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Nett IR, Mulas C, Gatto L, Lilley KS, Smith A. Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency. EMBO Rep 2018; 19:e45642. [PMID: 29895711 PMCID: PMC6073214 DOI: 10.15252/embr.201745642] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 01/08/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signalling is implicated in initiation of embryonic stem (ES) cell differentiation. The pathway is subject to complex feedback regulation. Here, we examined the ERK-responsive phosphoproteome in ES cells and identified the negative regulator RSK1 as a prominent target. We used CRISPR/Cas9 to create combinatorial mutations in RSK family genes. Genotypes that included homozygous null mutations in Rps6ka1, encoding RSK1, resulted in elevated ERK phosphorylation. These RSK-depleted ES cells exhibit altered kinetics of transition into differentiation, with accelerated downregulation of naïve pluripotency factors, precocious expression of transitional epiblast markers and early onset of lineage specification. We further show that chemical inhibition of RSK increases ERK phosphorylation and expedites ES cell transition without compromising multilineage potential. These findings demonstrate that the ERK activation profile influences the dynamics of pluripotency progression and highlight the role of signalling feedback in temporal control of cell state transitions.
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Affiliation(s)
- Isabelle Re Nett
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laurent Gatto
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
- Computational Proteomics Unit, Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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2
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Proteomic patterns associated with heterosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:908-15. [PMID: 26721744 DOI: 10.1016/j.bbapap.2015.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/29/2015] [Accepted: 12/18/2015] [Indexed: 12/14/2022]
Abstract
Heterosis is characterized by higher seed yields, plant biomass or other traits in heterozygotes or hybrids compared with their genetically divergent parents, which are often homozygous. Despite extensive investigation of heterosis and its wide application in crops such as maize, rice, wheat and sorghum, its molecular basis is still enigmatic. In the past century, some pioneers have proposed multigene models referring to the complementation of allelic and gene expression variation, which is likely to be an important contributor to heterosis. In addition, there are potential interactions of epigenetic variation involved in heterosis via novel mechanisms. At the level of gene expression, many recent studies have revealed that the heterosis phenomenon can be deciphered not only at the transcriptional level but also at the proteomic level. This review presents an update on the information supporting the involvement of proteomic patterns in heterosis and a possible future direction of the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Guo B, Chen Y, Li C, Wang T, Wang R, Wang B, Hu S, Du X, Xing H, Song X, Yao Y, Sun Q, Ni Z. Maize (Zea mays L.) seedling leaf nuclear proteome and differentially expressed proteins between a hybrid and its parental lines. Proteomics 2014; 14:1071-87. [PMID: 24677780 DOI: 10.1002/pmic.201300147] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 01/10/2014] [Accepted: 01/24/2014] [Indexed: 12/27/2022]
Abstract
To better understand the underlying molecular basis of leaf development in maize, a reference map of nuclear proteins in basal region of seedling leaf was established using a combination of 2DE and MALDI-TOF-MS. In total, 441 reproducible protein spots in nuclear proteome of maize leaf basal region were detected with silver staining in a pH range of 3-10, among which 203 spots corresponding to 163 different proteins were identified. As expected, proteins implicated in RNA and protein-associated functions were overrepresented in nuclear proteome. Remarkably, a high percentage (10%) of proteins was identified to be involved in cell division and growth. In addition, comparative nuclear proteomic analysis in leaf basal region of highly heterotic hybrid Mo17/B73 and its parental lines was also performed and 52 of 445 (11.69%) detected protein spots were differentially expressed between the hybrid and its parental lines, among which 16 protein spots displayed nonadditively expressed pattern. These results indicated that hybridization between two parental lines can cause changes in the expression of a variety of nuclear proteins, which may be responsible for the observed leaf size heterosis.
