101
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Grimes M, Hall B, Foltz L, Levy T, Rikova K, Gaiser J, Cook W, Smirnova E, Wheeler T, Clark NR, Lachmann A, Zhang B, Hornbeck P, Ma'ayan A, Comb M. Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. Sci Signal 2018; 11:eaaq1087. [PMID: 29789295 PMCID: PMC6822907 DOI: 10.1126/scisignal.aaq1087] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein posttranslational modifications (PTMs) have typically been studied independently, yet many proteins are modified by more than one PTM type, and cell signaling pathways somehow integrate this information. We coupled immunoprecipitation using PTM-specific antibodies with tandem mass tag (TMT) mass spectrometry to simultaneously examine phosphorylation, methylation, and acetylation in 45 lung cancer cell lines compared to normal lung tissue and to cell lines treated with anticancer drugs. This simultaneous, large-scale, integrative analysis of these PTMs using a cluster-filtered network (CFN) approach revealed that cell signaling pathways were outlined by clustering patterns in PTMs. We used the t-distributed stochastic neighbor embedding (t-SNE) method to identify PTM clusters and then integrated each with known protein-protein interactions (PPIs) to elucidate functional cell signaling pathways. The CFN identified known and previously unknown cell signaling pathways in lung cancer cells that were not present in normal lung epithelial tissue. In various proteins modified by more than one type of PTM, the incidence of those PTMs exhibited inverse relationships, suggesting that molecular exclusive "OR" gates determine a large number of signal transduction events. We also showed that the acetyltransferase EP300 appears to be a hub in the network of pathways involving different PTMs. In addition, the data shed light on the mechanism of action of geldanamycin, an HSP90 inhibitor. Together, the findings reveal that cell signaling pathways mediated by acetylation, methylation, and phosphorylation regulate the cytoskeleton, membrane traffic, and RNA binding protein-mediated control of gene expression.
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Affiliation(s)
- Mark Grimes
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA.
| | | | - Lauren Foltz
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Tyler Levy
- Cell Signaling Technology, Danvers, MA 01923, USA
| | | | - Jeremiah Gaiser
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - William Cook
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Ekaterina Smirnova
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Travis Wheeler
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Neil R Clark
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS (Big Data to Knowledge Library of Integrated Network-based Cellular Signatures) Data Coordination and Integration Center, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS (Big Data to Knowledge Library of Integrated Network-based Cellular Signatures) Data Coordination and Integration Center, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Cell Signaling Technology, Danvers, MA 01923, USA
| | | | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS (Big Data to Knowledge Library of Integrated Network-based Cellular Signatures) Data Coordination and Integration Center, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Michael Comb
- Cell Signaling Technology, Danvers, MA 01923, USA
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102
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Kovary KM, Taylor B, Zhao ML, Teruel MN. Expression variation and covariation impair analog and enable binary signaling control. Mol Syst Biol 2018; 14:e7997. [PMID: 29759982 PMCID: PMC5951153 DOI: 10.15252/msb.20177997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 03/26/2018] [Accepted: 04/05/2018] [Indexed: 11/09/2022] Open
Abstract
Due to noise in the synthesis and degradation of proteins, the concentrations of individual vertebrate signaling proteins were estimated to vary with a coefficient of variation (CV) of approximately 25% between cells. Such high variation is beneficial for population-level regulation of cell functions but abolishes accurate single-cell signal transmission. Here, we measure cell-to-cell variability of relative protein abundance using quantitative proteomics of individual Xenopus laevis eggs and cultured human cells and show that variation is typically much lower, in the range of 5-15%, compatible with accurate single-cell transmission. Focusing on bimodal ERK signaling, we show that variation and covariation in MEK and ERK expression improves controllability of the percentage of activated cells, demonstrating how variation and covariation in expression enables population-level control of binary cell-fate decisions. Together, our study argues for a control principle whereby low expression variation enables accurate control of analog single-cell signaling, while increased variation, covariation, and numbers of pathway components are required to widen the stimulus range over which external inputs regulate binary cell activation to enable precise control of the fraction of activated cells in a population.
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Affiliation(s)
- Kyle M Kovary
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Brooks Taylor
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Michael L Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Mary N Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
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103
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Sonnett M, Yeung E, Wühr M. Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster. Anal Chem 2018; 90:5032-5039. [PMID: 29522331 PMCID: PMC6220677 DOI: 10.1021/acs.analchem.7b04713] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g., TMT) has enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice, existing multiplexing approaches suffer from key limitations. In its simple implementation (TMT-MS2), measurements are distorted by chemical noise leading to poor measurement accuracy. The current state-of-the-art (TMT-MS3) addresses this but requires specialized quadrupole-iontrap-Orbitrap instrumentation. The complement reporter ion approach (TMTc) produces high accuracy measurements and is compatible with many more instruments, like quadrupole-Orbitraps. However, the required deconvolution of the TMTc cluster leads to poor measurement precision. Here, we introduce TMTc+, which adds the modeling of the MS2-isolation step into the deconvolution algorithm. The resulting measurements are comparable in precision to TMT-MS3/MS2. The improved duty cycle and lower filtering requirements make TMTc+ more sensitive than TMT-MS3 and comparable with TMT-MS2. At the same time, unlike TMT-MS2, TMTc+ is exquisitely able to distinguish signal from chemical noise even outperforming TMT-MS3. Lastly, we compare TMTc+ to quantitative label-free proteomics of total HeLa lysate and find that TMTc+ quantifies 7.8k versus 3.9k proteins in a 5-plex sample. At the same time, the median coefficient of variation improves from 13% to 4%. Thus, TMTc+ advances quantitative proteomics by enabling accurate, sensitive, and precise multiplexed experiments on more commonly used instruments.
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Affiliation(s)
- Matthew Sonnett
- Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Eyan Yeung
- Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Martin Wühr
- Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
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104
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Milunovic-Jevtic A, Jevtic P, Levy DL, Gatlin JC. In vivo mitotic spindle scaling can be modulated by changing the levels of a single protein: the microtubule polymerase XMAP215. Mol Biol Cell 2018; 29:1311-1317. [PMID: 29851557 PMCID: PMC5994900 DOI: 10.1091/mbc.e18-01-0011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In many organisms, early embryonic development is characterized by a series of reductive cell divisions that result in rapid increases in cell number and concomitant decreases in cell size. Intracellular organelles, such as the nucleus and mitotic spindle, also become progressively smaller during this developmental window, but the molecular and mechanistic underpinnings of these scaling relationships are not fully understood. For the mitotic spindle, changes in cytoplasmic volume are sufficient to account for size scaling during early development in certain organisms. This observation is consistent with models that evoke a limiting component, whereby the smaller absolute number of spindle components in smaller cells limits spindle size. Here we investigate the role of a candidate factor for developmental spindle scaling, the microtubule polymerase XMAP215. Microinjection of additional XMAP215 protein into Xenopus laevis embryos was sufficient to induce the assembly of larger spindles during developmental stages 6.5, 7, and 8, whereas addition of a polymerase-incompetent XMAP215 mutant resulted in a downward shift in the in vivo spindle scaling curve. In sum, these results indicate that even small cells are able to produce larger spindles if microtubule growth rates are increased and suggest that structural components are not limiting.
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Affiliation(s)
- Ana Milunovic-Jevtic
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071.,Molecular and Cellular Life Sciences Program, University of Wyoming, Laramie, WY 82071
| | - Predrag Jevtic
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071.,Molecular and Cellular Life Sciences Program, University of Wyoming, Laramie, WY 82071
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071.,Molecular and Cellular Life Sciences Program, University of Wyoming, Laramie, WY 82071
| | - J C Gatlin
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071.,Molecular and Cellular Life Sciences Program, University of Wyoming, Laramie, WY 82071
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105
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Christov CP, Dingwell KS, Skehel M, Wilkes HS, Sale JE, Smith JC, Krude T. A NuRD Complex from Xenopus laevis Eggs Is Essential for DNA Replication during Early Embryogenesis. Cell Rep 2018; 22:2265-2278. [PMID: 29490265 PMCID: PMC5848848 DOI: 10.1016/j.celrep.2018.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/15/2018] [Accepted: 02/02/2018] [Indexed: 02/03/2023] Open
Abstract
DNA replication in the embryo of Xenopus laevis changes dramatically at the mid-blastula transition (MBT), with Y RNA-independent random initiation switching to Y RNA-dependent initiation at specific origins. Here, we identify xNuRD, an MTA2-containing assemblage of the nucleosome remodeling and histone deacetylation complex NuRD, as an essential factor in pre-MBT Xenopus embryos that overcomes a functional requirement for Y RNAs during DNA replication. Human NuRD complexes have a different subunit composition than xNuRD and do not support Y RNA-independent initiation of DNA replication. Blocking or immunodepletion of xNuRD inhibits DNA replication initiation in isolated nuclei in vitro and causes inhibition of DNA synthesis, developmental delay, and embryonic lethality in early embryos. xNuRD activity declines after the MBT, coinciding with dissociation of the complex and emergence of Y RNA-dependent initiation. Our data thus reveal an essential role for a NuRD complex as a DNA replication factor during early Xenopus development.
