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Edelbroek B, Westholm JO, Bergquist J, Söderbom F. Multi-omics analysis of aggregative multicellularity. iScience 2024; 27:110659. [PMID: 39224513 PMCID: PMC11367525 DOI: 10.1016/j.isci.2024.110659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/14/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
All organisms have to carefully regulate their gene expression, not least during development. mRNA levels are often used as proxy for protein output; however, this approach ignores post-transcriptional effects. In particular, mRNA-protein correlation remains elusive for organisms that exhibit aggregative rather than clonal multicellularity. We addressed this issue by generating a paired transcriptomics and proteomics time series during the transition from uni-to multicellular stage in the social ameba Dictyostelium discoideum. Our data reveals that mRNA and protein levels correlate highly during unicellular growth, but decrease when multicellular development is initiated. This accentuates that transcripts alone cannot accurately predict protein levels. The dataset provides a useful resource to study gene expression during aggregative multicellular development. Additionally, our study provides an example of how to analyze and visualize mRNA and protein levels, which should be broadly applicable to other organisms and conditions.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Neurochemistry, Uppsala University, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
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2
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Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024; 27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Maternal-to-zygotic transition (MZT) is central to early embryogenesis. However, its underlying molecular mechanisms are still not well described. Here, we revealed the expression dynamics of 5,000 proteins across four stages of zebrafish embryos during MZT, representing one of the most systematic surveys of proteome landscape of the zebrafish embryos during MZT. Nearly 700 proteins were differentially expressed and were divided into six clusters according to their expression patterns. The proteome expression profiles accurately reflect the main events that happen during the MZT, i.e., zygotic genome activation (ZGA), clearance of maternal mRNAs, and initiation of cellular differentiation and organogenesis. MZT is modulated by many proteins at multiple levels in a collaborative fashion, i.e., transcription factors, histones, histone-modifying enzymes, RNA helicases, and P-body proteins. Significant discrepancies were discovered between zebrafish proteome and transcriptome profiles during the MZT. The proteome dynamics database will be a valuable resource for bettering our understanding of MZT.
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Affiliation(s)
- Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - William Poulos
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Jose B. Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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3
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Reddien PW. The purpose and ubiquity of turnover. Cell 2024; 187:2657-2681. [PMID: 38788689 DOI: 10.1016/j.cell.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Turnover-constant component production and destruction-is ubiquitous in biology. Turnover occurs across organisms and scales, including for RNAs, proteins, membranes, macromolecular structures, organelles, cells, hair, feathers, nails, antlers, and teeth. For many systems, turnover might seem wasteful when degraded components are often fully functional. Some components turn over with shockingly high rates and others do not turn over at all, further making this process enigmatic. However, turnover can address fundamental problems by yielding powerful properties, including regeneration, rapid repair onset, clearance of unpredictable damage and errors, maintenance of low constitutive levels of disrepair, prevention of stable hazards, and transitions. I argue that trade-offs between turnover benefits and metabolic costs, combined with constraints on turnover, determine its presence and rates across distinct contexts. I suggest that the limits of turnover help explain aging and that turnover properties and the basis for its levels underlie this fundamental component of life.
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Affiliation(s)
- Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
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4
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Xiang K, Ly J, Bartel DP. Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos. Dev Cell 2024; 59:1058-1074.e11. [PMID: 38460509 DOI: 10.1016/j.devcel.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/28/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
During oocyte maturation and early embryogenesis, changes in mRNA poly(A)-tail lengths strongly influence translation, but how these tail-length changes are orchestrated has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with millions of 3' UTR sequence variants) in frog oocytes and embryos and in fish embryos. Contrasting to previously proposed cytoplasmic polyadenylation elements (CPEs), we found that a shorter element, UUUUA, together with the polyadenylation signal (PAS), specify cytoplasmic polyadenylation, and we identified contextual features that modulate the activity of both elements. In maturing oocytes, this tail lengthening occurs against a backdrop of global deadenylation and the action of C-rich elements that specify tail-length-independent translational repression. In embryos, cytoplasmic polyadenylation becomes more permissive, and additional elements specify waves of stage-specific deadenylation. Together, these findings largely explain the complex tapestry of tail-length changes observed in early frog and fish development, with strong evidence of conservation in both mice and humans.
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Affiliation(s)
- Kehui Xiang
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jimmy Ly
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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5
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Frese AN, Mariossi A, Levine MS, Wühr M. Quantitative proteome dynamics across embryogenesis in a model chordate. iScience 2024; 27:109355. [PMID: 38510129 PMCID: PMC10951915 DOI: 10.1016/j.isci.2024.109355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
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Affiliation(s)
- Alexander N. Frese
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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6
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Fan D, Cong Y, Liu J, Zhang H, Du Z. Spatiotemporal analysis of mRNA-protein relationships enhances transcriptome-based developmental inference. Cell Rep 2024; 43:113928. [PMID: 38461413 DOI: 10.1016/j.celrep.2024.113928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/31/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Elucidating the complex relationships between mRNA and protein expression at high spatiotemporal resolution is critical for unraveling multilevel gene regulation and enhancing mRNA-based developmental analyses. In this study, we conduct a single-cell analysis of mRNA and protein expression of transcription factors throughout C. elegans embryogenesis. Initially, cellular co-presence of mRNA and protein is low, increasing to a medium-high level (73%) upon factoring in delayed protein synthesis and long-term protein persistence. These factors substantially affect mRNA-protein concordance, leading to potential inaccuracies in mRNA-reliant gene detection and specificity characterization. Building on the learned relationship, we infer protein presence from mRNA expression and demonstrate its utility in identifying tissue-specific genes and elucidating relationships between genes and cells. This approach facilitates identifying the role of sptf-1/SP7 in neuronal lineage development. Collectively, this study provides insights into gene expression dynamics during rapid embryogenesis and approaches for improving the efficacy of transcriptome-based developmental analyses.
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Affiliation(s)
- Duchangjiang Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yulin Cong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyi Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Haoye Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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7
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Chen Y, Huang JH, Phong C, Ferrell JE. Viscosity-dependent control of protein synthesis and degradation. Nat Commun 2024; 15:2149. [PMID: 38459041 PMCID: PMC10923802 DOI: 10.1038/s41467-024-46447-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
It has been proposed that the concentration of proteins in the cytoplasm maximizes the speed of important biochemical reactions. Here we have used Xenopus egg extracts, which can be diluted or concentrated to yield a range of cytoplasmic protein concentrations, to test the effect of cytoplasmic concentration on mRNA translation and protein degradation. We find that protein synthesis rates are maximal in ~1x cytoplasm, whereas protein degradation continues to rise to a higher optimal concentration of ~1.8x. We show that this difference in optima can be attributed to a greater sensitivity of translation to cytoplasmic viscosity. The different concentration optima could produce a negative feedback homeostatic system, where increasing the cytoplasmic protein concentration above the 1x physiological level increases the viscosity of the cytoplasm, which selectively inhibits translation and drives the system back toward the 1x set point.
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Affiliation(s)
- Yuping Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Jo-Hsi Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Connie Phong
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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8
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Baxi AB, Li J, Quach VM, Pade LR, Moody SA, Nemes P. Cell lineage-guided mass spectrometry reveals increased energy metabolism and reactive oxygen species in the vertebrate organizer. Proc Natl Acad Sci U S A 2024; 121:e2311625121. [PMID: 38300871 PMCID: PMC10861879 DOI: 10.1073/pnas.2311625121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024] Open
Abstract
Molecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been mostly limited to transcripts and a few proteins, the latter due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog (X. laevis), a popular model of development, has long been known to be the origin of signals that pattern the mesoderm and central nervous system. Molecular screens of the SMO have identified several genes responsible for the ability of the SMO to establish the body axis. Nonetheless, a comprehensive study of proteins and metabolites produced specifically in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the remainder of the embryo using high-resolution mass spectrometry (HRMS). Quantification of ~4,600 proteins and a panel of targeted metabolites documented differential expression for 460 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the SMO. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO. Chemical perturbation of the redox gradient perturbed mesoderm involution during early gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.
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Affiliation(s)
- Aparna B. Baxi
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
- Department of Anatomy and Cell Biology,School of Medical and Health Sciences,The George Washington University, Washington, DC20037
| | - Jie Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
| | - Vi M. Quach
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
| | - Leena R. Pade
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
| | - Sally A. Moody
- Department of Anatomy and Cell Biology,School of Medical and Health Sciences,The George Washington University, Washington, DC20037
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
- Department of Anatomy and Cell Biology,School of Medical and Health Sciences,The George Washington University, Washington, DC20037
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9
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Li X, Xie F, Li R, Li L, Ren M, Jin M, Zhou J, Wang C, Li S. Integrated 4D Analysis of Intramuscular Fat Deposition: Quantitative Proteomic and Transcriptomic Studies in Wannanhua Pig Longissimus Dorsi Muscle. Animals (Basel) 2024; 14:167. [PMID: 38200898 PMCID: PMC10778203 DOI: 10.3390/ani14010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Wannanhua (WH) is a pig breed indigenous to Anhui Province, China. This breed has a high intramuscular fat (IMF) content, making it an ideal model for investigating lipid deposition mechanisms in pigs. IMF content is one of the main indicators of meat quality in pigs and is regulated by multiple genes and metabolic pathways. Building upon our prior transcriptomic investigation, the present study focused on the longissimus dorsi muscle tissue of Wannanhua (WH) pigs in the rapid fat-deposition stages (120 and 240 days of age). Employing 4D label-free quantitative proteomic analysis, we identified 106 differentially expressed proteins (DEPs). Parallel reaction monitoring (PRM) technology was used to verify the DEPs, and the results showed that the 4D label-free results were reliable and valid. Functional enrichment and protein-protein interaction analyses showed that the DEPs were mainly involved in the skeletal-muscle-associated structural proteins, mitochondria, energy metabolism, and fatty acid metabolism. By integrating transcriptomic data, we identified seven candidate genes including ACADL, ACADM, ANKRD2, MYOZ2, TNNI1, UCHL1, and ART3 that play a regulatory role in fat deposition and muscle development. These findings establish a theoretical foundation for future analyses of lipid deposition traits, contributing to potential enhancements in pig meat quality during breeding and advancing the selection process for Chinese indigenous breeds.
