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Mulas C, Stammers M, Salomaa SI, Heinzen C, Suter DM, Smith A, Chalut KJ. ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition. Development 2024; 151:dev203106. [PMID: 39069943 DOI: 10.1242/dev.203106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 07/30/2024]
Abstract
Naïve epiblast cells in the embryo and pluripotent stem cells in vitro undergo developmental progression to a formative state competent for lineage specification. During this transition, transcription factors and chromatin are rewired to encode new functional features. Here, we examine the role of mitogen-activated protein kinase (ERK1/2) signalling in pluripotent state transition. We show that a primary consequence of ERK activation in mouse embryonic stem cells is elimination of Nanog, which precipitates breakdown of the naïve state gene regulatory network. Variability in pERK dynamics results in heterogeneous loss of Nanog and metachronous state transition. Knockdown of Nanog allows exit without ERK activation. However, transition to formative pluripotency does not proceed and cells collapse to an indeterminate identity. This outcome is due to failure to maintain expression of the central pluripotency factor Oct4. Thus, during formative transition ERK signalling both dismantles the naïve state and preserves pluripotency. These results illustrate how a single signalling pathway can both initiate and secure transition between cell states.
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Affiliation(s)
- Carla Mulas
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Randall Centre for Cell and Molecular Biology, King's College London, London SE1 1YR, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
| | - Melanie Stammers
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Siiri I Salomaa
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
| | - Constanze Heinzen
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt 60439, Germany
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Austin Smith
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Kevin J Chalut
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
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Ascensao JA, Denk J, Lok K, Yu Q, Wetmore KM, Hallatschek O. Rediversification following ecotype isolation reveals hidden adaptive potential. Curr Biol 2024; 34:855-867.e6. [PMID: 38325377 PMCID: PMC10911448 DOI: 10.1016/j.cub.2024.01.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/09/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about whether communities can regenerate ecological diversity following ecotype removal or extinction and how the rediversified communities would compare to the original ones. Here, we show that simple two-ecotype communities from the E. coli long-term evolution experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different from the original community in ways relevant to the mechanism of ecotype coexistence-for example, in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, although the rediversified community showed unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species where there are even more potential niches, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.
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Affiliation(s)
- Joao A Ascensao
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Jonas Denk
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Kristen Lok
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Present affiliation: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - QinQin Yu
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Present affiliation: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Oskar Hallatschek
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
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Pavlou A, Cinquemani E, Geiselmann J, de Jong H. Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity. Biophys J 2022; 121:4179-4188. [PMID: 36146937 PMCID: PMC9675035 DOI: 10.1016/j.bpj.2022.09.021] [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: 11/23/2021] [Revised: 06/13/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
Fluorescent proteins (FPs) are a powerful tool to quantitatively monitor gene expression. The dynamics of a promoter and its regulation can be inferred from fluorescence data. The interpretation of fluorescent data, however, is strongly dependent on the maturation of FPs since different proteins mature in distinct ways. We propose a novel approach for analyzing fluorescent reporter data by incorporating maturation dynamics in the reconstruction of promoter activities. Our approach consists of developing and calibrating mechanistic maturation models for distinct FPs. These models are then used alongside a Bayesian approach to estimate promoter activities from fluorescence data. We demonstrate by means of targeted experiments in Escherichia coli that our approach provides robust estimates and that accounting for maturation is, in many cases, essential for the interpretation of gene expression data.
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Affiliation(s)
- Antrea Pavlou
- University Grenoble Alpes, Inria, Grenoble, France; University Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | | | - Johannes Geiselmann
- University Grenoble Alpes, Inria, Grenoble, France; University Grenoble Alpes, CNRS, LIPhy, Grenoble, France.