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Affiliation(s)
- Christo P Christov
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Kevin S Dingwell
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London, NW1 1AT, UK
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Helen S Wilkes
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - James C Smith
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London, NW1 1AT, UK
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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106
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Abstract
The creation of mutant lines by genome editing is accelerating genetic analysis in many organisms. CRISPR/Cas9 methods have been adapted for use in the African clawed frog, Xenopus, a longstanding model organism for biomedical research. Traditional breeding schemes for creating homozygous mutant lines with CRISPR/Cas9-targeted mutagenesis have several time-consuming and laborious steps. To facilitate the creation of mutant embryos, particularly to overcome the obstacles associated with knocking out genes that are essential for embryogenesis, a new method called leapfrogging was developed. This technique leverages the robustness of Xenopus embryos to "cut and paste" embryological methods. Leapfrogging utilizes the transfer of primordial germ cells (PGCs) from efficiently-mutagenized donor embryos into PGC-ablated wildtype siblings. This method allows for the efficient mutation of essential genes by creating chimeric animals with wildtype somatic cells that carry a mutant germline. When two F0 animals carrying "leapfrog transplants" (i.e., mutant germ cells) are intercrossed, they produce homozygous, or compound heterozygous, null F1 embryos, thus saving a full generation time to obtain phenotypic data. Leapfrogging also provides a new approach for analyzing maternal effect genes, which are refractory to F0 phenotypic analysis following CRISPR/Cas9 mutagenesis. This manuscript details the method of leapfrogging, with special emphasis on how to successfully perform PGC transplantation.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine;
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107
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Jevtić P, Milunović-Jevtić A, Dilsaver MR, Gatlin JC, Levy DL. Use of Xenopus cell-free extracts to study size regulation of subcellular structures. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2018; 60:277-288. [PMID: 27759156 DOI: 10.1387/ijdb.160158dl] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Striking size variations are prominent throughout biology, at the organismal, cellular, and subcellular levels. Important fundamental questions concern organelle size regulation and how organelle size is regulated relative to cell size, also known as scaling. Uncovering mechanisms of organelle size regulation will inform the functional significance of size as well as the implications of misregulated size, for instance in the case of nuclear enlargement in cancer. Xenopus egg and embryo extracts are powerful cell-free systems that have been utilized extensively for mechanistic and functional studies of various organelles and subcellular structures. The open biochemical nature of the extract permits facile manipulation of its composition, and in recent years extract approaches have illuminated mechanisms of organelle size regulation. This review largely focuses on in vitro Xenopus studies that have identified regulators of nuclear and spindle size. We also discuss potential relationships between size scaling of the nucleus and spindle, size regulation of other subcellular structures, and extract experiments that have clarified developmental timing mechanisms. We conclude by offering some future prospects, notably the integration of Xenopus extract with microfluidic technology.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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108
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Jenness C, Giunta S, Müller MM, Kimura H, Muir TW, Funabiki H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc Natl Acad Sci U S A 2018; 115:E876-E885. [PMID: 29339483 PMCID: PMC5798369 DOI: 10.1073/pnas.1717509115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutations in CDCA7, the SNF2 family protein HELLS (LSH), or the DNA methyltransferase DNMT3b cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. While it has been speculated that DNA methylation defects cause this disease, little is known about the molecular function of CDCA7 and its functional relationship to HELLS and DNMT3b. Systematic analysis of how the cell cycle, H3K9 methylation, and the mitotic kinase Aurora B affect proteomic profiles of chromatin in Xenopus egg extracts revealed that HELLS and CDCA7 form a stoichiometric complex on chromatin, in a manner sensitive to Aurora B. Although HELLS alone fails to remodel nucleosomes, we demonstrate that the HELLS-CDCA7 complex possesses nucleosome remodeling activity. Furthermore, CDCA7 is essential for loading HELLS onto chromatin, and CDCA7 harboring patient ICF mutations fails to recruit the complex to chromatin. Together, our study identifies a unique bipartite nucleosome remodeling complex where the functional remodeling activity is split between two proteins and thus delineates the defective pathway in ICF syndrome.
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Affiliation(s)
- Christopher Jenness
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Manuel M Müller
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065;
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109
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Lee-Liu D, Sun L, Dovichi NJ, Larraín J. Quantitative Proteomics After Spinal Cord Injury (SCI) in a Regenerative and a Nonregenerative Stage in the Frog Xenopus laevis. Mol Cell Proteomics 2018; 17:592-606. [PMID: 29358338 PMCID: PMC5880103 DOI: 10.1074/mcp.ra117.000215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/30/2017] [Indexed: 12/31/2022] Open
Abstract
The capacity to regenerate the spinal cord after an injury is a coveted trait that only a limited group of nonmammalian organisms can achieve. In Xenopus laevis, this capacity is only present during larval or tadpole stages, but is absent during postmetamorphic frog stages. This provides an excellent model for comparative studies between a regenerative and a nonregenerative stage to identify the cellular and molecular mechanisms that explain this difference in regenerative potential. Here, we used iTRAQ chemistry to obtain a quantitative proteome of the spinal cord 1 day after a transection injury in regenerative and nonregenerative stage animals, and used sham operated animals as controls. We quantified a total of 6,384 proteins, with 172 showing significant differential expression in the regenerative stage and 240 in the nonregenerative stage, with an overlap of only 14 proteins. Functional enrichment analysis revealed that although the regenerative stage downregulated synapse/vesicle and mitochondrial proteins, the nonregenerative stage upregulated lipid metabolism proteins, and downregulated ribosomal and translation control proteins. Furthermore, STRING network analysis showed that proteins belonging to these groups are highly interconnected, providing interesting candidates for future functional studies. Data are available via ProteomeXchange with identifier PXD006993.
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Affiliation(s)
- Dasfne Lee-Liu
- From the ‡Center for Aging and Regeneration, Millennium Nucleus in Regenerative Biology, Faculty of Biological Sciences, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Liangliang Sun
- §Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Norman J Dovichi
- ¶Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Juan Larraín
- From the ‡Center for Aging and Regeneration, Millennium Nucleus in Regenerative Biology, Faculty of Biological Sciences, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile ;
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110
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Abstract
The oocytes, embryos, and cell-free lysates of the frog Xenopus laevis have emerged as powerful models for quantitative proteomic experiments. In the accompanying paper (Chapter 13) we describe how to prepare samples and acquire multiplexed proteomics spectra from those. As an illustrative example we use a 10-stage developmental time series from the egg to stage 35 (just before hatching). Here, we outline how to convert the ~700,000 acquired mass spectra from this time series into protein expression dynamics for ~9000 proteins. We first outline a preliminary quality-control analysis to discover any errors that occurred during sample preparation. We discuss how peptide and protein identification error rates are controlled, and how peptide and protein species are quantified. Our analysis relies on the freely available MaxQuant proteomics pipeline. Finally, we demonstrate how to start interpreting this large dataset by clustering and gene-set enrichment analysis.
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Affiliation(s)
- Matthew Sonnett
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Meera Gupta
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Thao Nguyen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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111
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Gupta M, Sonnett M, Ryazanova L, Presler M, Wühr M. Quantitative Proteomics of Xenopus Embryos I, Sample Preparation. Methods Mol Biol 2018; 1865:175-194. [PMID: 30151767 DOI: 10.1007/978-1-4939-8784-9_13] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Xenopus oocytes and embryos are model systems optimally suited for quantitative proteomics. This is due to the availability of large amount of protein material and the ease of physical manipulation. Furthermore, facile in vitro fertilization provides superbly synchronized embryos for cell cycle and developmental stages. Here, we detail protocols developed over the last few years for sample preparation of multiplexed proteomics with TMT-tags followed by quantitative mass spectrometry analysis using the MultiNotch MS3 approach. In this approach, each condition is barcoded with an isobaric tag at the peptide level. After barcoding, samples are combined and the relative abundance of ~100,000 peptides is quantified on a mass spectrometer. High reproducibility of the sample preparation process prior to peptides being tagged and combined is of upmost importance for obtaining unbiased data. Otherwise, differences in sample handling can inadvertently appear as biological changes. We detail and exemplify the application of our sample workflow on an embryonic time-series of ten developmental stages of Xenopus laevis embryos ranging from the egg to stage 35 (just before hatching). Our accompanying paper (Chapter 14 ) details a bioinformatics pipeline to analyze the quality of the given sample preparation and strategies to convert spectra of X. laevis peptides into biologically interpretable data.