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Affiliation(s)
- Xiaojin Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Fei Xie
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ruidong Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Lei Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Man Ren
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Mengmeng Jin
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Ju Zhou
- Kunshan Animal Health Supervision Institute, Kunshan 215300, China;
| | - Chonglong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shenghe Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
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10
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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11
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Heo G, Lee SH, Kim JD, Lee GH, Sim JM, Zhou D, Guo J, Cui XS. GRP78 acts as a cAMP/PKA signaling modulator through the MC4R pathway in porcine embryonic development. FASEB J 2023; 37:e23274. [PMID: 37917004 DOI: 10.1096/fj.202301356r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/23/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023]
Abstract
Glucose-regulated protein 78 (GRP78) binds to and stabilizes melanocortin 4 receptor (MC4R), which activates protein kinase A (PKA) by regulating G proteins. GRP78 is primarily used as a marker for endoplasmic reticulum stress; however, its other functions have not been well studied. Therefore, in this study, we aimed to investigate the function of GRP78 during porcine embryonic development. The developmental quality of porcine embryos, expression of cell cycle proteins, and function of mitochondria were evaluated by inhibiting the function of GRP78. Porcine oocytes were activated to undergo parthenogenesis, and blastocysts were obtained after 7 days of in vitro culture. GRP78 function was inhibited by adding 20 μM HA15 to the in vitro culture medium. The inhibition in GRP78 function led to a decrease in G proteins release, which subsequently downregulated the cyclic adenosine monophosphate (cAMP)/PKA pathway. Ultimately, inhibition of GRP78 function induced the inhibition of CDK1 and cyclin B expression and disruption of the cell cycle. In addition, inhibition of GRP78 function regulated DRP1 and SIRT1 expression, resulting in mitochondrial dysfunction. This study provides new insights into the role of GRP78 in porcine embryonic development, particularly its involvement in the regulation of the MC4R pathway and downstream cAMP/PKA signaling. The results suggest that the inhibition of GRP78 function in porcine embryos by HA15 treatment may have negative effects on embryo quality and development. This study also demonstrated that GRP78 plays a crucial role in the functioning of MC4R, which releases the G protein during porcine embryonic development.
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Affiliation(s)
- Geun Heo
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Song-Hee Lee
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Ji-Dam Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Gyu-Hyun Lee
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jae-Min Sim
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Dongjie Zhou
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jing Guo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xiang-Shun Cui
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
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12
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Nguyen TA, Heng JWJ, Ng YT, Sun R, Fisher S, Oguz G, Kaewsapsak P, Xue S, Reversade B, Ramasamy A, Eisenberg E, Tan MH. Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus. BMC Biol 2023; 21:251. [PMID: 37946231 PMCID: PMC10636886 DOI: 10.1186/s12915-023-01756-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Xenopus has served as a valuable model system for biomedical research over the past decades. Notably, ADAR was first detected in frog oocytes and embryos as an activity that unwinds RNA duplexes. However, the scope of A-to-I RNA editing by the ADAR enzymes in Xenopus remains underexplored. RESULTS Here, we identify millions of editing events in Xenopus with high accuracy and systematically map the editome across developmental stages, adult organs, and species. We report diverse spatiotemporal patterns of editing with deamination activity highest in early embryogenesis before zygotic genome activation and in the ovary. Strikingly, editing events are poorly conserved across different Xenopus species. Even sites that are detected in both X. laevis and X. tropicalis show largely divergent editing levels or developmental profiles. In protein-coding regions, only a small subset of sites that are found mostly in the brain are well conserved between frogs and mammals. CONCLUSIONS Collectively, our work provides fresh insights into ADAR activity in vertebrates and suggest that species-specific editing may play a role in each animal's unique physiology or environmental adaptation.
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Affiliation(s)
- Tram Anh Nguyen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Jia Wei Joel Heng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Yan Ting Ng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rui Sun
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Shira Fisher
- Faculty of Life Sciences, The Mina and Everard Goodman, Bar-Ilan University, Ramat Gan, Israel
| | - Gokce Oguz
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Pornchai Kaewsapsak
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Bruno Reversade
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medical Genetics, School of Medicine (KUSoM), Koç University, Istanbul, Turkey
| | - Adaikalavan Ramasamy
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore.
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.
- HP-NTU Digital Manufacturing Corporate Lab, Nanyang Technological University, Singapore, Singapore.
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13
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Stepler KE, Hannah SC, Taneyhill LA, Nemes P. Deep Proteome of the Developing Chick Midbrain. J Proteome Res 2023; 22:3264-3274. [PMID: 37616547 DOI: 10.1021/acs.jproteome.3c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The epithelial-to-mesenchymal transition (EMT) and migration of cranial neural crest cells within the midbrain are critical processes that permit proper craniofacial patterning in the early embryo. Disruptions in these processes not only impair development but also lead to various diseases, underscoring the need for their detailed understanding at the molecular level. The chick embryo has served historically as an excellent model for human embryonic development, including cranial neural crest cell EMT and migration. While these developmental events have been characterized transcriptionally, studies at the protein level have not been undertaken to date. Here, we applied mass spectrometry (MS)-based proteomics to establish a deep proteomics profile of the chick midbrain region during early embryonic development. Our proteomics method combines optimal lysis conditions, offline fractionation, separation on a nanopatterned stationary phase (μPAC) using nanoflow liquid chromatography, and detection using quadrupole-ion trap-Orbitrap tribrid high-resolution tandem MS. Identification of >5900 proteins and >450 phosphoproteins in this study marks the deepest coverage of the chick midbrain proteome to date. These proteins have known roles in pathways related to neural crest cell EMT and migration such as signaling, proteolysis/extracellular matrix remodeling, and transcriptional regulation. This study offers valuable insight into important developmental processes occurring in the midbrain region and demonstrates the utility of proteomics for characterization of tissue microenvironments during chick embryogenesis.
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Affiliation(s)
- Kaitlyn E Stepler
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Seth C Hannah
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Lisa A Taneyhill
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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14
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Baxi AB, Nemes P, Moody SA. Time-resolved quantitative proteomic analysis of the developing Xenopus otic vesicle reveals putative congenital hearing loss candidates. iScience 2023; 26:107665. [PMID: 37670778 PMCID: PMC10475516 DOI: 10.1016/j.isci.2023.107665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/16/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023] Open
Abstract
Over 200 genes are known to underlie human congenital hearing loss (CHL). Although transcriptomic approaches have identified candidate regulators of otic development, little is known about the abundance of their protein products. We used a multiplexed quantitative mass spectrometry-based proteomic approach to determine protein abundances over key stages of Xenopus otic morphogenesis to reveal a dynamic expression of cytoskeletal, integrin signaling, and extracellular matrix proteins. We correlated these dynamically expressed proteins to previously published lists of putative downstream targets of human syndromic hearing loss genes: SIX1 (BOR syndrome), CHD7 (CHARGE syndrome), and SOX10 (Waardenburg syndrome). We identified transforming growth factor beta-induced (Tgfbi), an extracellular integrin-interacting protein, as a putative target of Six1 that is required for normal otic vesicle formation. Our findings demonstrate the application of this Xenopus dataset to understanding the dynamic regulation of proteins during otic development and to discovery of additional candidates for human CHL.
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Affiliation(s)
- Aparna B. Baxi
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
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15
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Yan J, Ding Y, Peng Z, Qin L, Gu J, Wan C. Systematic Proteomics Study on the Embryonic Development of Danio rerio. J Proteome Res 2023; 22:2814-2826. [PMID: 37500539 DOI: 10.1021/acs.jproteome.3c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The early development of zebrafish (Danio rerio) is a complex and dynamic physiological process involving cell division, differentiation, and movement. Currently, the genome and transcriptome techniques have been widely used to study the embryonic development of zebrafish. However, the research of proteomics based on proteins that directly execute functions is relatively vacant. In this work, we apply label-free quantitative proteomics to explore protein profiling during zebrafish's embryogenesis, and a total of 5961 proteins were identified at 10 stages of zebrafish's early development. The identified proteins were divided into 11 modules according to weighted gene coexpression network analysis (WGCNA), and the characteristics between modules were significantly different. For example, mitochondria-related functions enriched the early development of zebrafish. Primordial germ cell-related proteins were identified at the 4-cell stage, while the eye development event is dominated at 5 days post fertilization (dpf). By combining with published transcriptomics data, we discovered some proteins that may be involved in activating zygotic genes. Meanwhile, 137 novel proteins were identified. This study comprehensively analyzed the dynamic processes in the embryonic development of zebrafish from the perspective of proteomics. It provided solid data support for further understanding of the molecular mechanism of its development.
