1
|
Hong J, He H, Xu Y, Wang S, Luo C. An integrative temperature-controlled microfluidic system for budding yeast heat shock response analysis at the single-cell level. LAB ON A CHIP 2024; 24:3658-3667. [PMID: 38915274 DOI: 10.1039/d4lc00313f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cells can respond and adapt to complex forms of environmental change. Budding yeast is widely used as a model system for these stress response studies. In these studies, the precise control of the environment with high temporal resolution is most important. However, there is a lack of single-cell research platforms that enable precise control of the temperature and form of cell growth. This has hindered our understanding of cellular coping strategies in the face of diverse forms of temperature change. Here, we developed a novel temperature-controlled microfluidic platform that integrates a microheater (using liquid metal) and a thermocouple (liquid metal vs. conductive PDMS) on a chip. Three forms of temperature changes (step, gradient, and periodical oscillations) were realized by automated equipment. The platform has the advantages of low cost and a simple fabrication process. Moreover, we investigated the nuclear entry and exit behaviors of the transcription factor Msn2 in yeast in response to heat stress (37 °C) with different heating modes. The feasibility of this temperature-controlled platform for studying the protein dynamic behavior of yeast cells was demonstrated.
Collapse
Affiliation(s)
- Jie Hong
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Hao He
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Yinjia Xu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
| | - Shujing Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| |
Collapse
|
2
|
Nambiar A, Dubinkina V, Liu S, Maslov S. FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi. PLoS Comput Biol 2023; 19:e1011563. [PMID: 37971967 PMCID: PMC10653424 DOI: 10.1371/journal.pcbi.1011563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 09/30/2023] [Indexed: 11/19/2023] Open
Abstract
mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE-a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.
Collapse
Affiliation(s)
- Ananthan Nambiar
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
| | - Veronika Dubinkina
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, California, United States of America
| | - Simon Liu
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Sergei Maslov
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, United States of America
| |
Collapse
|
3
|
Hahn L, Walczak AM, Mora T. Dynamical Information Synergy in Biochemical Signaling Networks. PHYSICAL REVIEW LETTERS 2023; 131:128401. [PMID: 37802943 DOI: 10.1103/physrevlett.131.128401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/28/2023] [Indexed: 10/08/2023]
Abstract
Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules, rather than just their instantaneous concentrations. Here, we analytically calculate the information contained in these dynamics for a number of paradigmatic cases in the linear regime, for both static and time-dependent input signals. When considering oscillatory output dynamics, we report on the emergence of synergy between successive measurements, meaning that the joint information in two measurements exceeds the sum of the individual information. We extend our analysis numerically beyond the scope of linear input encoding to reveal synergetic effects in the cases of frequency or damping modulation, both of which are relevant to classical biochemical signaling systems.
Collapse
Affiliation(s)
- Lauritz Hahn
- Laboratoire de Physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, Paris, France
| |
Collapse
|
4
|
Sarkar S, Rammohan J. Nearly maximal information gain due to time integration in central dogma reactions. iScience 2023; 26:106767. [PMID: 37235057 PMCID: PMC10206154 DOI: 10.1016/j.isci.2023.106767] [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: 09/27/2022] [Revised: 02/21/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Living cells process information about their environment through the central dogma processes of transcription and translation, which drive the cellular response to stimuli. Here, we study the transfer of information from environmental input to the transcript and protein expression levels. Evaluation of both experimental and analogous simulation data reveals that transcription and translation are not two simple information channels connected in series. Instead, we demonstrate that the central dogma reactions often create a time-integrating information channel, where the translation channel receives and integrates multiple outputs from the transcription channel. This information channel model of the central dogma provides new information-theoretic selection criteria for the central dogma rate constants. Using the data for four well-studied species we show that their central dogma rate constants achieve information gain because of time integration while also keeping the loss because of stochasticity in translation relatively low (<0.5 bits).