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Affiliation(s)
- Meera Gupta
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Matthew Sonnett
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lillia Ryazanova
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Marc Presler
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Martin Wühr
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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112
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Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S. Protein Expression Landscape of Mouse Embryos during Pre-implantation Development. Cell Rep 2017; 21:3957-3969. [DOI: 10.1016/j.celrep.2017.11.111] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/08/2017] [Accepted: 11/29/2017] [Indexed: 12/31/2022] Open
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113
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Nguyen PA, Field CM, Mitchison TJ. Prc1E and Kif4A control microtubule organization within and between large Xenopus egg asters. Mol Biol Cell 2017; 29:304-316. [PMID: 29187577 PMCID: PMC5996955 DOI: 10.1091/mbc.e17-09-0540] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/13/2017] [Accepted: 11/22/2017] [Indexed: 11/11/2022] Open
Abstract
The cleavage furrow in Xenopus zygotes is positioned by two large microtubule asters that grow out from the poles of the first mitotic spindle. Where these asters meet at the midplane, they assemble a disk-shaped interaction zone consisting of anti-parallel microtubule bundles coated with chromosome passenger complex (CPC) and centralspindlin that instructs the cleavage furrow. Here we investigate the mechanism that keeps the two asters separate and forms a distinct boundary between them, focusing on the conserved cytokinesis midzone proteins Prc1 and Kif4A. Prc1E, the egg orthologue of Prc1, and Kif4A were recruited to anti-parallel bundles at interaction zones between asters in Xenopus egg extracts. Prc1E was required for Kif4A recruitment but not vice versa. Microtubule plus-end growth slowed and terminated preferentially within interaction zones, resulting in a block to interpenetration that depended on both Prc1E and Kif4A. Unexpectedly, Prc1E and Kif4A were also required for radial order of large asters growing in isolation, apparently to compensate for the direction-randomizing influence of nucleation away from centrosomes. We propose that Prc1E and Kif4, together with catastrophe factors, promote "anti-parallel pruning" that enforces radial organization within asters and generates boundaries to microtubule growth between asters.
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Affiliation(s)
- P A Nguyen
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Marine Biological Laboratory, Woods Hole, MA 02543
| | - C M Field
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Marine Biological Laboratory, Woods Hole, MA 02543
| | - T J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 .,Marine Biological Laboratory, Woods Hole, MA 02543
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114
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Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. Proc Natl Acad Sci U S A 2017; 114:E10838-E10847. [PMID: 29183978 DOI: 10.1073/pnas.1709207114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Fertilization releases the meiotic arrest and initiates the events that prepare the egg for the ensuing developmental program. Protein degradation and phosphorylation are known to regulate protein activity during this process. However, the full extent of protein loss and phosphoregulation is still unknown. We examined absolute protein and phosphosite dynamics of the fertilization response by mass spectrometry-based proteomics in electroactivated eggs. To do this, we developed an approach for calculating the stoichiometry of phosphosites from multiplexed proteomics that is compatible with dynamic, stable, and multisite phosphorylation. Overall, the data suggest that degradation is limited to a few low-abundance proteins. However, this degradation promotes extensive dephosphorylation that occurs over a wide range of abundances during meiotic exit. We also show that eggs release a large amount of protein into the medium just after fertilization, most likely related to the blocks to polyspermy. Concomitantly, there is a substantial increase in phosphorylation likely tied to calcium-activated kinases. We identify putative degradation targets and components of the slow block to polyspermy. The analytical approaches demonstrated here are broadly applicable to studies of dynamic biological systems.
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115
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Wang S, Xiao Y, Zhang DD, Wong PK. A gapmer aptamer nanobiosensor for real-time monitoring of transcription and translation in single cells. Biomaterials 2017; 156:56-64. [PMID: 29190498 DOI: 10.1016/j.biomaterials.2017.11.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/23/2017] [Accepted: 11/21/2017] [Indexed: 12/22/2022]
Abstract
Transcription and translation are under tight spatiotemporal regulation among cells to coordinate multicellular organization. Methods that allow massively parallel detection of gene expression dynamics at the single cell level are required for elucidating the complex regulatory mechanisms. Here we present a multiplex nanobiosensor for real-time monitoring of protein and mRNA expression dynamics in live cells based on gapmer aptamers and complementary locked nucleic acid probes. Using the multiplex nanobiosensor, we quantified spatiotemporal dynamics of vascular endothelial growth factor A mRNA and protein expressions in single human endothelial cells during microvascular self-organization. Our results revealed distinct gene regulatory processes in the heterogeneous cell subpopulations.
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Affiliation(s)
- Shue Wang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | - Yuan Xiao
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ 85721, USA; Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ 85721, USA
| | - Pak Kin Wong
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ 85721, USA; Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; Department of Mechanical Engineering and Department of Surgery, The Pennsylvania State University, University Park, PA 16802, USA.
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116
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Peuchen EH, Cox OF, Sun L, Hebert AS, Coon JJ, Champion MM, Dovichi NJ, Huber PW. Phosphorylation Dynamics Dominate the Regulated Proteome during Early Xenopus Development. Sci Rep 2017; 7:15647. [PMID: 29142207 PMCID: PMC5688136 DOI: 10.1038/s41598-017-15936-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/03/2017] [Indexed: 01/08/2023] Open
Abstract
The earliest stages of animal development are largely controlled by changes in protein phosphorylation mediated by signaling pathways and cyclin-dependent kinases. In order to decipher these complex networks and to discover new aspects of regulation by this post-translational modification, we undertook an analysis of the X. laevis phosphoproteome at seven developmental stages beginning with stage VI oocytes and ending with two-cell embryos. Concurrent measurement of the proteome and phosphoproteome enabled measurement of phosphosite occupancy as a function of developmental stage. We observed little change in protein expression levels during this period. We detected the expected phosphorylation of MAP kinases, translational regulatory proteins, and subunits of APC/C that validate the accuracy of our measurements. We find that more than half the identified proteins possess multiple sites of phosphorylation that are often clustered, where kinases work together in a hierarchical manner to create stretches of phosphorylated residues, which may be a means to amplify signals or stabilize a particular protein conformation. Conversely, other proteins have opposing sites of phosphorylation that seemingly reflect distinct changes in activity during this developmental timeline.
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Affiliation(s)
- Elizabeth H Peuchen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Olivia F Cox
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Alex S Hebert
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.
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117
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Torán JL, Aguilar S, López JA, Torroja C, Quintana JA, Santiago C, Abad JL, Gomes-Alves P, Gonzalez A, Bernal JA, Jiménez-Borreguero LJ, Alves PM, R-Borlado L, Vázquez J, Bernad A. CXCL6 is an important paracrine factor in the pro-angiogenic human cardiac progenitor-like cell secretome. Sci Rep 2017; 7:12490. [PMID: 28970523 PMCID: PMC5624898 DOI: 10.1038/s41598-017-11976-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/29/2017] [Indexed: 12/22/2022] Open
Abstract
Studies in recent years have established that the principal effects in cardiac cell therapy are associated with paracrine/autocrine factors. We combined several complementary techniques to define human cardiac progenitor cell (CPC) secretome constituted by 914 proteins/genes; 51% of these are associated with the exosomal compartment. To define the set of proteins specifically or highly differentially secreted by CPC, we compared human mesenchymal stem cells and dermal fibroblasts; the study defined a group of growth factors, cytokines and chemokines expressed at high to medium levels by CPC. Among them, IL-1, GROa (CXCL1), CXCL6 (GCP2) and IL-8 are examples whose expression was confirmed by most techniques used. ELISA showed that CXCL6 is significantly overexpressed in CPC conditioned medium (CM) (18- to 26-fold) and western blot confirmed expression of its receptors CXCR1 and CXCR2. Addition of anti-CXCL6 completely abolished migration in CPC-CM compared with anti-CXCR2, which promoted partial inhibition, and anti-CXCR1, which was inefficient. Anti-CXCL6 also significantly inhibited CPC CM angiogenic activity. In vivo evaluation also supported a relevant role for angiogenesis. Altogether, these results suggest a notable angiogenic potential in CPC-CM and identify CXCL6 as an important paracrine factor for CPC that signals mainly through CXCR2.