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Affiliation(s)
- Jiahao Yan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Yuhe Ding
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Zhao Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Lu Qin
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Jingyu Gu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
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16
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Gu L, Li X, Zhu W, Shen Y, Wang Q, Liu W, Zhang J, Zhang H, Li J, Li Z, Liu Z, Li C, Wang H. Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition. J Pharm Anal 2023; 13:942-954. [PMID: 37719194 PMCID: PMC10499587 DOI: 10.1016/j.jpha.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 09/19/2023] Open
Abstract
Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development. However, the single-cell or low-input proteomic research in this field is relatively underdeveloped because of the higher threshold of the starting material for mammalian embryo samples and the lack of hypersensitive proteome technology. In this study, a comprehensive solution of ultrasensitive proteome technology (CS-UPT) was developed for single-cell or low-input mouse oocyte/embryo samples. The deep coverage and high-throughput routes significantly reduced the starting material and were selected by investigators based on their demands. Using the deep coverage route, we provided the first large-scale snapshot of the very early stage of mouse maternal-to-zygotic transition, including almost 5,500 protein groups from 20 mouse oocytes or zygotes for each sample. Moreover, significant protein regulatory networks centered on transcription factors and kinases between the MII oocyte and 1-cell embryo provided rich insights into minor zygotic genome activation.
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Affiliation(s)
- Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xumiao Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wencheng Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Yi Shen
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenjun Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Junfeng Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Huiping Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziyi Li
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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17
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Zhang H, Ji S, Zhang K, Chen Y, Ming J, Kong F, Wang L, Wang S, Zou Z, Xiong Z, Xu K, Lin Z, Huang B, Liu L, Fan Q, Jin S, Deng H, Xie W. Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition. Genome Biol 2023; 24:166. [PMID: 37443062 PMCID: PMC10347836 DOI: 10.1186/s13059-023-02997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic genome activation. How the transcriptome, translatome, and proteome are coordinated during this critical developmental window remains poorly understood. RESULTS Utilizing a highly sensitive and quantitative mass spectrometry approach, we obtain high-quality proteome data spanning seven mouse stages, from full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. Integrative analyses reveal distinct proteome reprogramming compared to that of the transcriptome or translatome. FGO to 8-cell proteomes are dominated by FGO-stockpiled proteins, while the transcriptome and translatome are more dynamic. FGO-originated proteins frequently persist to blastocyst while corresponding transcripts are already downregulated or decayed. Improved concordance between protein and translation or transcription is observed for genes starting translation upon meiotic resumption, as well as those transcribed and translated only in embryos. Concordance between protein and transcription/translation is also observed for proteins with short half-lives. We built a kinetic model that predicts protein dynamics by incorporating both initial protein abundance in FGOs and translation kinetics across developmental stages. CONCLUSIONS Through integrative analyses of datasets generated by ultrasensitive methods, our study reveals that the proteome shows distinct dynamics compared to the translatome and transcriptome during mouse OET. We propose that the remarkably stable oocyte-originated proteome may help save resources to accommodate the demanding needs of growing embryos. This study will advance our understanding of mammalian OET and the fundamental principles governing gene expression.
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Affiliation(s)
- Hongmei Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jia Ming
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shun Wang
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
- Hubei Key Laboratory of Computational Science, Wuhan University, Wuhan, China
| | - Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bo Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310002, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Suoqin Jin
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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18
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Baxi AB, Li J, Quach VM, Nemes P. Cell Lineage-Guided Microanalytical Mass Spectrometry Reveals Increased Energy Metabolism and Reactive Oxygen Species in the Vertebrate Organizer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548174. [PMID: 37461553 PMCID: PMC10350060 DOI: 10.1101/2023.07.07.548174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2024]
Abstract
Molecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been limited to transcripts and some proteins due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog ( X. laevis ), a popular model of development, has long been discovered to induce the patterning of the central nervous system. Molecular screens on the tissue have identified several genes, such as goosecoid, chordin, and noggin, with independent ability to establish a body axis. A comprehensive study of proteins and metabolites produced in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the rest of the embryo using liquid chromatography high-resolution mass spectrometry (HRMS). Quantification of ∼4,600 proteins and a panel of metabolites documented differential expression for ∼450 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation (OXPHOS) and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the Organizer. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO tissue. Chemical perturbation of the redox gradient affected mesoderm involution during early tissue movements of gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.
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19
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Ozadam H, Tonn T, Han CM, Segura A, Hoskins I, Rao S, Ghatpande V, Tran D, Catoe D, Salit M, Cenik C. Single-cell quantification of ribosome occupancy in early mouse development. Nature 2023:10.1038/s41586-023-06228-9. [PMID: 37344592 DOI: 10.1038/s41586-023-06228-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
Translation regulation is critical for early mammalian embryonic development1. However, previous studies had been restricted to bulk measurements2, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells.
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Affiliation(s)
- Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Crystal M Han
- Department of Mechanical Engineering, San Jose State University, San Jose, CA, USA
| | - Alia Segura
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Vighnesh Ghatpande
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Duc Tran
- Department of Chemical and Materials Engineering, San Jose State University, San Jose, CA, USA
| | - David Catoe
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
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20
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van den Berg PR, Bérenger-Currias NMLP, Budnik B, Slavov N, Semrau S. Integration of a multi-omics stem cell differentiation dataset using a dynamical model. PLoS Genet 2023; 19:e1010744. [PMID: 37167320 DOI: 10.1371/journal.pgen.1010744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/23/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023] Open
Abstract
Stem cell differentiation is a highly dynamic process involving pervasive changes in gene expression. The large majority of existing studies has characterized differentiation at the level of individual molecular profiles, such as the transcriptome or the proteome. To obtain a more comprehensive view, we measured protein, mRNA and microRNA abundance during retinoic acid-driven differentiation of mouse embryonic stem cells. We found that mRNA and protein abundance are typically only weakly correlated across time. To understand this finding, we developed a hierarchical dynamical model that allowed us to integrate all data sets. This model was able to explain mRNA-protein discordance for most genes and identified instances of potential microRNA-mediated regulation. Overexpression or depletion of microRNAs identified by the model, followed by RNA sequencing and protein quantification, were used to follow up on the predictions of the model. Overall, our study shows how multi-omics integration by a dynamical model could be used to nominate candidate regulators.
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Affiliation(s)
| | | | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, Leiden, Zuid-Holland, The Netherlands
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21
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Chen Y, Huang JH, Phong C, Ferrell JE. Protein homeostasis from diffusion-dependent control of protein synthesis and degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538146. [PMID: 37162886 PMCID: PMC10168264 DOI: 10.1101/2023.04.24.538146] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
It has been proposed that the concentration of proteins in the cytoplasm maximizes the speed of important biochemical reactions. Here we have used the Xenopus extract system, which can be diluted or concentrated to yield a range of cytoplasmic protein concentrations, to test the effect of cytoplasmic concentration on mRNA translation and protein degradation. We found that protein synthesis rates are maximal in ~1x cytoplasm, whereas protein degradation continues to rise to an optimal concentration of ~1.8x. This can be attributed to the greater sensitivity of translation to cytoplasmic viscosity, perhaps because it involves unusually large macromolecular complexes like polyribosomes. The different concentration optima sets up a negative feedback homeostatic system, where increasing the cytoplasmic protein concentration above the 1x physiological level increases the viscosity of the cytoplasm, which selectively inhibits translation and drives the system back toward the 1x set point.
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Affiliation(s)
- Yuping Chen
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
- These authors contributed equally
- Corresponding authors
| | - Jo-Hsi Huang
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
- These authors contributed equally
| | - Connie Phong
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
| | - James E. Ferrell
- Dept. of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305
- Dept. of Biochemistry, Stanford University School of Medicine, Stanford CA 94305
- Corresponding authors
- Lead contact
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22
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Sakura F, Noma K, Asano T, Tanita K, Toyofuku E, Kato K, Tsumura M, Nihira H, Izawa K, Mitsui-Sekinaka K, Konno R, Kawashima Y, Mizoguchi Y, Karakawa S, Hayakawa S, Kawaguchi H, Imai K, Nonoyama S, Yasumi T, Ohnishi H, Kanegane H, Ohara O, Okada S. A complementary approach for genetic diagnosis of inborn errors of immunity using proteogenomic analysis. PNAS NEXUS 2023; 2:pgad104. [PMID: 37077884 PMCID: PMC10109033 DOI: 10.1093/pnasnexus/pgad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Advances in next-generation sequencing technology have identified many genes responsible for inborn errors of immunity (IEI). However, there is still room for improvement in the efficiency of genetic diagnosis. Recently, RNA sequencing and proteomics using peripheral blood mononuclear cells (PBMCs) have gained attention, but only some studies have integrated these analyses in IEI. Moreover, previous proteomic studies for PBMCs have achieved limited coverage (approximately 3000 proteins). More comprehensive data are needed to gain valuable insights into the molecular mechanisms underlying IEI. Here, we propose a state-of-the-art method for diagnosing IEI using PBMCs proteomics integrated with targeted RNA sequencing (T-RNA-seq), providing unique insights into the pathogenesis of IEI. This study analyzed 70 IEI patients whose genetic etiology had not been identified by genetic analysis. In-depth proteomics identified 6498 proteins, which covered 63% of 527 genes identified in T-RNA-seq, allowing us to examine the molecular cause of IEI and immune cell defects. This integrated analysis identified the disease-causing genes in four cases undiagnosed in previous genetic studies. Three of them could be diagnosed by T-RNA-seq, while the other could only be diagnosed by proteomics. Moreover, this integrated analysis showed high protein-mRNA correlations in B- and T-cell-specific genes, and their expression profiles identified patients with immune cell dysfunction. These results indicate that integrated analysis improves the efficiency of genetic diagnosis and provides a deep understanding of the immune cell dysfunction underlying the etiology of IEI. Our novel approach demonstrates the complementary role of proteogenomic analysis in the genetic diagnosis and characterization of IEI.