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Huang Y, Jin M, Yan W, Wu Q, Niu Y, Zou C, Jia C, Chang Z, Huang J, Jiang D, Gao H. A point mutant in the promoter of transglutaminase gene dramatically increased yield of microbial transglutaminase from Streptomyces mobaraensis TX1. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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WellInverter: a web application for the analysis of fluorescent reporter gene data. BMC Bioinformatics 2019; 20:309. [PMID: 31185910 PMCID: PMC6558888 DOI: 10.1186/s12859-019-2920-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
Background Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly parallelized way. The extraction of useful information from the resulting large amounts of data is not easy to achieve, because the fluorescence and absorbance measurements are only indirectly related to promoter activities and protein concentrations, requiring mathematical models of the expression of reporter genes for their interpretation. Although the principles of the analysis of reporter gene data are well-established today, there is a lack of general-purpose bioinformatics tools based on generic measurement models and sound inference procedures. This has motivated the development of WellInverter, a web application based on well-known methods for regularized linear inversion. Results We present a new version of WellInverter that considerably improves the performance and usability of the original application. In particular, we have put in place a parallel computing architecture with a load balancer to distribute analysis queries over several back-end servers, we have completely redesigned the graphical user interface to better support the different analysis steps, and we have developed a plug-in system for the parsing of data files produced by microplate readers from different manufacturers. We illustrate the functioning of WellInverter by analyzing data of the expression of a fluorescent reporter gene controlled by a phage promoter in growing Escherichia coli populations. We show that the expression pattern in different growth media, supporting different growth rates, corresponds to the pattern expected for a constitutive gene. Conclusions The new version of WellInverter is a robust, easy-to-use and scalable web application, which has been deployed on two publicly accessible web servers and which can also be installed locally. A demo version of the application with two sample datasets is available on-line. Electronic supplementary material The online version of this article (10.1186/s12859-019-2920-4) contains supplementary material, which is available to authorized users.
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Vogel S, Schäfer C, Hess S, Folz-Donahue K, Nelles M, Minassian A, Schwarz MK, Kukat C, Ehrlich M, Zaehres H, Kloppenburg P, Hoehn M, Aswendt M. The in vivo timeline of differentiation of engrafted human neural progenitor cells. Stem Cell Res 2019; 37:101429. [DOI: 10.1016/j.scr.2019.101429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/18/2019] [Accepted: 03/22/2019] [Indexed: 01/19/2023] Open
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Maury J, Kannan S, Jensen NB, Öberg FK, Kildegaard KR, Forster J, Nielsen J, Workman CT, Borodina I. Glucose-Dependent Promoters for Dynamic Regulation of Metabolic Pathways. Front Bioeng Biotechnol 2018; 6:63. [PMID: 29872655 PMCID: PMC5972318 DOI: 10.3389/fbioe.2018.00063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/30/2018] [Indexed: 11/13/2022] Open
Abstract
For an industrial fermentation process, it can be advantageous to decouple cell growth from product formation. This decoupling would allow for the rapid accumulation of biomass without inhibition from product formation, after which the fermentation can be switched to a mode where cells would grow minimally and primarily act as catalysts to convert substrate into desired product. The switch in fermentation mode should preferably be accomplished without the addition of expensive inducers. A common cell factory Saccharomyces cerevisiae is a Crabtree-positive yeast and is typically fermented at industrial scale under glucose-limited conditions to avoid the formation of ethanol. In this work, we aimed to identify and characterize promoters that depend on glucose concentration for use as dynamic control elements. Through analysis of mRNA data of S. cerevisiae grown in chemostats under glucose excess or limitation, we identified 34 candidate promoters that strongly responded to glucose presence or absence. These promoters were characterized in small-scale batch and fed-batch cultivations using a quickly maturing rapidly degrading green fluorescent protein yEGFP3-Cln2PEST as a reporter. Expressing 3-hydroxypropionic acid (3HP) pathway from a set of selected regulated promoters allowed for suppression of 3HP production during glucose-excess phase of a batch cultivation with subsequent activation in glucose-limiting conditions. Regulating the 3HP pathway by the ICL1 promoter resulted in 70% improvement of 3HP titer in comparison to PGK1 promoter.
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Affiliation(s)
- Jérôme Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Soumya Kannan
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Niels B Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Fredrik K Öberg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kanchana R Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Jochen Forster
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Irina Borodina
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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