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MESH Headings
- Animals
- Antibodies, Neutralizing/pharmacology
- Cell Movement
- Chemokine CXCL1/genetics
- Chemokine CXCL1/metabolism
- Chemokine CXCL6/antagonists & inhibitors
- Chemokine CXCL6/genetics
- Chemokine CXCL6/metabolism
- Culture Media, Conditioned/chemistry
- Culture Media, Conditioned/metabolism
- Fibroblasts/cytology
- Fibroblasts/drug effects
- Fibroblasts/metabolism
- Gene Expression Regulation
- Human Umbilical Vein Endothelial Cells/cytology
- Human Umbilical Vein Endothelial Cells/drug effects
- Human Umbilical Vein Endothelial Cells/metabolism
- Humans
- Interleukin-1/genetics
- Interleukin-1/metabolism
- Interleukin-8/genetics
- Interleukin-8/metabolism
- Male
- Mesenchymal Stem Cells/cytology
- Mesenchymal Stem Cells/drug effects
- Mesenchymal Stem Cells/metabolism
- Mice
- Mice, Inbred C57BL
- Myocardium/cytology
- Myocardium/metabolism
- Neovascularization, Physiologic/genetics
- Paracrine Communication/genetics
- Proteome/genetics
- Proteome/metabolism
- Receptors, Interleukin-8A/antagonists & inhibitors
- Receptors, Interleukin-8A/genetics
- Receptors, Interleukin-8A/metabolism
- Receptors, Interleukin-8B/antagonists & inhibitors
- Receptors, Interleukin-8B/genetics
- Receptors, Interleukin-8B/metabolism
- Signal Transduction
- Stem Cells/cytology
- Stem Cells/drug effects
- Stem Cells/metabolism
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Affiliation(s)
- José Luis Torán
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Cardiovascular Development and Repair Department, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Susana Aguilar
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Cardiovascular Development and Repair Department, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Juan Antonio López
- Cardiovascular Proteomics Laboratory, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernaández Almagro 3, 28029, Madrid, Spain
| | - Carlos Torroja
- Bioinformatics Unit, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Juan Antonio Quintana
- Cardiovascular Development and Repair Department, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Cell and Developmental Biology, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Cesar Santiago
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - José Luis Abad
- Coretherapix SLU, Santiago Grisolia 2, 28769, Tres Cantos, Madrid, Spain
| | - Patricia Gomes-Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
| | - Andrés Gonzalez
- Myocardial pathophysiology, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Juan Antonio Bernal
- Myocardial pathophysiology, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Luis Jesús Jiménez-Borreguero
- Cell and Developmental Biology, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Hospital de la Princesa, Diego de León 62, 28006, Madrid, Spain
| | - Paula Marques Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
| | - Luis R-Borlado
- Coretherapix SLU, Santiago Grisolia 2, 28769, Tres Cantos, Madrid, Spain
| | - Jesús Vázquez
- Cardiovascular Proteomics Laboratory, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernaández Almagro 3, 28029, Madrid, Spain
| | - Antonio Bernad
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Cardiovascular Development and Repair Department, Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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118
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Owens DA, Butler AM, Aguero TH, Newman KM, Van Booven D, King ML. High-throughput analysis reveals novel maternal germline RNAs crucial for primordial germ cell preservation and proper migration. Development 2017; 144:292-304. [PMID: 28096217 DOI: 10.1242/dev.139220] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 11/25/2016] [Indexed: 01/10/2023]
Abstract
During oogenesis, hundreds of maternal RNAs are selectively localized to the animal or vegetal pole, including determinants of somatic and germline fates. Although microarray analysis has identified localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high-throughput RNA-sequencing analysis to comprehensively interrogate animal and vegetal pole RNAs in the fully grown Xenopus laevis oocyte. We identified 411 (198 annotated) and 27 (15 annotated) enriched mRNAs at the vegetal and animal pole, respectively. Ninety were novel mRNAs over 4-fold enriched at the vegetal pole and six were over 10-fold enriched at the animal pole. Unlike mRNAs, microRNAs were not asymmetrically distributed. Whole-mount in situ hybridization confirmed that all 17 selected mRNAs were localized. Biological function and network analysis of vegetally enriched transcripts identified protein-modifying enzymes, receptors, ligands, RNA-binding proteins, transcription factors and co-factors with five defining hubs linking 47 genes in a network. Initial functional studies of maternal vegetally localized mRNAs show that sox7 plays a novel and important role in primordial germ cell (PGC) development and that ephrinB1 (efnb1) is required for proper PGC migration. We propose potential pathways operating at the vegetal pole that highlight where future investigations might be most fruitful.
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Affiliation(s)
- Dawn A Owens
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Amanda M Butler
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Tristan H Aguero
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Karen M Newman
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Derek Van Booven
- The Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Mary Lou King
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
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119
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McGuire SH, Rietman EA, Siegelmann H, Tuszynski JA. Gibbs free energy as a measure of complexity correlates with time within C. elegans embryonic development. J Biol Phys 2017; 43:551-563. [PMID: 28929407 DOI: 10.1007/s10867-017-9469-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/23/2017] [Indexed: 12/19/2022] Open
Abstract
We investigate free energy behavior in the nematode Caenorhabditis elegans during embryonic development. Our approach utilizes publicly available gene expression data, which gives us a picture of developmental changes in protein concentration and, resultantly, chemical potential and free energy. Our results indicate a clear global relationship between Gibbs free energy and time spent in development and provide thermodynamic indicators of the large-scale biological events of cell division and differentiation.
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Affiliation(s)
- Samuel H McGuire
- College of Information and Computer Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Edward A Rietman
- College of Information and Computer Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Hava Siegelmann
- College of Information and Computer Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jack A Tuszynski
- Department of Oncology, Cross Cancer Institute, University of Alberta Edmonton, Edmonton, Alberta, Canada. .,Department of Physics, University Of Alberta, Edmonton, Alberta, TG6 2J1, Canada.
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120
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Onjiko RM, Plotnick DO, Moody SA, Nemes P. Metabolic Comparison of Dorsal versus Ventral Cells Directly in the Live 8-cell Frog Embryo by Microprobe Single-cell CE-ESI-MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:4964-4970. [PMID: 29062391 PMCID: PMC5650250 DOI: 10.1039/c7ay00834a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-cell mass spectrometry (MS) empowers the characterization of metabolomic changes as cells differentiate to different tissues during early embryogenesis. Using whole-cell dissection and capillary electrophoresis electrospray ionization (CE-ESI) MS, we recently uncovered metabolic cell-to-cell differences in the 8- and 16-cell embryo of the South African clawed frog (Xenopus laevis), raising the question whether metabolic cell heterogeneity is also detectable across the dorsal-ventral axis of the 8-cell embryo. Here, we tested this hypothesis directly in the live embryo by quantifying single-cell metabolism between the left dorsal-animal (D1L) and left ventral-animal (V1L) cell pairs in the same embryo using microprobe single-cell CE-ESI-MS in the positive ion mode. After quantifying ~70 molecular features, including 52 identified metabolites, that were reproducibly detected in both cells among n = 5 different embryos, we employed supervised multivariate data analysis based on partial least squares discriminant analysis (PLSDA) to compare metabolism between the cell types. Statistical analysis revealed that asparagine, glycine betaine, and a yet-unidentified molecule were statistically significantly enriched in the D1L cell compared to V1L (p < 0.05 and fold change ≥ 1.5). These results demonstrate that cells derived from the same hemisphere (animal pole) harbor different metabolic activity along the dorsal-ventral axis as early as the 8-cell stage. Apart from providing new evidence of metabolic cell heterogeneity during early embryogenesis, this study demonstrates that microprobe single-cell CE-ESI-MS enables the analysis of multiple single cells in the same live vertebrate embryo.
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Affiliation(s)
- Rosemary M. Onjiko
- Department of Chemistry, The George Washington University, Washington DC, 20052
| | - David O. Plotnick
- Department of Chemistry, The George Washington University, Washington DC, 20052
| | - Sally A. Moody
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington DC, 20052
| | - Peter Nemes
- Department of Chemistry, The George Washington University, Washington DC, 20052
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121
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Wang M, Ly M, Lugowski A, Laver JD, Lipshitz HD, Smibert CA, Rissland OS. ME31B globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-to-zygotic transition. eLife 2017; 6:27891. [PMID: 28875934 PMCID: PMC5779226 DOI: 10.7554/elife.27891] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/04/2017] [Indexed: 12/27/2022] Open
Abstract
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). We show that the RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay. In a process dependent on the PNG kinase, levels of ME31B and its partners, Cup and Trailer Hitch (TRAL), decrease by over 10-fold during the MZT, leading to a change in the composition of mRNA-protein complexes. We propose that ME31B is a global repressor whose regulatory impact changes based on its biological context.