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Affiliation(s)
- Fumiaki Sakura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Kosuke Noma
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Takaki Asano
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Kay Tanita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo City, Tokyo 113-0034, Japan
| | - Etsushi Toyofuku
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo City, Tokyo 113-0034, Japan
| | - Kentaro Kato
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Hiroshi Nihira
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Kazushi Izawa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Kanako Mitsui-Sekinaka
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa City, Saitama 359-8513, Japan
| | - Ryo Konno
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu City, Chiba 292-0818, Japan
| | - Yusuke Kawashima
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu City, Chiba 292-0818, Japan
| | - Yoko Mizoguchi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Shuhei Karakawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Seiichi Hayakawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Hiroshi Kawaguchi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Kohsuke Imai
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa City, Saitama 359-8513, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa City, Saitama 359-8513, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu City 501-1112, Japan
| | - Hirokazu Kanegane
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo City, Tokyo 113-0034, Japan
| | - Osamu Ohara
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu City, Chiba 292-0818, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
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23
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Ren F, Zhou Q, Meng Y, Guo W, Tang Q, Mei J. RNA binding proteins are potential novel biomarkers of egg quality in yellow catfish. BMC Genomics 2023; 24:121. [PMID: 36927412 PMCID: PMC10018890 DOI: 10.1186/s12864-023-09220-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Egg quality is a major concern in fish reproduction and development. An effective evaluation of egg quality prior to fertilization is helpful in improving the fertilization rate and survival rate of the larva. In this study, we aim to identify quality instructors from the combination study of fertilization rate, hatching rate, embryo malformation rate and gene expression profile. RESULTS Eggs from 25 female fish were fertilized with sperm from the same fish. The egg quality was determined by the fertilization rates, hatching rate and embryo malformation rate and divided into three categories, low-quality (< 35%), medium-quality (35 to 75%), and high-quality (> 75%). Due to the distinct difference in fertilization, hatching and embryo malformation rate between low-quality eggs and high-quality eggs, these two groups were considered for the identification of quality markers. Then RNA-seq was performed for the originally preserved eggs from the low-quality group and high-quality group. We profiled the differentially expressed genes and identified a group of RNA-binding proteins (RBPs) as potential regulators. Gene function analysis indicated that most of these genes were enriched in RNA-regulated pathways including RNA processing. The RBPs were more related to egg quality from the PLS-DA analysis. Finally, gene expression was validated by qRT-PCR. CONCLUSIONS We found a cluster of RBP genes including igf2bp3, zar1, elavl1, rbm25b and related regulatory factors including yy1, sirt1, anp32e, btg4 as novel biomarkers of egg quality.
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Affiliation(s)
- Fan Ren
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quan Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yinglu Meng
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjie Guo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Tang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
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24
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Ash2l, an obligatory component of H3K4 methylation complexes, regulates neural crest development. Dev Biol 2022; 492:14-24. [PMID: 36162552 DOI: 10.1016/j.ydbio.2022.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023]
Abstract
The vertebrate nervous system develops from embryonic neural plate and neural crest. Although genetic mechanisms governing vertebrate neural development have been investigated in depth, epigenetic regulation of this process remains less understood. Redundancy of epigenetic factors and early lethality of animals deficient in critical epigenetic components pose major challenges in characterization of epigenetic factors in vertebrate neural development. In this study, we use the amphibian model Xenopus laevis to investigate the roles of non-redundant, obligatory components of all histone H3K4 activating methylation complexes (COMPASS, also known as SET1/MLL complexes) in early neural development. The two genes that we focus on, Ash2l and Dpy30, regulate mesendodermal differentiation in mouse embryonic stem cells and cause early embryonic lethality when removed from mouse embryos. Using targeted knockdown of the genes in dorsal ectoderm of Xenopus that gives rise to future nervous system, we show here that ash2l and dpy30 are required for neural and neural crest marker expression in Xenopus late neurula embryos but are dispensable for early neural and neural plate border gene expression. Co-immunoprecipitation assays reveal that Dpy30 and Ash2L associate with the neural plate border transcription factors, such as Msx1 and Tfap2a. Chromatin immunoprecipitation (ChIP) assay further demonstrates that Ash2L and the H3K4me3 active histone mark accumulate at the promoter regions of the neural crest gene sox10 in a Tfap2a-dependent manner. Collectively, our data suggest that Ash2l and Dpy30 interact with specific transcription factors to recruit COMPASS complexes to the regulatory regions of neural crest specification genes to control their expression and influence development of the nervous system during vertebrate embryogenesis.
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25
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Differential nuclear import sets the timing of protein access to the embryonic genome. Nat Commun 2022; 13:5887. [PMID: 36202846 PMCID: PMC9537182 DOI: 10.1038/s41467-022-33429-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/16/2022] [Indexed: 02/02/2023] Open
Abstract
The development of a fertilized egg to an embryo requires the proper temporal control of gene expression. During cell differentiation, timing is often controlled via cascades of transcription factors (TFs). However, in early development, transcription is often inactive, and many TF levels stay constant, suggesting that alternative mechanisms govern the observed rapid and ordered onset of gene expression. Here, we find that in early embryonic development access of maternally deposited nuclear proteins to the genome is temporally ordered via importin affinities, thereby timing the expression of downstream targets. We quantify changes in the nuclear proteome during early development and find that nuclear proteins, such as TFs and RNA polymerases, enter the nucleus sequentially. Moreover, we find that the timing of nuclear proteins' access to the genome corresponds to the timing of downstream gene activation. We show that the affinity of proteins to importin is a major determinant in the timing of protein entry into embryonic nuclei. Thus, we propose a mechanism by which embryos encode the timing of gene expression in early development via biochemical affinities. This process could be critical for embryos to organize themselves before deploying the regulatory cascades that control cell identities.
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26
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Iegorova V, Naraine R, Psenicka M, Zelazowska M, Sindelka R. Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis. Front Cell Dev Biol 2022; 10:982732. [PMID: 36204678 PMCID: PMC9531136 DOI: 10.3389/fcell.2022.982732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
The oocyte is a unique cell, from which develops a complex organism comprising of germ layers, tissues and organs. In some vertebrate species it is known that the asymmetrical localization of biomolecules within the oocyte is what drives the spatial differentiation of the daughter cells required for embryogenesis. This asymmetry is first established to produce an animal-vegetal (A-V) axis which reflects the future specification of the ectoderm, mesoderm, and endoderm layers. Several pathways for localization of vegetal maternal transcripts have already been described using a few animal models. However, there is limited information about transcripts that are localized to the animal pole, even though there is accumulating evidence indicating its active establishment. Here, we performed comparative TOMO-Seq analysis on two holoblastic cleavage models: Xenopus laevis and Acipenser ruthenus oocytes during oogenesis. We found that there were many transcripts that have a temporal preference for the establishment of localization. In both models, we observed vegetal transcript gradients that were established during either the early or late oogenesis stages and transcripts that started their localization during the early stages but became more pronounced during the later stages. We found that some animal gradients were already established during the early stages, however the majority were formed during the later stages of oogenesis. Some of these temporally localized transcripts were conserved between the models, while others were species specific. Additionally, temporal de novo transcription and also degradation of transcripts within the oocyte were observed, pointing to an active remodeling of the maternal RNA pool.
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Affiliation(s)
- Viktoriia Iegorova
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Ravindra Naraine
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Martin Psenicka
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czechia
| | - Monika Zelazowska
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Radek Sindelka
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- *Correspondence: Radek Sindelka,
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27
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Huang Y, Zhou L, Hou C, Guo D. The dynamic proteome in Arabidopsis thaliana early embryogenesis. Development 2022; 149:276287. [DOI: 10.1242/dev.200715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The morphology of the flowering plant is established during early embryogenesis. In recent years, many studies have focused on transcriptional profiling in plant embryogenesis, but the dynamic landscape of the Arabidopsis thaliana proteome remains elusive. In this study, Arabidopsis embryos at 2/4-cell, 8-cell, 16-cell, 32-cell, globular and heart stages were collected for nanoproteomic analysis. In total, 5386 proteins were identified. Of these, 1051 proteins were universally identified in all developmental stages and a range of 27 to 2154 proteins was found to be stage specific. These proteins could be grouped into eight clusters according to their expression levels. Gene Ontology enrichment analysis showed that genes involved in ribosome biogenesis and auxin-activated signalling were enriched during early embryogenesis, indicating that active translation and auxin signalling are important events in Arabidopsis embryo development. Combining RNA-sequencing data with the proteomics analysis, the correlation between mRNA and protein was evaluated. An overall positive correlation was found between mRNA and protein. This work provides a comprehensive landscape of the Arabidopsis proteome in early embryogenesis. Some important proteins/transcription factors identified through network analysis may serve as potential targets for future investigation.