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Affiliation(s)
- Baojian Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Chuan Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Tianya Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Rui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Bo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Sha Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Xiaofen Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Xiao Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
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4
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Barthéléry M, Jaishankar A, Salli U, Freeman WM, Vrana KE. 2-D DIGE identification of differentially expressed heterogeneous nuclear ribonucleoproteins and transcription factors during neural differentiation of human embryonic stem cells. Proteomics Clin Appl 2012; 3:505-14. [PMID: 21136975 DOI: 10.1002/prca.200800109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Neural stem cells (NSC) are progenitors that can give rise to all neural lineages. They are found in specific niches of fetal and adult brains and grow in vitro as non-adherent colonies, the neurospheres. These cells express the intermediate filament nestin, commonly considered an NSC marker. NSC can be derived as neurospheres from human embryonic stem cells (hESC). The mechanisms of cellular programming that hESC undergo during differentiation remain obscure. To investigate the commitment process of hESC during directed neural differentiation, we compared the nuclear proteomes of hESC and hESC-derived neurospheres. We used 2-D DIGE to conduct a quantitative comparison of hESC and NSC nuclear proteins and detected 1521 protein spots matched across three gels. Statistical analysis (ANOVA n = 3 with false discovery correction) revealed that only 2.1% of the densitometric signal was significantly changed. The ranges of average ratios varied from 1.2- to 11-fold at a statistically significant p-value <0.05. MS/MS identified 15 regulated proteins previously shown to be involved in chromatin remodeling, mRNA processing and gene expression regulation. Notably, three members of the heterogeneous nuclear ribonucleoprotein family (AUF-1, and FBP-1 and FBP-2) register a 54, 70 and 99% increased expression, highlighting them as potential markers for NSC in vitro derivation. By contrast, Cpsf-6 virtually disappears with differentiation with an 11-fold drop in NSC, highlighting this protein as a novel marker for undifferentiated ESC.
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Affiliation(s)
- Miguel Barthéléry
- Pennsylvania State University College of Medicine, Department of Pharmacology, Hummelstown, PA, USA
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Sarkar P, Collier TS, Randall SM, Muddiman DC, Rao BM. The subcellular proteome of undifferentiated human embryonic stem cells. Proteomics 2012; 12:421-30. [DOI: 10.1002/pmic.201100507] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 10/31/2011] [Accepted: 11/14/2011] [Indexed: 11/11/2022]
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Kuster DWD, Merkus D, Jorna HJJ, Dekkers DHW, Duncker DJ, Verhoeven AJM. Nuclear protein extraction from frozen porcine myocardium. J Physiol Biochem 2011; 67:165-73. [PMID: 21061196 DOI: 10.1007/s13105-010-0059-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 10/15/2010] [Indexed: 01/04/2023]
Abstract
Protocols for the extraction of nuclear proteins have been developed for cultured cells and fresh tissue, but sometimes only frozen tissue is available. We have optimized the homogenization procedure and subsequent fractionation protocol for the preparation of nuclear protein extracts from frozen porcine left ventricular (LV) tissue. This method gave a highly reproducible protein yield (6.5±0.7% of total protein; mean±SE, n=9) and a 6-fold enrichment of the nuclear marker protein B23. The nuclear protein extracts were essentially devoid of cytosolic, myofilament, and histone proteins. Compared to nuclear extracts from fresh LV tissue, some loss of nuclear proteins to the cytosolic fraction was observed. Using this method, we studied the distribution of tyrosine phosphorylated signal transducer and activator of transcription 3 (PY-STAT3) in LV tissue of animals treated with the β-agonist dobutamine. Upon treatment, PY-STAT3 increased 30.2±8.5-fold in total homogenates, but only 6.9±2.1-fold (n=4, P=0.03) in nuclear protein extracts. Of all PY-STAT3 formed, only a minor fraction appeared in the nuclear fraction. This simple and reproducible protocol yielded nuclear protein extracts that were highly enriched in nuclear proteins with almost complete removal of cytosolic and myofilament proteins. This nuclear protein extraction protocol is therefore well-suited for nuclear proteome analysis of frozen heart tissue collected in biobanks.