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Affiliation(s)
- Miranda Wang
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael Ly
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Andrew Lugowski
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Olivia S Rissland
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States.,RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, United States
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122
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Tandon P, Conlon F, Furlow JD, Horb ME. Expanding the genetic toolkit in Xenopus: Approaches and opportunities for human disease modeling. Dev Biol 2017; 426:325-335. [PMID: 27109192 PMCID: PMC5074924 DOI: 10.1016/j.ydbio.2016.04.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/23/2016] [Accepted: 04/12/2016] [Indexed: 11/29/2022]
Abstract
The amphibian model Xenopus, has been used extensively over the past century to study multiple aspects of cell and developmental biology. Xenopus offers advantages of a non-mammalian system, including high fecundity, external development, and simple housing requirements, with additional advantages of large embryos, highly conserved developmental processes, and close evolutionary relationship to higher vertebrates. There are two main species of Xenopus used in biomedical research, Xenopus laevis and Xenopus tropicalis; the common perception is that both species are excellent models for embryological and cell biological studies, but only Xenopus tropicalis is useful as a genetic model. The recent completion of the Xenopus laevis genome sequence combined with implementation of genome editing tools, such as TALENs (transcription activator-like effector nucleases) and CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated nucleases), greatly facilitates the use of both Xenopus laevis and Xenopus tropicalis for understanding gene function in development and disease. In this paper, we review recent advances made in Xenopus laevis and Xenopus tropicalis with TALENs and CRISPR-Cas and discuss the various approaches that have been used to generate knockout and knock-in animals in both species. These advances show that both Xenopus species are useful for genetic approaches and in particular counters the notion that Xenopus laevis is not amenable to genetic manipulations.
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Affiliation(s)
- Panna Tandon
- University of North Carolina McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, United States.
| | - Frank Conlon
- University of North Carolina McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, United States
| | - J David Furlow
- Deparment of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95616, United States
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, United States.
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123
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Whitworth GB, Misaghi BC, Rosenthal DM, Mills EA, Heinen DJ, Watson AH, Ives CW, Ali SH, Bezold K, Marsh-Armstrong N, Watson FL. Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis. Dev Biol 2017; 426:360-373. [PMID: 27471010 PMCID: PMC5897040 DOI: 10.1016/j.ydbio.2016.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 11/29/2022]
Abstract
Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.
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Affiliation(s)
- G B Whitworth
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - B C Misaghi
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - D M Rosenthal
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - E A Mills
- Johns Hopkins University School of Medicine, Solomon H. Snyder Dept. of Neuroscience and Hugo Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
| | - D J Heinen
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - A H Watson
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - C W Ives
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - S H Ali
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - K Bezold
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - N Marsh-Armstrong
- Johns Hopkins University School of Medicine, Solomon H. Snyder Dept. of Neuroscience and Hugo Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
| | - F L Watson
- Department of Biology, Washington and Lee University, Lexington, VA, United States.
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124
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Eroshkin FM, Martynova NY, Bayramov AV, Ermakova GV, Ivanova AS, Korotkova DD, Zaraisky AG. Interaction of secreted factor Agr2 with its potential receptors from the family of three-finger proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017030049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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125
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Suzuki A, Yoshida H, van Heeringen SJ, Takebayashi-Suzuki K, Veenstra GJC, Taira M. Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis. Dev Biol 2017; 426:336-359. [DOI: 10.1016/j.ydbio.2016.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/10/2016] [Accepted: 09/19/2016] [Indexed: 12/13/2022]
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126
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Lombard-Banek C, Portero EP, Onjiko RM, Nemes P. New-generation mass spectrometry expands the toolbox of cell and developmental biology. Genesis 2017; 55. [PMID: 28095647 DOI: 10.1002/dvg.23012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 12/01/2016] [Accepted: 12/03/2016] [Indexed: 12/12/2022]
Abstract
Systems cell biology understanding of development requires characterization of all the molecules produced in the biological system. Decades of research and new-generation sequencing provided functional information on key genes and transcripts. However, there is less information available on how differential gene expression translates into the domains of functionally important proteins, peptides, and metabolites, and how changes in these molecules impact development. Mass spectrometry (MS) is the current technology of choice for the detection and quantification of large numbers of proteins and metabolites, because it requires no use of antibodies, functional probes, or a priori knowledge of molecules produced in the system. This review focuses on recent technologies that have improved MS sensitivity for proteins and metabolites and enabled new functionalities to assess their temporal and spatial changes during vertebrate embryonic development. This review highlights case studies, in which new-generation MS tools have enabled the study of hundreds-to-thousands of proteins and metabolites in tissues, cell populations, and single cells in model systems of vertebrate development, particularly the frog (Xenopus), zebrafish, and mouse. New-generation MS expands the toolbox of cell and developmental studies, raising exciting potentials to advance basic and translational research in the life sciences.
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Affiliation(s)
| | - Erika P Portero
- Department of Chemistry, The George Washington University, Washington, DC, 20052
| | - Rosemary M Onjiko
- Department of Chemistry, The George Washington University, Washington, DC, 20052
| | - Peter Nemes
- Department of Chemistry, The George Washington University, Washington, DC, 20052
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127
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Savova V, Pearl EJ, Boke E, Nag A, Adzhubei I, Horb ME, Peshkin L. Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis. Dev Biol 2017; 424:181-188. [PMID: 28283406 PMCID: PMC5405699 DOI: 10.1016/j.ydbio.2017.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/28/2017] [Accepted: 02/28/2017] [Indexed: 11/29/2022]
Abstract
We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele-specific analysis. This data provides a catalogue of coding variation, which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Further, we specifically compare the variation in the progeny of four crosses: inbred genomic (J)-strain, outbred albino (B)-strain, and two hybrid crosses of J and B strains. We identify a subset of mutations specific to the B strain, which allows us to investigate the selection pressures affecting duplicated genes in this allotetraploid. From these crosses we find the ratio of non-synonymous to synonymous mutations is lower in duplicated genes, which suggests that they are under greater purifying selection. Surprisingly, we also find that function-altering ("damaging") mutations constitute a greater fraction of the non-synonymous variants in this group, which suggests a role for subfunctionalization in coding variation affecting duplicated genes.
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Affiliation(s)
- Virginia Savova
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Esther J Pearl
- National Xenopus Resource and Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Elvan Boke
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anwesha Nag
- Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215, USA
| | - Ivan Adzhubei
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marko E Horb
- National Xenopus Resource and Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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128
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Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY, Butter F. The developmental proteome of Drosophila melanogaster. Genome Res 2017; 27:1273-1285. [PMID: 28381612 PMCID: PMC5495078 DOI: 10.1101/gr.213694.116] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/30/2017] [Indexed: 01/12/2023]
Abstract
Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila’s life cycle, resulting in 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9f3Ψ as a protein-coding gene, and to obtain evidence of 268 small proteins. Moreover, the comparison with available transcriptomic data uncovered examples of poor correlation between mRNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes provide a powerful resource and can be explored in detail in our interactive web interface.
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Affiliation(s)
- Nuria Casas-Vila
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Alina Bluhm
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sergi Sayols
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Nadja Dinges
- RNA Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Mario Dejung
- Proteomics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Tina Altenhein
- Institute of Genetics, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599
| | - Benjamin Altenhein
- Institute of Genetics, Johannes Gutenberg University, 55128 Mainz, Germany.,Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | | | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
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129
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Hasley A, Chavez S, Danilchik M, Wühr M, Pelegri F. Vertebrate Embryonic Cleavage Pattern Determination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:117-171. [PMID: 27975272 PMCID: PMC6500441 DOI: 10.1007/978-3-319-46095-6_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pattern of the earliest cell divisions in a vertebrate embryo lays the groundwork for later developmental events such as gastrulation, organogenesis, and overall body plan establishment. Understanding these early cleavage patterns and the mechanisms that create them is thus crucial for the study of vertebrate development. This chapter describes the early cleavage stages for species representing ray-finned fish, amphibians, birds, reptiles, mammals, and proto-vertebrate ascidians and summarizes current understanding of the mechanisms that govern these patterns. The nearly universal influence of cell shape on orientation and positioning of spindles and cleavage furrows and the mechanisms that mediate this influence are discussed. We discuss in particular models of aster and spindle centering and orientation in large embryonic blastomeres that rely on asymmetric internal pulling forces generated by the cleavage furrow for the previous cell cycle. Also explored are mechanisms that integrate cell division given the limited supply of cellular building blocks in the egg and several-fold changes of cell size during early development, as well as cytoskeletal specializations specific to early blastomeres including processes leading to blastomere cohesion. Finally, we discuss evolutionary conclusions beginning to emerge from the contemporary analysis of the phylogenetic distributions of cleavage patterns. In sum, this chapter seeks to summarize our current understanding of vertebrate early embryonic cleavage patterns and their control and evolution.
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Affiliation(s)
- Andrew Hasley
- Laboratory of Genetics, University of Wisconsin-Madison, Genetics/Biotech Addition, Room 2424, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Shawn Chavez
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Department of Physiology & Pharmacology, Oregon Heath & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Department of Obstetrics & Gynecology, Oregon Heath & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Michael Danilchik
- Department of Integrative Biosciences, L499, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Martin Wühr
- Department of Molecular Biology & The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Icahn Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Genetics/Biotech Addition, Room 2424, 425-G Henry Mall, Madison, WI, 53706, USA.