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Affiliation(s)
- Yingzhang Huang
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
| | - Limeng Zhou
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
| | - Chunhui Hou
- Southern University of Science and Technology 2 Department of Biology , , Shenzhen 518055 , China
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
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28
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Chen F, Ma B, Lin Y, Luo X, Xu T, Zhang Y, Chen F, Li Y, Zhang Y, Luo B, Zhang Q, Xie X. Comparative maternal protein profiling of mouse biparental and uniparental embryos. Gigascience 2022; 11:6691138. [PMID: 36056732 PMCID: PMC9440387 DOI: 10.1093/gigascience/giac084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 12/25/2022] Open
Abstract
Background Maternal proteins have important roles during early embryonic development. However, our understanding of maternal proteins is still very limited. The integrated analysis of mouse uniparental (parthenogenetic) and biparental (fertilized) embryos at the protein level creates a protein expression landscape that can be used to explore preimplantation mouse development. Results Using label-free quantitative mass spectrometry (MS) analysis, we report on the maternal proteome of mouse parthenogenetic embryos at pronucleus, 2-cell, 4-cell, 8-cell, morula, and blastocyst stages and highlight dynamic changes in protein expression. In addition, comparison of proteomic profiles of parthenogenotes and fertilized embryos highlights the different fates of maternal proteins. Enrichment analysis uncovered a set of maternal proteins that are strongly correlated with the subcortical maternal complex, and we report that in parthenogenotes, some of these maternal proteins escape the fate of protein degradation. Moreover, we identified a new maternal factor-Fbxw24, and highlight its importance in early embryonic development. We report that Fbxw24 interacts with Ddb1-Cul4b and may regulate maternal protein degradation in mouse. Conclusions Our study provides an invaluable resource for mechanistic analysis of maternal proteins and highlights the role of the novel maternal factor Fbw24 in regulating maternal protein degradation during preimplantation embryo development.
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Affiliation(s)
- Fumei Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Buguo Ma
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yongda Lin
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Tao Xu
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yuan Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Fang Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yanfei Li
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yaoyao Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Bin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Qingmei Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xiaoxun Xie
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
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29
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Liu J, Zhang X, Ta X, Luo M, Chang X, Wang H. Fecal microbiome transplantation attenuates manganese-induced neurotoxicity through regulation of the apelin signaling pathway by inhibition of autophagy in mouse brain. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113925. [PMID: 35917710 DOI: 10.1016/j.ecoenv.2022.113925] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Manganese (Mn) is a common environmental pollutant. Mn exposure can lead to neurodegenerative diseases resembling Parkinson's disease, and has become a major public health concern. However, the mechanism of Mn-induced neurotoxicity in the brain is not clear. Fecal microbiome transplantation (FMT) may alleviate the neurotoxicity of Mn exposure by remodeling the gut microbiota. In this study, MnCl2 (manganese chloride) was administered to mice as in drinking water (Mn: 200 mg/L), and fecal matter from donor mice was administered by oral gavage every other day to the recipient mice. The Mn exposure model (Mn group) and FMT model (Mn+FMT group) were established and analyzed 5 weeks post-exposure. The Wipi1 gene exhibited the most significant increase associated with Mn exposure and Mn+FMT treatment groups based on transcriptome analysis. Combined analysis of transcriptomics and proteomics demonstrated that the apelin signaling pathway is the main pathway affected by FMT during Mn exposure. Immunofluorescence and Western blot showed that the expression of key proteins (Beclin-1, LC-3B, and PINK1) associated with autophagy in the hippocampus was robustly activated in the Mn exposure group, but attenuation was observed in Mn+FMT mice, suggesting a critical role of autophagy in neurotoxicity induced by Mn exposure. Our research provides evidence for the neurotoxic effects of Mn exposure through autophagy activation and provides an underlying mechanism of FMT protection against Mn-induced neurotoxicity through regulation of the apelin signaling pathway.
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Affiliation(s)
- Jingjing Liu
- Department of Toxicology, School of Public Health, Lanzhou University, Gansu 730000, China
| | - Xin Zhang
- Department of Toxicology, School of Public Health, Lanzhou University, Gansu 730000, China
| | - Xiaojuan Ta
- Department of Pathology, Lanzhou Second People's Hospital, Gansu 730000, China
| | - Miaomiao Luo
- Department of Obstetrics, Affiliated Hospital of Yan'an University, Shaanxi 716000, China
| | - Xuhong Chang
- Department of Toxicology, School of Public Health, Lanzhou University, Gansu 730000, China
| | - Hui Wang
- Department of Toxicology, School of Public Health, Lanzhou University, Gansu 730000, China.
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30
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Giuraniuc CV, Zain S, Ghafoor S, Hoppler S. A mathematical modelling portrait of Wnt signalling in early vertebrate embryogenesis. J Theor Biol 2022; 551-552:111239. [DOI: 10.1016/j.jtbi.2022.111239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022]
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31
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Mishra S, Levy DL. Nuclear F-actin and Lamin A antagonistically modulate nuclear shape. J Cell Sci 2022; 135:275607. [PMID: 35665815 PMCID: PMC9377710 DOI: 10.1242/jcs.259692] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/28/2022] [Indexed: 12/25/2022] Open
Abstract
Nuclear shape influences cell migration, gene expression and cell cycle progression, and is altered in disease states like laminopathies and cancer. What factors and forces determine nuclear shape? We find that nuclei assembled in Xenopus egg extracts in the presence of dynamic F-actin exhibit a striking bilobed nuclear morphology with distinct membrane compositions in the two lobes and accumulation of F-actin at the inner nuclear envelope. The addition of Lamin A (encoded by lmna), which is absent from Xenopus eggs, results in rounder nuclei, suggesting that opposing nuclear F-actin and Lamin A forces contribute to the regulation of nuclear shape. Nuclear F-actin also promotes altered nuclear shape in Lamin A-knockdown HeLa cells and, in both systems, abnormal nuclear shape is driven by formins and not Arp2/3 or myosin. Although the underlying mechanisms might differ in Xenopus and HeLa cells, we propose that nuclear F-actin filaments nucleated by formins impart outward forces that lead to altered nuclear morphology unless Lamin A is present. Targeting nuclear actin dynamics might represent a novel approach to rescuing disease-associated defects in nuclear shape.
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Affiliation(s)
- Sampada Mishra
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Daniel L. Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA,Author for correspondence ()
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32
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Gorbsky GJ, Daum JR, Sapkota H, Summala K, Yoshida H, Georgescu C, Wren JD, Peshkin L, Horb ME. Developing immortal cell lines from Xenopus embryos , four novel cell lines derived from Xenopus tropicalis. Open Biol 2022; 12:220089. [PMID: 35857907 PMCID: PMC9256088 DOI: 10.1098/rsob.220089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The diploid anuran Xenopus tropicalis has emerged as a key research model in cell and developmental biology. To enhance the usefulness of this species, we developed methods for generating immortal cell lines from Nigerian strain (NXR_1018, RRID:SCR_013731) X. tropicalis embryos. We generated 14 cell lines that were propagated for several months. We selected four morphologically distinct lines, XTN-6, XTN-8, XTN-10 and XTN-12 for further characterization. Karyotype analysis revealed that three of the lines, XTN-8, XTN-10 and XTN-12 were primarily diploid. XTN-6 cultures showed a consistent mixed population of diploid cells, cells with chromosome 8 trisomy, and cells containing a tetraploid content of chromosomes. The lines were propagated using conventional culture methods as adherent cultures at 30°C in a simple, diluted L-15 medium containing fetal bovine serum without use of a high CO2 incubator. Transcriptome analysis indicated that the four lines were distinct lineages. These methods will be useful in the generation of cell lines from normal and mutant strains of X. tropicalis as well as other species of Xenopus.
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Affiliation(s)
- Gary J. Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Depatment of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - John R. Daum
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Hem Sapkota
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Katja Summala
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Hitoshi Yoshida
- National Xenopus Resource and Eugene Bell Center for Regeneration Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Constantin Georgescu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Jonathan D. Wren
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Leonid Peshkin
- National Xenopus Resource and Eugene Bell Center for Regeneration Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Marko E. Horb
- National Xenopus Resource and Eugene Bell Center for Regeneration Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
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33
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Baxi AB, Pade LR, Nemes P. Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo. J Vis Exp 2022:10.3791/63586. [PMID: 35532271 PMCID: PMC9513837 DOI: 10.3791/63586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
Characterization of molecular events as cells give rise to tissues and organs raises a potential to better understand normal development and design efficient remedies for diseases. Technologies enabling accurate identification and quantification of diverse types and large numbers of proteins would provide still missing information on molecular mechanisms orchestrating tissue and organism development in space and time. Here, we present a mass spectrometry-based protocol that enables the measurement of thousands of proteins in identified cell lineages in Xenopus laevis (frog) embryos. The approach builds on reproducible cell-fate maps and established methods to identify, fluorescently label, track, and sample cells and their progeny (clones) from this model of vertebrate development. After collecting cellular contents using microsampling or isolating cells by dissection or fluorescence-activated cell sorting, proteins are extracted and processed for bottom-up proteomic analysis. Liquid chromatography and capillary electrophoresis are used to provide scalable separation for protein detection and quantification with high-resolution mass spectrometry (HRMS). Representative examples are provided for the proteomic characterization of neural-tissue fated cells. Cell-lineage-guided HRMS proteomics is adaptable to different tissues and organisms. It is sufficiently sensitive, specific, and quantitative to peer into the spatio-temporal dynamics of the proteome during vertebrate development.