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Affiliation(s)
- Diederik W D Kuster
- Department of Biochemistry, Cardiovascular Research Institute COEUR, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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Liu Y, He M, Sun X, Peng K, Zhao L. Alteration of nuclear protein profiling for NIH-3T3 cells exposed to H2O2. Cell Biochem Funct 2010; 28:578-84. [DOI: 10.1002/cbf.1693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Nasrabadi D, Larijani MR, Fathi A, Gourabi H, Dizaj AV, Baharvand H, Salekdeh GH. Nuclear proteome analysis of monkey embryonic stem cells during differentiation. Stem Cell Rev Rep 2010; 6:50-61. [PMID: 20091144 DOI: 10.1007/s12015-009-9109-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 12/02/2009] [Indexed: 12/18/2022]
Abstract
The nuclear proteome enables, manages, and regulates the genome by the collective actions and interactions of proteins found in the nucleus. We applied a proteomic approach to analyze a nuclear proteome during embryonic stem cell (ESC) proliferation, and 3 and 9 days after initiation of differentiation. The nuclei were isolated from cells and their proteins were separated using 2-DE. Out of about 560 protein spots reproducible detected on any give gel, 49 differentially expressed proteins were identified by Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI TOF/TOF) mass spectrometry. Of them, several nuclear located proteins involved in chromatin remodeling, transcription regulation, apoptosis, cell proliferation, and differentiation were identified including CTBP1, MM-1, RUVBL1, HCC-1, SGTA, SUMO2, and Galectin-1. Functional interaction analysis of differentially expressed proteins revealed that most of nuclear proteins had a direct interaction with c-Myc and p53.
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Affiliation(s)
- Davood Nasrabadi
- Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, P.O. Box: 19395-4644, Karaj, Iran
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9
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Qin H, Wang Y. Exploring DNA-binding proteins with in vivo chemical cross-linking and mass spectrometry. J Proteome Res 2009; 8:1983-91. [PMID: 19714816 DOI: 10.1021/pr8009319] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA-binding proteins are very important constituents of proteomes of all species and play crucial roles in transcription, DNA replication, recombination, repair, and other activities associated with DNA. Although a number of DNA-binding proteins have been identified, many proteins involved in gene regulation and DNA repair are likely still unknown because of their dynamic and/or weak interactions with DNA. In this report, we described an approach for the comprehensive identification of DNA-binding proteins with in vivo formaldehyde cross-linking and LC-MS/MS. DNA-binding proteins could be purified via the isolation of DNA-protein complexes and released from the complexes by reversing the cross-linking. By using this method, we were able to identify more than one hundred DNA-binding proteins, such as proteins involved in transcription, gene regulation, DNA replication and repair, and a large number of proteins that are potentially associated with DNA and DNA-binding proteins. This method should be generally applicable to the investigation of other nucleic acid-binding proteins, and hold great potential in the comprehensive study of gene regulation, DNA damage response and repair, as well as many other critical biological processes at proteomic level.
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Affiliation(s)
- Haibo Qin
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
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10
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Emerging molecular approaches in stem cell biology. Biotechniques 2009; 46:367-71. [PMID: 19480634 DOI: 10.2144/000113144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Stem cells are characterized by their ability to self-renew and differentiate into multiple adult cell types. Although substantial progress has been made over the last decade in understanding stem cell biology, recent technological advances in molecular and systems biology may hold the key to unraveling the mystery behind stem cell self-renewal and plasticity. The most notable of these advances is the ability to generate induced pluripotent cells from somatic cells. In this review, we discuss our current understanding of molecular similarities and differences among various stem cell types. Moreover, we survey the current state of systems biology and forecast future needs and direction in the stem cell field.
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11
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Jaishankar A, Barthelery M, Freeman WM, Salli U, Ritty TM, Vrana KE. Human Embryonic and Mesenchymal Stem Cells Express Different Nuclear Proteomes. Stem Cells Dev 2009; 18:793-802. [DOI: 10.1089/scd.2008.0156] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Amritha Jaishankar
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Miguel Barthelery
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Willard M. Freeman
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Ugur Salli
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Timothy M. Ritty
- Department of Orthopedics, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Kent E. Vrana
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
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