, a vitellogenin, and a juvenile hormone regulated protein. Here, a novel functional role for insect transferrin as an antioxidant protein is demonstrated. Stressors, such as heat shock, fungal challenge, and H(2)O(2) exposure, cause upregulation of the white-spotted flower chafer Protaetia brevitarsis (Coleoptera: Scarabaeidae) transferrin (PbTf) mRNA in the fat body and increases PbTf protein levels in the hemolymph. RNA interference (RNAi) treated PbTf reduction causes increased iron and H(2)O(2) levels in the hemolymph and results in induction of apoptotic cell death in the fat body during exposure to stress. The observed effects of PbTf RNAi suggest that PbTf inhibits stress-induced apoptosis by diminishing the Fenton reaction via the binding of iron, thus supporting an antioxidant role for PbTf in stress responses.
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Affiliation(s)
- Bo Yeon Kim
- College of Natural Resources and Life Science, Dong-A University, Busan 604-714, South Korea
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42
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Wong CC, Cheng KW, He QY, Chen F. Unraveling the molecular targets of natural products: Insights from genomic and proteomic analyses. Proteomics Clin Appl 2008; 2:338-54. [DOI: 10.1002/prca.200880002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Indexed: 11/11/2022]
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43
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Puri M, Goyal A, Senutovich N, Dowd SR, Minden JS. Building proteomic pathways using Drosophila ventral furrow formation as a model. MOLECULAR BIOSYSTEMS 2008; 4:1126-35. [DOI: 10.1039/b812153b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Burnham AJ, Gong L, Hardy RW. Heterogeneous nuclear ribonuclear protein K interacts with Sindbis virus nonstructural proteins and viral subgenomic mRNA. Virology 2007; 367:212-21. [PMID: 17561226 DOI: 10.1016/j.virol.2007.05.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 05/01/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
Alphaviruses are a group of arthropod-borne human and animal pathogens that can cause epidemics of significant public health and economic consequence. Alphavirus RNA synthesis requires four virally encoded nonstructural proteins and probably a number of cellular proteins. Using comparative two-dimensional electrophoresis we were able to identify proteins enriched in cytoplasmic membrane fractions containing viral RNA synthetic complexes following infection with Sindbis virus. Our studies demonstrated the following: (i) the host protein hnRNP K is enriched in cytoplasmic membrane fractions following Sindbis virus infection, (ii) viral nonstructural proteins co-immunoprecipitate with hnRNP K, (iii) nsP2 and hnRNP K co-localize in the cytoplasm of Sindbis virus infected cells, (iv) Sindbis virus subgenomic mRNA, but not genomic RNA co-immunoprecipitates with hnRNP K, (v) viral RNA does not appear to be required for the interaction of hnRNP K with the nonstructural proteins. Potential functions of hnRNP K during virus replication are discussed.
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Affiliation(s)
- Andrew J Burnham
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA
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45
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O'Keefe LV, Smibert P, Colella A, Chataway TK, Saint R, Richards RI. Know thy fly. Trends Genet 2007; 23:238-42. [PMID: 17395332 DOI: 10.1016/j.tig.2007.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 01/29/2007] [Accepted: 03/12/2007] [Indexed: 11/23/2022]
Abstract
The generation and analysis of mutants is central to studies of gene function in model organisms. Methods for random mutagenesis in Drosophila melanogaster have been available for many years, but an alternative approach--targeted mutagenesis using homologous recombination--has only recently been developed. This approach has the advantage of specificity, because genes of interest can be altered. One might expect with a gene-targeting approach that the frequency of background mutations would be minimal. Unfortunately, we have found that this is not the case. Although the possibility of background mutations arising during homologous-recombination-based gene targeting has been raised in the literature, it is not routinely taken into account when using this technique. Our experience suggests that it can be a considerable problem but that it has a relatively simple solution.
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Affiliation(s)
- Louise V O'Keefe
- ARC Special Research Centre for the Molecular Genetics of Development, School of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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46
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Abstract
Gliomas in the form of astrocytomas, anaplastic astrocytomas and glioblastomas are the most common brain tumors in humans. Early detection of these cancers is crucial for successful treatment. Proteomics promises the discovery of biomarkers and tumor markers for early detection and diagnosis. In the current study, a differential gel electrophoresis technology coupled with matrix-assisted laser desorption/ionization-time of flight and liquid chromatography-tandem mass spectroscopy was used to investigate tumor-specific changes in the proteome of human brain cancer. Fifty human brain tissues comprising varying diagnostic groups (non-tumor, grade I, grade II, grade III and grade IV) were run in duplicate together with an internal pool sample on each gel. The proteins of interest were automatically picked, in-gel digested and mass spectrometry fingerprinted. Two hundred and eleven protein spots were identified successfully and were collapsed into 91 unique proteins. Approximately 20 of those 91 unique proteins had, to our knowledge, not been reported previously as differentially expressed in human brain cancer. Alb protein, peroxiredoxin 4 and SH3 domain-binding glutamic acid-rich-like protein 3 were upregulated in glioblastoma multiform versus non-tumor tissues. However, aldolase C fructose-biphosphate, creatine kinase, B chain dihydrolipoyl dehydrogenase, enolase 2, fumarate hydratase, HSP60, lactoylglutathione lyase, lucine aminopeptidase, Mu-crystallin homolog, NADH-UO 24, neurofilament triplet L protein, septin 2, stathmin and vacuolar ATP synthase subunit E were downregulated in glioblastoma multiform compared with non-tumor tissues. These differentially expressed proteins provided novel information on the differences existing between normal brain and gliomas, and thus might prove to be useful molecular indicators of diagnostic or prognostic value.