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Affiliation(s)
- Aparna B Baxi
- Department of Chemistry & Biochemistry, University of Maryland; Department of Anatomy & Cell Biology, The George Washington University
| | - Leena R Pade
- Department of Chemistry & Biochemistry, University of Maryland
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland; Department of Anatomy & Cell Biology, The George Washington University;
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34
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Passos JRS, Guerreiro DD, Otávio KS, Dos Santos-Neto PC, Souza-Neves M, Cuadro F, Nuñez-Olivera R, Crispo M, Bezerra MJB, Silva RF, Lima LF, Figueiredo JR, Bustamante-Filho IC, Menchaca A, Moura AA. Global proteomic analysis of pre-implantational ovine embryos produced in-vitro. Reprod Domest Anim 2022; 57:784-797. [PMID: 35377953 DOI: 10.1111/rda.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
The present study was conducted to characterize the major proteome of pre-implantation (D6) ovine embryos produced in vitro. COCs were aspirated from antral follicles (2-6 mm), matured and fertilized in vitro, and cultured until day six. Proteins were extracted separately from three pools of 45 embryos and separately run in SDS-PAGE. Proteins from each pool were individually subjected to in-gel digestion followed by LC-MS/MS. Three "raw. files" and protein lists were produced by Pattern Lab software but only proteins present in all three lists were used for the bioinformatics analyses. https://david.ncifcrf.govThere were 2,262 proteins identified in the 6-day old ovine embryos, including albumin, zona pellucida glycoprotein 2, 3 and 4, peptidyl arginine deiminase 6, actin cytoplasmic 1, gamma-actin 1, pyruvate kinase, heat shock protein 90 and protein disulfide isomerase, among others. Major biological processes linked to the sheep embryo proteome were translation, protein transport and protein stabilization, and molecular functions, defined as ATP binding, oxygen carrier activity and oxygen binding. There were 42 enriched functional clusters according to the 2,147 genes (UniProt database). Ten selected clusters with potential association with embryo development included translation, structural constituent of ribosomes, ribosomes, nucleosomes, structural constituent of the cytoskeleton, microtubule-based process, translation initiation factor activity, regulation of translational initiation, cell body and nucleotide biosynthetic process. The most representative KEEG pathways were ribosome, oxidative phosphorylation, glutathione metabolism, gap junction, mineral absorption, DNA replication and cGMP-PKG signaling pathway. Analyses of functional clusters clearly showed differences associated with the proteome of pre-implantation (D6) sheep embryos generated after in vitro fertilization in comparison with in vivo counterparts (Sanchez et al., 2021; https://doi.org/10.1111/rda.13897), confirming that the quality of in vitro derived blastocysts are unlike those produced in vivo. The present study portrays the first comprehensive overview of the proteome of pre-implantational ovine embryos grown in vitro.
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Affiliation(s)
- J R S Passos
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - D D Guerreiro
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - K S Otávio
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - P C Dos Santos-Neto
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - M Souza-Neves
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - F Cuadro
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - R Nuñez-Olivera
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - M Crispo
- Unidad de Biotecnología en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - M J B Bezerra
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - R F Silva
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, CE, Brazil
| | - L F Lima
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, CE, Brazil
| | - J R Figueiredo
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, CE, Brazil
| | - I C Bustamante-Filho
- Laboratório de Biotecnologia, Universidade do Vale do Taquari, Lajeado, RS, Brazil
| | - A Menchaca
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay.,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria, Montevideo, Uruguay
| | - A A Moura
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
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Jiménez A, Lu D, Kalocsay M, Berberich MJ, Balbi P, Jambhekar A, Lahav G. Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations. Mol Syst Biol 2022; 18:e10588. [PMID: 35285572 PMCID: PMC8919251 DOI: 10.15252/msb.202110588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/16/2022] [Accepted: 02/19/2022] [Indexed: 12/21/2022] Open
Affiliation(s)
- Alba Jiménez
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Dan Lu
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Marian Kalocsay
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Laboratory of Systems Pharmacology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Matthew J Berberich
- Laboratory of Systems Pharmacology Blavatnik Institute at Harvard Medical School Boston MA USA
- Center for Protein Degradation Dana‐Farber Cancer Institute Boston MA USA
| | - Petra Balbi
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Ashwini Jambhekar
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Ludwig Center at Harvard Medical School Boston MA USA
| | - Galit Lahav
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Ludwig Center at Harvard Medical School Boston MA USA
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36
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Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
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37
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Zhao LW, Zhu YZ, Wu YW, Pi SB, Shen L, Fan HY. Nuclear poly(A) binding protein 1 (PABPN1) mediates zygotic genome activation-dependent maternal mRNA clearance during mouse early embryonic development. Nucleic Acids Res 2021; 50:458-472. [PMID: 34904664 PMCID: PMC8855302 DOI: 10.1093/nar/gkab1213] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
An embryo starts its life with maternal mRNA clearance, which is crucial for embryonic development. The elimination of maternal transcripts occurs by the joint action of two pathways: the maternally encoded mRNA decay pathway (M-decay) and the zygotic genome activation (ZGA)-dependent pathway (Z-decay). However, zygotic factors triggering maternal mRNA decay in early mammalian embryos remain largely unknown. In this study, we identified the zygotically encoded nuclear poly(A) binding protein 1 (PABPN1) as a factor required for maternal mRNA turnover, with a previously undescribed cytoplasmic function. Cytoplasmic PABPN1 docks on 3'-uridylated transcripts, downstream of terminal uridylyl transferases TUT4 and TUT7, and recruits 3'-5' exoribonuclease DIS3L2 to its targets, facilitating maternal mRNA decay. Pabpn1-knockout in mice resulted in preimplantation stage mortality due to early developmental arrest at the morula stage. Maternal mRNAs to be eliminated via the Z-decay pathway failed to be removed from Pabpn1-depleted embryos. Furthermore, PABPN1-mediated Z-decay is essential for major ZGA and regulates the expression of cell fate-determining factors in mouse preimplantation embryos. This study revealed an unforeseen cytoplasmic function of PABPN1 coupled with early embryonic development, characterized the presence of a zygotic destabilizer of maternal mRNA, and elucidated the Z-decay process mechanisms, which potentially contribute to human fertility.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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Ciardo D, Haccard O, Narassimprakash H, Cornu D, Guerrera IC, Goldar A, Marheineke K. Polo-like kinase 1 (Plk1) regulates DNA replication origin firing and interacts with Rif1 in Xenopus. Nucleic Acids Res 2021; 49:9851-9869. [PMID: 34469577 PMCID: PMC8464078 DOI: 10.1093/nar/gkab756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
The activation of eukaryotic DNA replication origins needs to be strictly controlled at multiple steps in order to faithfully duplicate the genome and to maintain its stability. How the checkpoint recovery and adaptation protein Polo-like kinase 1 (Plk1) regulates the firing of replication origins during non-challenged S phase remained an open question. Using DNA fiber analysis, we show that immunodepletion of Plk1 in the Xenopus in vitro system decreases replication fork density and initiation frequency. Numerical analyses suggest that Plk1 reduces the overall probability and synchrony of origin firing. We used quantitative chromatin proteomics and co-immunoprecipitations to demonstrate that Plk1 interacts with firing factors MTBP/Treslin/TopBP1 as well as with Rif1, a known regulator of replication timing. Phosphopeptide analysis by LC/MS/MS shows that the C-terminal domain of Rif1, which is necessary for its repressive action on origins through protein phosphatase 1 (PP1), can be phosphorylated in vitro by Plk1 on S2058 in its PP1 binding site. The phosphomimetic S2058D mutant interrupts the Rif1-PP1 interaction and modulates DNA replication. Collectively, our study provides molecular insights into how Plk1 regulates the spatio-temporal replication program and suggests that Plk1 controls origin activation at the level of large chromatin domains in vertebrates.
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Affiliation(s)
- Diletta Ciardo
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Olivier Haccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Hemalatha Narassimprakash
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - David Cornu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Ida Chiara Guerrera
- Proteomics platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris 75015, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kathrin Marheineke
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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39
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Slater PG, Palacios M, Larraín J. Xenopus, a Model to Study Wound Healing and Regeneration: Experimental Approaches. Cold Spring Harb Protoc 2021; 2021:pdb.top100966. [PMID: 33782095 DOI: 10.1101/pdb.top100966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Xenopus has been widely used as a model organism to study wound healing and regeneration. During early development and at tadpole stages, Xenopus is a quick healer and is able to regenerate multiple complex organs-abilities that decrease with the progression of metamorphosis. This unique capacity leads us to question which mechanisms allow and direct regeneration at stages before the beginning of metamorphosis and which ones are responsible for the loss of regenerative capacities during later stages. Xenopus is an ideal model to study regeneration and has contributed to the understanding of morphological, cellular, and molecular mechanisms involved in these processes. Nevertheless, there is still much to learn. Here we provide an overview on using Xenopus as a model organism to study regeneration and introduce protocols that can be used for studying wound healing and regeneration at multiple levels, thus enhancing our understanding of these phenomena.