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130
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Walentek P, Quigley IK. What we can learn from a tadpole about ciliopathies and airway diseases: Using systems biology in Xenopus to study cilia and mucociliary epithelia. Genesis 2017; 55:10.1002/dvg.23001. [PMID: 28095645 PMCID: PMC5276738 DOI: 10.1002/dvg.23001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022]
Abstract
Over the past years, the Xenopus embryo has emerged as an incredibly useful model organism for studying the formation and function of cilia and ciliated epithelia in vivo. This has led to a variety of findings elucidating the molecular mechanisms of ciliated cell specification, basal body biogenesis, cilia assembly, and ciliary motility. These findings also revealed the deep functional conservation of signaling, transcriptional, post-transcriptional, and protein networks employed in the formation and function of vertebrate ciliated cells. Therefore, Xenopus research can contribute crucial insights not only into developmental and cell biology, but also into the molecular mechanisms underlying cilia related diseases (ciliopathies) as well as diseases affecting the ciliated epithelium of the respiratory tract in humans (e.g., chronic lung diseases). Additionally, systems biology approaches including transcriptomics, genomics, and proteomics have been rapidly adapted for use in Xenopus, and broaden the applications for current and future translational biomedical research. This review aims to present the advantages of using Xenopus for cilia research, highlight some of the evolutionarily conserved key concepts and mechanisms of ciliated cell biology that were elucidated using the Xenopus model, and describe the potential for Xenopus research to address unresolved questions regarding the molecular mechanisms of ciliopathies and airway diseases.
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Affiliation(s)
- Peter Walentek
- Department of Molecular and Cell Biology; Genetics, Genomics and Development Division; Developmental and Regenerative Biology Group; University of California, Berkeley, CA 94720, USA
| | - Ian K. Quigley
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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131
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Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016; 165:535-50. [PMID: 27104977 DOI: 10.1016/j.cell.2016.03.014] [Citation(s) in RCA: 1811] [Impact Index Per Article: 226.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 12/30/2022]
Abstract
The question of how genomic information is expressed to determine phenotypes is of central importance for basic and translational life science research and has been studied by transcriptomic and proteomic profiling. Here, we review the relationship between protein and mRNA levels under various scenarios, such as steady state, long-term state changes, and short-term adaptation, demonstrating the complexity of gene expression regulation, especially during dynamic transitions. The spatial and temporal variations of mRNAs, as well as the local availability of resources for protein biosynthesis, strongly influence the relationship between protein levels and their coding transcripts. We further discuss the buffering of mRNA fluctuations at the level of protein concentrations. We conclude that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
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Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Beyer
- Cellular Networks and Systems Biology, University of Cologne, CECAD, Joseph-Stelzmann-Strasse 26, Cologne 50931, Germany.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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132
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Pontes AH, de Sousa MV. Mass Spectrometry-Based Approaches to Understand the Molecular Basis of Memory. Front Chem 2016; 4:40. [PMID: 27790611 PMCID: PMC5064248 DOI: 10.3389/fchem.2016.00040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/27/2016] [Indexed: 01/15/2023] Open
Abstract
The central nervous system is responsible for an array of cognitive functions such as memory, learning, language, and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS) have enabled the identification and quantification of thousands of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS)-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.
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Affiliation(s)
- Arthur H Pontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia Brasilia, Brazil
| | - Marcelo V de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia Brasilia, Brazil
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133
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Lombard-Banek C, Moody SA, Nemes P. High-Sensitivity Mass Spectrometry for Probing Gene Translation in Single Embryonic Cells in the Early Frog ( Xenopus) Embryo. Front Cell Dev Biol 2016; 4:100. [PMID: 27761436 PMCID: PMC5050209 DOI: 10.3389/fcell.2016.00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/29/2016] [Indexed: 01/01/2023] Open
Abstract
Direct measurement of protein expression with single-cell resolution promises to deepen the understanding of the basic molecular processes during normal and impaired development. High-resolution mass spectrometry provides detailed coverage of the proteomic composition of large numbers of cells. Here we discuss recent mass spectrometry developments based on single-cell capillary electrophoresis that extend discovery proteomics to sufficient sensitivity to enable the measurement of proteins in single cells. The single-cell mass spectrometry system is used to detect a large number of proteins in single embryonic cells in the 16-cell embryo of the South African clawed frog (Xenopus laevis) that give rise to distinct tissue types. Single-cell measurements of protein expression provide complementary information on gene transcription during early development of the vertebrate embryo, raising a potential to understand how differential gene expression coordinates normal cell heterogeneity during development.
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Affiliation(s)
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, The George Washington University Washington, DC, USA
| | - Peter Nemes
- Department of Chemistry, The George Washington University Washington, DC, USA
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134
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Lee-Liu D, Méndez-Olivos EE, Muñoz R, Larraín J. The African clawed frog Xenopus laevis: A model organism to study regeneration of the central nervous system. Neurosci Lett 2016; 652:82-93. [PMID: 27693567 DOI: 10.1016/j.neulet.2016.09.054] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/18/2016] [Accepted: 09/28/2016] [Indexed: 12/20/2022]
Abstract
While an injury to the central nervous system (CNS) in humans and mammals is irreversible, amphibians and teleost fish have the capacity to fully regenerate after severe injury to the CNS. Xenopus laevis has a high potential to regenerate the brain and spinal cord during larval stages (47-54), and loses this capacity during metamorphosis. The optic nerve has the capacity to regenerate throughout the frog's lifespan. Here, we review CNS regeneration in frogs, with a focus in X. laevis, but also provide some information about X. tropicalis and other frogs. We start with an overview of the anatomy of the Xenopus CNS, including the main supraspinal tracts that emerge from the brain stem, which play a key role in motor control and are highly conserved across vertebrates. We follow with the advantages of using Xenopus, a classical laboratory model organism, with increasing availability of genetic tools like transgenesis and genome editing, and genomic sequences for both X. laevis and X. tropicalis. Most importantly, Xenopus provides the possibility to perform intra-species comparative experiments between regenerative and non-regenerative stages that allow the identification of which factors are permissive for neural regeneration, and/or which are inhibitory. We aim to provide sufficient evidence supporting how useful Xenopus can be to obtain insights into our understanding of CNS regeneration, which, complemented with studies in mammalian vertebrate model systems, can provide a collaborative road towards finding novel therapeutic approaches for injuries to the CNS.
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Affiliation(s)
- Dasfne Lee-Liu
- Center for Aging and Regeneration, Millennium Nucleus in Regenerative Biology, Faculty of Biological Sciences, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile.
| | - Emilio E Méndez-Olivos
- Center for Aging and Regeneration, Millennium Nucleus in Regenerative Biology, Faculty of Biological Sciences, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Rosana Muñoz
- Center for Aging and Regeneration, Millennium Nucleus in Regenerative Biology, Faculty of Biological Sciences, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Juan Larraín
- Center for Aging and Regeneration, Millennium Nucleus in Regenerative Biology, Faculty of Biological Sciences, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile.
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135
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Shah VV, Soibam B, Ritter RA, Benham A, Oomen J, Sater AK. MicroRNAs and ectodermal specification I. Identification of miRs and miR-targeted mRNAs in early anterior neural and epidermal ectoderm. Dev Biol 2016; 426:200-210. [PMID: 27623002 DOI: 10.1016/j.ydbio.2016.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 08/13/2016] [Accepted: 08/16/2016] [Indexed: 11/25/2022]
Abstract
The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks (GRNs) that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectodermal lineages in Xenopus. We used next-generation sequencing to identify over 170 miRs expressed in midgastrula ectoderm expressing either noggin or a constitutively active BMP receptor, reflecting anterior neural or epidermal ectoderm, respectively; 125 had not previously been identified in Xenopus. We identified the locations of the pre-miR sequences in the X. laevis genome. Neural and epidermal ectoderm express broadly similar sets of miRs. To identify targets of miR-dependent translational control, we co-immunoprecipitated Argonaute-Ribonucleoprotein (Ago-RNP) complexes from early neural and epidermal ectoderm and sequenced the associated RNA. The Ago-RNP RNAs from these tissues represent overlapping, yet distinct, subsets of genes. Moreover, the profile of Ago-RNP associated genes differs substantially from the profile of total RNAs in these tissues. We generated target predictions for the "high confidence" Ago-RNP RNAs using the identified ectodermal miRs; These RNAs generally had target sites for multiple miRs. Oct4 orthologues, as well as many of their previously identified transcriptional targets, are represented in the Ago-RNP pool in both tissues, suggesting that miR-dependent regulation contributes to the downregulation of the oct4 gene regulatory network and the reduction in ectodermal pluripotency.