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Affiliation(s)
- Ashraf A Khalil
- Department of Protein Technology, Mubarak City for Scientific Research, Alexandria 21934, Egypt.
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47
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Inaba K, Nomura M, Nakajima A, Hozumi A. Functional proteomics inCiona intestinalis: A breakthrough in the exploration of the molecular and cellular mechanism of ascidian development. Dev Dyn 2007; 236:1782-9. [PMID: 17373714 DOI: 10.1002/dvdy.21121] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Ascidians have been providing a unique experimental system for a variety of fields, including reproductive biology, developmental biology, neurobiology, immunology, and evolutional biology. Recent progress in the genome sequencing of Ciona intestinalis has led to the development of a great tool for investigating the gene functions and expressions involved in several biological events in ascidians. The disclosure of genomic information has ushered in the postgenomic era, spearheaded by extensive protein analysis. The characterization of the function, localization, and molecular interaction of cellular proteins results in a more direct description of the molecular mechanism underlying several biological processes. Proteomics in ascidians, however, has just recently appeared and is not well established yet. In this study, we give an outline of the technical processes used in proteomics and review the recent status of ascidian proteomics.
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Affiliation(s)
- Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan.
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48
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Abstract
Two-dimensional difference gel electrophoresis (2D DIGE) is a modified form of 2D electrophoresis (2DE) that allows one to compare two or three protein samples simultaneously on the same gel. The proteins in each sample are covalently tagged with different color fluorescent dyes that are designed to have no effect on the relative migration of proteins during electrophoresis. Proteins that are common to the samples appear as 'spots' with a fixed ratio of fluorescent signals, whereas proteins that differ between the samples have different fluorescence ratios. With the appropriate imaging system, DIGE is capable of reliably detecting as little as 0.5 fmol of protein, and protein differences down to +/- 15%, over a >10,000-fold protein concentration range. DIGE combined with digital image analysis therefore greatly improves the statistical assessment of proteome variation. Here we describe a protocol for conducting DIGE experiments, which takes 2-3 d to complete.
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Affiliation(s)
- Surya Viswanathan
- Department of Biological Science, Carnegie Mellon University, Mellon Institute, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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49
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Lee KS, Kim BY, Kim HJ, Seo SJ, Yoon HJ, Choi YS, Kim I, Han YS, Je YH, Lee SM, Kim DH, Sohn HD, Jin BR. Transferrin inhibits stress-induced apoptosis in a beetle. Free Radic Biol Med 2006; 41:1151-61. [PMID: 16962940 DOI: 10.1016/j.freeradbiomed.2006.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 06/27/2006] [Accepted: 07/01/2006] [Indexed: 11/23/2022]
Abstract
Transferrin in insects is known as an iron transporter, an antibiotic agent, a vitellogenin, and a juvenile hormone-regulated protein. We show here a novel functional role for insect transferrin. Stresses, such as iron overload, bacterial or fungal challenge, cold or heat shock, wounding, and H2O2 or paraquat exposure, cause upregulation of the beetle Apriona germari transferrin (AgTf) gene in the fat body and epidermis, and they cause increased AgTf protein levels. RNA interference (RNAi)-mediated AgTf reduction results in rapid induction of apoptotic cell death in the fat body during exposure to heat stress. The observed effect of AgTf RNAi indicates that AgTf inhibits heat stress-induced apoptotic cell death, suggesting a functional role for AgTf in defense and stress responses in the beetle.
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Affiliation(s)
- Kwang Sik Lee
- College of Natural Resources and Life Science, Dong-A University, Busan 604-714, Korea
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50
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Hernández G, Vazquez-Pianzola P. Functional diversity of the eukaryotic translation initiation factors belonging to eIF4 families. Mech Dev 2006; 122:865-76. [PMID: 15922571 DOI: 10.1016/j.mod.2005.04.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 04/06/2005] [Accepted: 04/07/2005] [Indexed: 02/04/2023]
Abstract
Protein synthesis in eukaryotic cells is fundamental for gene expression. This process involves the binding of an mRNA molecule to the small ribosomal subunit in a group of reactions catalyzed by eukaryotic translation initiation factors (eIF) eIF4. To date, the role of each of the four eIF4, i.e. eIF4E, eIF4G, eIF4A and eIF4B, is well established. However, with the advent of genome-wide sequencing projects of various organisms, families of genes for each translation initiation factor have been identified. Intriguingly, recent studies have now established that certain eIF4 proteins can promote or inhibit translation of specific mRNAs, and also that some of them are active in processes other than translation. In addition, there is evidence of tissue- and developmental-stage-specific expression for some of these proteins. These new findings point to an additional level of complexity in the translation initiation process. In this review, we analyze the latest advances concerning the functionality of members of the eIF4 families in eukaryotic organisms and discuss the implications of this in the context of our current understanding of regulation of the translation initiation process.
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Affiliation(s)
- Greco Hernández
- Max-Planck-Institut für Biophysikalische Chemie, Abt. Molekulare Biologie, Am Fassberg 11, 37077 Göttingen, Germany.
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