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Affiliation(s)
- Paula G Slater
- Center for Aging and Regeneration, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago de Chile, Chile 7820436
| | - Miriam Palacios
- Center for Aging and Regeneration, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago de Chile, Chile 7820436
| | - Juan Larraín
- Center for Aging and Regeneration, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago de Chile, Chile 7820436
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40
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Neiers F, Saliou JM, Briand L, Robichon A. Adaptive Variation of Buchnera Endosymbiont Density in Aphid Host Acyrthosiphon pisum Controlled by Environmental Conditions. ACS OMEGA 2021; 6:17902-17914. [PMID: 34308025 PMCID: PMC8296009 DOI: 10.1021/acsomega.1c01465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The scarcity of transcriptional regulatory genes in Buchnera aphidicola, an obligate endosymbiont in aphids, suggests the stability of expressed gene patterns and metabolic pathways. This observation argues in favor of the hypothesis that this endosymbiont bacteria might contribute little to the host adaptation when aphid hosts are facing challenging fluctuating environment. Finding evidence for the increased expression or silenced genes involved in metabolic pathways under the pressure of stress conditions and/or a given environment has been challenging for experimenters with this bacterial symbiotic model. Transcriptomic data have shown that Buchnera gene expression changes are confined to a narrow range when the aphids face brutal environmental variations. In this report, we demonstrate that instead of manipulating individual genes, the conditions may act on the relative mass of endosymbiont corresponding to the needs of the host. The control of the fluctuating number of endosymbiont cells per individual host appears to be an unexpected regulatory modality that contributes to the adaptation of aphids to their environment. This feature may account for the success of the symbiotic advantages in overcoming the drastic changes in temperature and food supplies during evolution.
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Affiliation(s)
- Fabrice Neiers
- Centre des Sciences
du Goût et de l’Alimentation (CSGA), Université de Bourgogne-Franche Comté, CNRS, INRA, 21000 Dijon, France
| | - Jean-Michel Saliou
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, US 41—UMS 2014—PLBS, F-59000 Lille, France
| | - Loïc Briand
- Centre des Sciences
du Goût et de l’Alimentation (CSGA), Université de Bourgogne-Franche Comté, CNRS, INRA, 21000 Dijon, France
| | - Alain Robichon
- ISA, Université Côte
dʼAzur, INRA, CNRS, 06903 Sophia Antipolis, France
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41
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Blitz IL, Nakayama T. CRISPR-Cas9 Mutagenesis in Xenopus tropicalis for Phenotypic Analyses in the F 0 Generation and Beyond. Cold Spring Harb Protoc 2021; 2022:pdb.prot106971. [PMID: 34244352 DOI: 10.1101/pdb.prot106971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas9 mutagenesis is being widely used to create targeted loss-of-function mutations in the diploid frog Xenopus tropicalis Here we describe a simple mutagenesis protocol using microinjection of Cas9 protein or mRNA, together with synthetic guide RNAs (sgRNAs) targeting specific DNA sequences, into the early embryo. Cas9-catalyzed double-strand breaks undergo error-prone repair, resulting in production of short insertions and/or deletions. Thus, careful selection of target sites can lead to mutations that impair normal function of the protein product. CRISPR-Cas9 can be used to create either mosaic loss-of-function Xenopus embryos that display F0 generation phenotypes or mutant lines for downstream analysis. In addition to describing how to mutagenize genes using CRISPR-Cas9, we also discuss a simple method to determine the mutagenesis efficiency, some potential problems that can arise, and possible solutions to overcome them. The protocol described here should be applicable to other amphibians and, in principle, many other organisms.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA
| | - Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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42
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Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1644. [PMID: 33565275 PMCID: PMC8647923 DOI: 10.1002/wrna.1644] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Regulation of protein synthesis is a vital step in controlling gene expression, especially during development. Over the last 10 years, it has become clear that rather than being homogeneous machines responsible for mRNA translation, ribosomes are highly heterogeneous and can play an active part in translational regulation. These "specialized ribosomes" comprise of specific protein and/or rRNA components, which are required for the translation of particular mRNAs. However, while there is extensive evidence for ribosome heterogeneity, support for specialized functions is limited. Recent work in a variety of developmental model organisms has shed some light on the biological relevance of ribosome heterogeneity. Tissue-specific expression of ribosomal components along with phenotypic analysis of ribosomal gene mutations indicate that ribosome heterogeneity and potentially specialization are common in key development processes like embryogenesis, spermatogenesis, oogenesis, body patterning, and neurogenesis. Several examples of ribosome specialization have now been proposed but strong links between ribosome heterogeneity, translation of specific mRNAs by defined mechanisms, and role of these translation events remain elusive. Furthermore, several studies have indicated that heterogeneous ribosome populations are a product of tissue-specific expression rather than specialized function and that ribosomal protein phenotypes are the result of extra-ribosomal function or overall reduced ribosome levels. Many important questions still need to be addressed in order to determine the functional importance of ribosome heterogeneity to development and disease, which is likely to vary across systems. It will be essential to dissect these issues to fully understand diseases caused by disruptions to ribosomal composition, such as ribosomopathies. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Structure/Function RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Karl Norris
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Julie Louise Aspden
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
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43
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Philpott A. The Use of Xenopus for Cell Biology Applications. Cold Spring Harb Protoc 2021; 2021:pdb.top105528. [PMID: 33782096 DOI: 10.1101/pdb.top105528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Problems of cell biology and the molecular controls underpinning them have been studied in the remarkably versatile Xenopus systems for many years. This versatility is showcased in several accompanying protocols, which are introduced here. One protocol demonstrates how the Xenopus embryonic ectoderm can be used to study the effects of mechanical cell deformation; another illustrates how the developing eye can be used as a platform for determining cell-cycle length. Two protocols show how extracts from Xenopus embryos can be exploited to characterize the behavior of specific intracellular proteins-specifically, to determine protein phosphorylation status and the ability to bind to chromatin. Finally, because specific antibodies to Xenopus proteins are pivotal reagents for cell biology and biochemistry applications, four protocols describing how to generate, purify, and assay the specificity of antibodies raised against Xenopus proteins are included in hopes of stimulating the expansion of these critical resources across the Xenopus community.
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Affiliation(s)
- Anna Philpott
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom; .,Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, CB2 0AW, United Kingdom
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44
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Baxi AB, Pade LR, Nemes P. Mass spectrometry based proteomics for developmental neurobiology in the amphibian Xenopus laevis. Curr Top Dev Biol 2021; 145:205-231. [PMID: 34074530 PMCID: PMC8314003 DOI: 10.1016/bs.ctdb.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The South African clawed frog (Xenopus laevis), a prominent vertebrate model in cell and developmental biology, has been instrumental in studying molecular mechanisms of neural development and disease. Recently, high-resolution mass spectrometry (HRMS), a bioanalytical technology, has expanded the molecular toolbox of protein detection and characterization (proteomics). This chapter overviews the characteristics, advantages, and challenges of this biological model and technology. Discussions are offered on their combined use to aid studies on cell differentiation and development of neural tissues. Finally, the emerging integration of proteomics and other 'omic technologies is reflected on to generate new knowledge, drive and test new hypotheses, and ultimately, advance the understanding of neural development during states of health and disease.
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Affiliation(s)
- Aparna B Baxi
- Department of Chemistry & Biochemistry, University of Maryland, College Park, College Park, MD, United States; Department of Anatomy and Cell Biology, The George Washington University, Washington, DC, United States
| | - Leena R Pade
- Department of Chemistry & Biochemistry, University of Maryland, College Park, College Park, MD, United States
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, College Park, MD, United States; Department of Anatomy and Cell Biology, The George Washington University, Washington, DC, United States.
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45
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Modeling the role for nuclear import dynamics in the early embryonic cell cycle. Biophys J 2021; 120:4277-4286. [PMID: 34022240 DOI: 10.1016/j.bpj.2021.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 11/21/2022] Open
Abstract
Nuclear composition determines nuclear function. The early embryos of many species begin life with large pools of maternally provided components that become rapidly imported into an increasing number of nuclei as the cells undergo repeated cleavage divisions. Because early cell cycles are too fast for nuclei to achieve steady-state nucleocytoplasmic partitioning, the composition of cleavage stage nuclei is likely dominated by nuclear import. The end of the rapid cleavage stage and onset of major zygotic transcription, known as the mid-blastula transition (MBT), is controlled by the ratio of nuclei/cytoplasm, indicating that changes in nuclear composition likely mediate MBT timing. Here, we explore how different nuclear import regimes can affect protein accumulation in the nucleus in the early Drosophila embryo. We find that nuclear import differs dramatically for a general nuclear cargo (NLS (nuclear localization signal)-mRFP) and a proposed MBT regulator (histone H3). We show that nuclear import rates of NLS-mRFP in a given nucleus remain relatively unchanged throughout the cleavage cycles, whereas those of H3 halve with each cycle. We model these two distinct modes of nuclear import as "nucleus-limited" and "import-limited" and examine how the two different modes can contribute to different protein accumulation dynamics. Finally, we incorporate these distinct modes of nuclear import into a model for cell-cycle regulation at the MBT and find that the import-limited H3 dynamics contribute to increased robustness and allow for stepwise cell-cycle slowing at the MBT.