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Affiliation(s)
- Vrutant V Shah
- Dept. of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | | | - Ruth A Ritter
- Dept. of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | | | - Jamina Oomen
- Program in Genetics, Stony Brook University, Stony Brook, NY, United States
| | - Amy K Sater
- Dept. of Biology and Biochemistry, University of Houston, Houston, TX, United States.
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136
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Qi ST, Ma JY, Wang ZB, Guo L, Hou Y, Sun QY. N6-Methyladenosine Sequencing Highlights the Involvement of mRNA Methylation in Oocyte Meiotic Maturation and Embryo Development by Regulating Translation in Xenopus laevis. J Biol Chem 2016; 291:23020-23026. [PMID: 27613873 DOI: 10.1074/jbc.m116.748889] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Indexed: 11/06/2022] Open
Abstract
During the oogenesis of Xenopus laevis, oocytes accumulate maternal materials for early embryo development. As the transcription activity of the oocyte is silenced at the fully grown stage and the global genome is reactivated only by the mid-blastula embryo stage, the translation of maternal mRNAs accumulated during oocyte growth should be accurately regulated. Previous evidence has illustrated that the poly(A) tail length and RNA binding elements mediate RNA translation regulation in the oocyte. Recently, RNA methylation has been found to exist in various systems. In this study, we sequenced the N6-methyladenosine (m6A) modified mRNAs in fully grown germinal vesicle-stage and metaphase II-stage oocytes. As a result, we identified 4207 mRNAs with m6A peaks in germinal vesicle-stage or metaphase II-stage oocytes. When we integrated the mRNA methylation data with transcriptome and proteome data, we found that the highly methylated mRNAs showed significantly lower protein levels than those of the hypomethylated mRNAs, although the RNA levels showed no significant difference. We also found that the hypomethylated mRNAs were mainly enriched in the cell cycle and translation pathways, whereas the highly methylated mRNAs were mainly associated with protein phosphorylation. Our results suggest that oocyte mRNA methylation can regulate cellular translation and cell division during oocyte meiotic maturation and early embryo development.
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Affiliation(s)
- Shu-Tao Qi
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China and
| | - Jun-Yu Ma
- the College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhen-Bo Wang
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China and
| | - Lei Guo
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China and
| | - Yi Hou
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China and
| | - Qing-Yuan Sun
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China and .,the College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
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137
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Incorporation of non-canonical amino acids into the developing murine proteome. Sci Rep 2016; 6:32377. [PMID: 27572480 PMCID: PMC5004113 DOI: 10.1038/srep32377] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/09/2016] [Indexed: 12/25/2022] Open
Abstract
Analysis of the developing proteome has been complicated by a lack of tools that can be easily employed to label and identify newly synthesized proteins within complex biological mixtures. Here, we demonstrate that the methionine analogs azidohomoalanine and homopropargylglycine can be globally incorporated into the proteome of mice through facile intraperitoneal injections. These analogs contain bio-orthogonal chemical handles to which fluorescent tags can be conjugated to identify newly synthesized proteins. We show these non-canonical amino acids are incorporated into various tissues in juvenile mice and in a concentration dependent manner. Furthermore, administration of these methionine analogs to pregnant dams during a critical stage of murine development, E10.5-12.5 when many tissues are assembling, does not overtly disrupt development as assessed by proteomic analysis and normal parturition and growth of pups. This successful demonstration that non-canonical amino acids can be directly administered in vivo will enable future studies that seek to characterize the murine proteome during growth, disease and repair.
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138
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Lombard-Banek C, Reddy S, Moody SA, Nemes P. Label-free Quantification of Proteins in Single Embryonic Cells with Neural Fate in the Cleavage-Stage Frog (Xenopus laevis) Embryo using Capillary Electrophoresis Electrospray Ionization High-Resolution Mass Spectrometry (CE-ESI-HRMS). Mol Cell Proteomics 2016; 15:2756-68. [PMID: 27317400 PMCID: PMC4974349 DOI: 10.1074/mcp.m115.057760] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/16/2016] [Indexed: 12/12/2022] Open
Abstract
Quantification of protein expression in single cells promises to advance a systems-level understanding of normal development. Using a bottom-up proteomic workflow and multiplexing quantification by tandem mass tags, we recently demonstrated relative quantification between single embryonic cells (blastomeres) in the frog (Xenopus laevis) embryo. In this study, we minimize derivatization steps to enhance analytical sensitivity and use label-free quantification (LFQ) for single Xenopus cells. The technology builds on a custom-designed capillary electrophoresis microflow-electrospray ionization high-resolution mass spectrometry platform and LFQ by MaxLFQ (MaxQuant). By judiciously tailoring performance to peptide separation, ionization, and data-dependent acquisition, we demonstrate an ∼75-amol (∼11 nm) lower limit of detection and quantification for proteins in complex cell digests. The platform enabled the identification of 438 nonredundant protein groups by measuring 16 ng of protein digest, or <0.2% of the total protein contained in a blastomere in the 16-cell embryo. LFQ intensity was validated as a quantitative proxy for protein abundance. Correlation analysis was performed to compare protein quantities between the embryo and n = 3 different single D11 blastomeres, which are fated to develop into the nervous system. A total of 335 nonredundant protein groups were quantified in union between the single D11 cells spanning a 4 log-order concentration range. LFQ and correlation analysis detected expected proteomic differences between the whole embryo and blastomeres, and also found translational differences between individual D11 cells. LFQ on single cells raises exciting possibilities to study gene expression in other cells and models to help better understand cell processes on a systems biology level.
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Affiliation(s)
| | - Sushma Reddy
- From the ‡Department of Chemistry and ¶Thomas Jefferson High School for Science and Technology, Alexandria, Virginia
| | - Sally A Moody
- §Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC
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139
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Blitz IL, Fish MB, Cho KWY. Leapfrogging: primordial germ cell transplantation permits recovery of CRISPR/Cas9-induced mutations in essential genes. Development 2016; 143:2868-75. [PMID: 27385011 PMCID: PMC5004912 DOI: 10.1242/dev.138057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/15/2016] [Indexed: 01/07/2023]
Abstract
CRISPR/Cas9 genome editing is revolutionizing genetic loss-of-function analysis but technical limitations remain that slow progress when creating mutant lines. First, in conventional genetic breeding schemes, mosaic founder animals carrying mutant alleles are outcrossed to produce F1 heterozygotes. Phenotypic analysis occurs in the F2 generation following F1 intercrosses. Thus, mutant analyses will require multi-generational studies. Second, when targeting essential genes, efficient mutagenesis of founders is often lethal, preventing the acquisition of mature animals. Reducing mutagenesis levels may improve founder survival, but results in lower, more variable rates of germline transmission. Therefore, an efficient approach to study lethal mutations would be useful. To overcome these shortfalls, we introduce 'leapfrogging', a method combining efficient CRISPR mutagenesis with transplantation of mutated primordial germ cells into a wild-type host. Tested using Xenopus tropicalis, we show that founders containing transplants transmit mutant alleles with high efficiency. F1 offspring from intercrosses between F0 animals that carry embryonic lethal alleles recapitulate loss-of-function phenotypes, circumventing an entire generation of breeding. We anticipate that leapfrogging will be transferable to other species.
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Affiliation(s)
- Ira L Blitz
- 4410 Natural Sciences Building 2, Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Margaret B Fish
- 4410 Natural Sciences Building 2, Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Ken W Y Cho
- 4410 Natural Sciences Building 2, Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
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140
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Rentzsch F, Technau U. Genomics and development of Nematostella vectensis and other anthozoans. Curr Opin Genet Dev 2016; 39:63-70. [PMID: 27318695 DOI: 10.1016/j.gde.2016.05.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/14/2016] [Accepted: 05/30/2016] [Indexed: 01/10/2023]
Abstract
Due to their rather simple body plan with only few organs and a low number of cell types, cnidarians have long been recognized as an important animal group for evolutionary comparisons of animal body plans. Recent studies have shown, however, that the genomes of cnidarians and their epigenetic and posttranscriptional regulation are more complex than their morphology might suggest. How these complex genomes are deployed during embryonic development is an open question. With a focus on the sea anemone Nematostella vectensis we describe new findings about the development of the nervous system from neural progenitor cells and how Wnt and BMP signalling control axial patterning. These studies show that beyond evolutionary comparisons, cnidarian model organisms can provide new insights into generic questions in developmental biology.