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46
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Yilmaz O, Patinote A, Com E, Pineau C, Bobe J. Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs. BMC Genomics 2021; 22:308. [PMID: 33910518 PMCID: PMC8082894 DOI: 10.1186/s12864-021-07606-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND We previously reported the results of CRISPR/Cas9 knock-out (KO) of type-I and type-III vitellogenins (Vtgs) in zebrafish, which provided the first experimental evidence on essentiality and disparate functioning of Vtgs at different stages during early development. However, the specific contributions of different types of Vtg to major cellular processes remained to be investigated. The present study employed liquid chromatography and tandem mass spectrometry (LC-MS/MS) to meet this deficit. Proteomic profiles of zebrafish eggs lacking three type-I Vtgs simultaneously (vtg1-KO), or lacking only type III Vtg (vtg3-KO) were compared to those of wild type (Wt) eggs. Obtained spectra were searched against a zebrafish proteome database and identified proteins were quantified based on normalized spectral counts. RESULTS The vtg-KO caused severe changes in the proteome of 1-cell stage zebrafish eggs. These changes were disclosed by molecular signatures that highly resembled the proteomic phenotype of poor quality zebrafish eggs reported in our prior studies. Proteomic profiles of vtg-KO eggs and perturbations in abundances of hundreds of proteins revealed unique, noncompensable contributions of multiple Vtgs to protein and in energy homeostasis. The lack of this contribution appears to have a significant impact on endoplasmic reticulum and mitochondrial functions, and thus embryonic development, even after zygotic genome activation. Increased endoplasmic reticulum stress, Redox/Detox activities, glycolysis/gluconeogenesis, enrichment in cellular proliferation and in human neurodegenerative disease related activities in both vtg1- and vtg3-KO eggs were found to be indicators of the aforementioned conditions. Distinctive increase in apoptosis and Parkinson disease pathways, as well as the decrease in lipid metabolism related activities in vtg3-KO eggs implies compelling roles of Vtg3, the least abundant form of Vtgs in vertebrate eggs, in mitochondrial activities. Several differentially abundant proteins representing the altered molecular mechanisms have been identified as strong candidate markers for studying the details of these mechanisms during early embryonic development in zebrafish and possibly other vertebrates. CONCLUSIONS These findings indicate that the global egg proteome is subject to extensive modification depending on the presence or absence of specific Vtgs and that these modifications can have a major impact on developmental competence.
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Affiliation(s)
- Ozlem Yilmaz
- INRAE, LPGP, 35000, Rennes, France.
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway.
| | | | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset-UMR_S 1085, F-35042, Rennes cedex, France
- Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset-UMR_S 1085, F-35042, Rennes cedex, France
- Protim, Univ Rennes, F-35042, Rennes cedex, France
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47
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Cao WX, Kabelitz S, Gupta M, Yeung E, Lin S, Rammelt C, Ihling C, Pekovic F, Low TCH, Siddiqui NU, Cheng MHK, Angers S, Smibert CA, Wühr M, Wahle E, Lipshitz HD. Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition. Cell Rep 2021; 31:107783. [PMID: 32579915 PMCID: PMC7372737 DOI: 10.1016/j.celrep.2020.107783] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/06/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
In animal embryos, the maternal-to-zygotic transition (MZT) hands developmental control from maternal to zygotic gene products. We show that the maternal proteome represents more than half of the protein-coding capacity of Drosophila melanogaster’s genome, and that 2% of this proteome is rapidly degraded during the MZT. Cleared proteins include the post-transcriptional repressors Cup, Trailer hitch (TRAL), Maternal expression at 31B (ME31B), and Smaug (SMG). Although the ubiquitin-proteasome system is necessary for clearance of these repressors, distinct E3 ligase complexes target them: the C-terminal to Lis1 Homology (CTLH) complex targets Cup, TRAL, and ME31B for degradation early in the MZT and the Skp/Cullin/F-box-containing (SCF) complex targets SMG at the end of the MZT. Deleting the C-terminal 233 amino acids of SMG abrogates F-box protein interaction and confers immunity to degradation. Persistent SMG downregulates zygotic re-expression of mRNAs whose maternal contribution is degraded by SMG. Thus, clearance of SMG permits an orderly MZT. Cao et al. show that 2% of the proteome is degraded in early Drosophila embryos, including a repressive ribonucleoprotein complex. Two E3 ubiquitin ligases separately act on distinct components of this complex to phase their clearance. Failure to degrade a key component, the Smaug RNA-binding protein, disrupts an orderly maternal-to-zygotic transition.
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Affiliation(s)
- Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sarah Kabelitz
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Meera Gupta
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Eyan Yeung
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Sichun Lin
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Christian Ihling
- Institute of Pharmacy and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Filip Pekovic
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Timothy C H Low
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Najeeb U Siddiqui
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Matthew H K Cheng
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Martin Wühr
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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48
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Na Y, Kim H, Choi Y, Shin S, Jung JH, Kwon SC, Kim VN, Kim JS. FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo. Nucleic Acids Res 2021; 49:e28. [PMID: 33332543 PMCID: PMC7968992 DOI: 10.1093/nar/gkaa1194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/11/2020] [Accepted: 11/24/2020] [Indexed: 02/05/2023] Open
Abstract
RNA-protein interaction is central to post-transcriptional gene regulation. Identification of RNA-binding proteins relies mainly on UV-induced crosslinking (UVX) followed by the enrichment of RNA-protein conjugates and LC-MS/MS analysis. However, UVX has limited applicability in tissues of multicellular organisms due to its low penetration depth. Here, we introduce formaldehyde crosslinking (FAX) as an alternative chemical crosslinking for RNA interactome capture (RIC). Mild FAX captures RNA-protein interaction with high specificity and efficiency in cell culture. Unlike UVX-RIC, FAX-RIC robustly detects proteins that bind to structured RNAs or uracil-poor RNAs (e.g. AGO1, STAU1, UPF1, NCBP2, EIF4E, YTHDF proteins and PABP), broadening the coverage. Applied to Xenopus laevis oocytes and embryos, FAX-RIC provided comprehensive and unbiased RNA interactome, revealing dynamic remodeling of RNA-protein complexes. Notably, translation machinery changes during oocyte-to-embryo transition, for instance, from canonical eIF4E to noncanonical eIF4E3. Furthermore, using Mus musculus liver, we demonstrate that FAX-RIC is applicable to mammalian tissue samples. Taken together, we report that FAX can extend the RNA interactome profiling into multicellular organisms.
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Affiliation(s)
- Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae Hun Jung
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - S Chul Kwon
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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49
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Exner CRT, Willsey HR. Xenopus leads the way: Frogs as a pioneering model to understand the human brain. Genesis 2021; 59:e23405. [PMID: 33369095 PMCID: PMC8130472 DOI: 10.1002/dvg.23405] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022]
Abstract
From its long history in the field of embryology to its recent advances in genetics, Xenopus has been an indispensable model for understanding the human brain. Foundational studies that gave us our first insights into major embryonic patterning events serve as a crucial backdrop for newer avenues of investigation into organogenesis and organ function. The vast array of tools available in Xenopus laevis and Xenopus tropicalis allows interrogation of developmental phenomena at all levels, from the molecular to the behavioral, and the application of CRISPR technology has enabled the investigation of human disorder risk genes in a higher-throughput manner. As the only major tetrapod model in which all developmental stages are easily manipulated and observed, frogs provide the unique opportunity to study organ development from the earliest stages. All of these features make Xenopus a premier model for studying the development of the brain, a notoriously complex process that demands an understanding of all stages from fertilization to organogenesis and beyond. Importantly, core processes of brain development are conserved between Xenopus and human, underlining the advantages of this model. This review begins by summarizing discoveries made in amphibians that form the cornerstones of vertebrate neurodevelopmental biology and goes on to discuss recent advances that have catapulted our understanding of brain development in Xenopus and in relation to human development and disease. As we engage in a new era of patient-driven gene discovery, Xenopus offers exceptional potential to uncover conserved biology underlying human brain disorders and move towards rational drug design.
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Affiliation(s)
- Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143, USA
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50
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Kakebeen AD, Huebner RJ, Shindo A, Kwon K, Kwon T, Wills AE, Wallingford JB. A temporally resolved transcriptome for developing "Keller" explants of the Xenopus laevis dorsal marginal zone. Dev Dyn 2021; 250:717-731. [PMID: 33368695 DOI: 10.1002/dvdy.289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Explanted tissues from vertebrate embryos reliably develop in culture and have provided essential paradigms for understanding embryogenesis, from early embryological investigations of induction, to the extensive study of Xenopus animal caps, to the current studies of mammalian gastruloids. Cultured explants of the Xenopus dorsal marginal zone ("Keller" explants) serve as a central paradigm for studies of convergent extension cell movements, yet we know little about the global patterns of gene expression in these explants. RESULTS In an effort to more thoroughly develop this important model system, we provide here a time-resolved bulk transcriptome for developing Keller explants. CONCLUSIONS The dataset reported here provides a useful resource for those using Keller explants for studies of morphogenesis and provide genome-scale insights into the temporal patterns of gene expression in an important tissue when explanted and grown in culture.
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Affiliation(s)
- Anneke D Kakebeen
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Robert J Huebner
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
| | - Asako Shindo
- Division of Biological Science, Nagoya University, Nagoya, Japan
| | - Kujin Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, (UNIST), Ulsan, Republic of Korea
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, (UNIST), Ulsan, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Andrea E Wills
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
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