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Affiliation(s)
- Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5008 Bergen, Norway.
| | - Ulrich Technau
- Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
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141
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Gaur S, Mandelbaum M, Herold M, Majumdar HD, Neilson KM, Maynard TM, Mood K, Daar IO, Moody SA. Neural transcription factors bias cleavage stage blastomeres to give rise to neural ectoderm. Genesis 2016; 54:334-49. [PMID: 27092474 PMCID: PMC4912902 DOI: 10.1002/dvg.22943] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 01/23/2023]
Abstract
The decision by embryonic ectoderm to give rise to epidermal versus neural derivatives is the result of signaling events during blastula and gastrula stages. However, there also is evidence in Xenopus that cleavage stage blastomeres contain maternally derived molecules that bias them toward a neural fate. We used a blastomere explant culture assay to test whether maternally deposited transcription factors bias 16-cell blastomere precursors of epidermal or neural ectoderm to express early zygotic neural genes in the absence of gastrulation interactions or exogenously supplied signaling factors. We found that Foxd4l1, Zic2, Gmnn, and Sox11 each induced explants made from ventral, epidermis-producing blastomeres to express early neural genes, and that at least some of the Foxd4l1 and Zic2 activities are required at cleavage stages. Similarly, providing extra Foxd4l1 or Zic2 to explants made from dorsal, neural plate-producing blastomeres significantly increased the expression of early neural genes, whereas knocking down either significantly reduced them. These results show that maternally delivered transcription factors bias cleavage stage blastomeres to a neural fate. We demonstrate that mouse and human homologs of Foxd4l1 have similar functional domains compared to the frog protein, as well as conserved transcriptional activities when expressed in Xenopus embryos and blastomere explants. genesis 54:334-349, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Shailly Gaur
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Max Mandelbaum
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Mona Herold
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Himani Datta Majumdar
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Karen M. Neilson
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | | | - Kathy Mood
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Ira O. Daar
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Sally A. Moody
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
- George Washington University Institute for Neuroscience
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142
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Yan X, Hoek TA, Vale RD, Tanenbaum ME. Dynamics of Translation of Single mRNA Molecules In Vivo. Cell 2016; 165:976-89. [PMID: 27153498 PMCID: PMC4889334 DOI: 10.1016/j.cell.2016.04.034] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/04/2016] [Accepted: 04/11/2016] [Indexed: 11/16/2022]
Abstract
Regulation of mRNA translation, the process by which ribosomes decode mRNAs into polypeptides, is used to tune cellular protein levels. Currently, methods for observing the complete process of translation from single mRNAs in vivo are unavailable. Here, we report the long-term (>1 hr) imaging of single mRNAs undergoing hundreds of rounds of translation in live cells, enabling quantitative measurements of ribosome initiation, elongation, and stalling. This approach reveals a surprising heterogeneity in the translation of individual mRNAs within the same cell, including rapid and reversible transitions between a translating and non-translating state. Applying this method to the cell-cycle gene Emi1, we find strong overall repression of translation initiation by specific 5' UTR sequences, but individual mRNA molecules in the same cell can exhibit dramatically different translational efficiencies. The ability to observe translation of single mRNA molecules in live cells provides a powerful tool to study translation regulation.
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Affiliation(s)
- Xiaowei Yan
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Tim A Hoek
- Hubrecht Institute, The Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht 3584CT, the Netherlands
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Marvin E Tanenbaum
- Hubrecht Institute, The Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht 3584CT, the Netherlands.
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143
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Peuchen EH, Sun L, Dovichi NJ. Optimization and comparison of bottom-up proteomic sample preparation for early-stage Xenopus laevis embryos. Anal Bioanal Chem 2016; 408:4743-9. [PMID: 27137514 DOI: 10.1007/s00216-016-9564-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/22/2016] [Accepted: 04/14/2016] [Indexed: 01/21/2023]
Abstract
Xenopus laevis is an important model organism in developmental biology. While there is a large literature on changes in the organism's transcriptome during development, the study of its proteome is at an embryonic state. Several papers have been published recently that characterize the proteome of X. laevis eggs and early-stage embryos; however, proteomic sample preparation optimizations have not been reported. Sample preparation is challenging because a large fraction (~90 % by weight) of the egg or early-stage embryo is yolk. We compared three common protein extraction buffer systems, mammalian Cell-PE LB(TM) lysing buffer (NP40), sodium dodecyl sulfate (SDS), and 8 M urea, in terms of protein extraction efficiency and protein identifications. SDS extracts contained the highest concentration of proteins, but this extract was dominated by a high concentration of yolk proteins. In contrast, NP40 extracts contained ~30 % of the protein concentration as SDS extracts, but excelled in discriminating against yolk proteins, which resulted in more protein and peptide identifications. We then compared digestion methods using both SDS and NP40 extraction methods with one-dimensional reverse-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS). NP40 coupled to a filter-aided sample preparation (FASP) procedure produced nearly twice the number of protein and peptide identifications compared to alternatives. When NP40-FASP samples were subjected to two-dimensional RPLC-ESI-MS/MS, a total of 5171 proteins and 38,885 peptides were identified from a single stage of embryos (stage 2), increasing the number of protein identifications by 23 % in comparison to other traditional protein extraction methods.
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Affiliation(s)
| | - Liangliang Sun
- University of Notre Dame, Stepan Chemistry 425, Notre Dame, IN, 46556, USA
| | - Norman J Dovichi
- University of Notre Dame, Stepan Chemistry 425, Notre Dame, IN, 46556, USA.
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144
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Vize PD, Zorn AM. Xenopus genomic data and browser resources. Dev Biol 2016; 426:194-199. [PMID: 27039265 DOI: 10.1016/j.ydbio.2016.03.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/26/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
Abstract
The two species of Xenopus most commonly used in biomedical research are the diploid Xenopus (Silurana) tropicalis and the tetraploid Xenopus laevis. The X. tropicalis genome sequence has been available since 2010 and this year the X. laevis, genome from two distinct genetic backgrounds has been published. Multiple genome assemblies available for both species and transcriptomic and epigenetic data sets are growing rapidly, all of which are available from a variety of web resources. This review describes the contents of these resources, how to locate and download genomic data, and also how to view and manipulate these data on various public genome browsers, with an emphasis on Xenbase, the Xenopus model organism database.
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Affiliation(s)
- Peter D Vize
- Departments of Biological Science and Computer Science, University of Calgary, Alberta, Canada.
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
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145
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Ding Y, Colozza G, Zhang K, Moriyama Y, Ploper D, Sosa EA, Benitez MDJ, De Robertis EM. Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. Dev Biol 2016; 426:176-187. [PMID: 27016259 PMCID: PMC5033668 DOI: 10.1016/j.ydbio.2016.02.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/14/2016] [Accepted: 02/26/2016] [Indexed: 12/31/2022]
Abstract
RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the X. laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.
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Affiliation(s)
- Yi Ding
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Gabriele Colozza
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Kelvin Zhang
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Yuki Moriyama
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Diego Ploper
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Eric A Sosa
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Maria D J Benitez
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Edward M De Robertis
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
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146
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Abstract
Xenopus has been one of the earliest and most important vertebrate model organisms for investigating the role and structure of basal bodies. Early transmission electron microscopy studies in Xenopus revealed the fine structures of Xenopus basal bodies and their accessory structures. Subsequent investigations using multiciliated cells in the Xenopus epidermis have further revealed many important features regarding the transcriptional regulation of basal body amplification as well as the regulation of basal body/cilia polarity. Future basal body research using Xenopus is expected to focus on the application of modern genome editing techniques (CRISPR/TALEN) to characterize the components of basal body proteins and their molecular functions.
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Affiliation(s)
- Siwei Zhang
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Brian J Mitchell
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
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147
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Vuković LD, Jevtić P, Zhang Z, Stohr BA, Levy DL. Nuclear size is sensitive to NTF2 protein levels in a manner dependent on Ran binding. J Cell Sci 2016; 129:1115-27. [PMID: 26823604 DOI: 10.1242/jcs.181263] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022] Open
Abstract
Altered nuclear size is associated with many cancers, and determining whether cancer-associated changes in nuclear size contribute to carcinogenesis necessitates an understanding of mechanisms of nuclear size regulation. Although nuclear import rates generally positively correlate with nuclear size, NTF2 levels negatively affect nuclear size, despite the role of NTF2 (also known as NUTF2) in nuclear recycling of the import factor Ran. We show that binding of Ran to NTF2 is required for NTF2 to inhibit nuclear expansion and import of large cargo molecules in Xenopus laevis egg and embryo extracts, consistent with our observation that NTF2 reduces the diameter of the nuclear pore complex (NPC) in a Ran-binding-dependent manner. Furthermore, we demonstrate that ectopic NTF2 expression in Xenopus embryos and mammalian tissue culture cells alters nuclear size. Finally, we show that increases in nuclear size during melanoma progression correlate with reduced NTF2 expression, and increasing NTF2 levels in melanoma cells is sufficient to reduce nuclear size. These results show a conserved capacity for NTF2 to impact on nuclear size, and we propose that NTF2 might be a new cancer biomarker.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Zhaojie Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Bradley A Stohr
- Department of Pathology, University of California, San Francisco, CA 94143, USA
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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