Collapse
Affiliation(s)
- Swarnavo Sarkar
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jayan Rammohan
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| |
Collapse
|
5
|
Jeknić S, Kudo T, Song JJ, Covert MW. An optimized reporter of the transcription factor hypoxia-inducible factor 1α reveals complex HIF-1α activation dynamics in single cells. J Biol Chem 2023; 299:104599. [PMID: 36907438 PMCID: PMC10124923 DOI: 10.1016/j.jbc.2023.104599] [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: 10/18/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 03/13/2023] Open
Abstract
Immune cells adopt a variety of metabolic states to support their many biological functions, which include fighting pathogens, removing tissue debris, and tissue remodeling. One of the key mediators of these metabolic changes is the transcription factor hypoxia-inducible factor 1α (HIF-1α). Single-cell dynamics have been shown to be an important determinant of cell behavior; however, despite the importance of HIF-1α, little is known about its single-cell dynamics or their effect on metabolism. To address this knowledge gap, here we optimized a HIF-1α fluorescent reporter and applied it to study single-cell dynamics. First, we showed that single cells are likely able to differentiate multiple levels of prolyl hydroxylase inhibition, a marker of metabolic change, via HIF-1α activity. We then applied a physiological stimulus known to trigger metabolic change, interferon-γ, and observed heterogeneous, oscillatory HIF-1α responses in single cells. Finally, we input these dynamics into a mathematical model of HIF-1α-regulated metabolism and discovered a profound difference between cells exhibiting high versus low HIF-1α activation. Specifically, we found cells with high HIF-1α activation are able to meaningfully reduce flux through the tricarboxylic acid cycle and show a notable increase in the NAD+/NADH ratio compared with cells displaying low HIF-1α activation. Altogether, this work demonstrates an optimized reporter for studying HIF-1α in single cells and reveals previously unknown principles of HIF-1α activation.
Collapse
Affiliation(s)
- Stevan Jeknić
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Joanna J Song
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, California, USA.
| |
Collapse
|
6
|
Aspert T, Hentsch D, Charvin G. DetecDiv, a generalist deep-learning platform for automated cell division tracking and survival analysis. eLife 2022; 11:79519. [PMID: 35976090 PMCID: PMC9444243 DOI: 10.7554/elife.79519] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Automating the extraction of meaningful temporal information from sequences of microscopy images represents a major challenge to characterize dynamical biological processes. So far, strong limitations in the ability to quantitatively analyze single-cell trajectories have prevented large-scale investigations to assess the dynamics of entry into replicative senescence in yeast. Here, we have developed DetecDiv, a microfluidic-based image acquisition platform combined with deep learning-based software for high-throughput single-cell division tracking. We show that DetecDiv can automatically reconstruct cellular replicative lifespans with high accuracy and performs similarly with various imaging platforms and geometries of microfluidic traps. In addition, this methodology provides comprehensive temporal cellular metrics using time-series classification and image semantic segmentation. Last, we show that this method can be further applied to automatically quantify the dynamics of cellular adaptation and real-time cell survival upon exposure to environmental stress. Hence, this methodology provides an all-in-one toolbox for high-throughput phenotyping for cell cycle, stress response, and replicative lifespan assays.
Collapse
Affiliation(s)
- Théo Aspert
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Didier Hentsch
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Gilles Charvin
- Department of Developmental Biology and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| |
Collapse
|
7
|
Guerra P, Vuillemenot LAPE, van Oppen YB, Been M, Milias-Argeitis A. TORC1 and PKA activity towards ribosome biogenesis oscillates in synchrony with the budding yeast cell cycle. J Cell Sci 2022; 135:276358. [PMID: 35975715 DOI: 10.1242/jcs.260378] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 10/15/2022] Open
Abstract
Recent studies have revealed that the growth rate of budding yeast and mammalian cells varies during the cell cycle. By linking a multitude of signals to cell growth, the highly conserved Target of Rapamycin Complex 1 (TORC1) and Protein Kinase A (PKA) pathways are prime candidates for mediating the dynamic coupling between growth and division. However, measurements of TORC1 and PKA activity during the cell cycle are still lacking. Following the localization dynamics of two TORC1 and PKA targets via time-lapse microscopy in hundreds of yeast cells, we found that the activity of these pathways towards ribosome biogenesis fluctuates in synchrony with the cell cycle even under constant external conditions. Mutations of upstream TORC1 and PKA regulators suggested that internal metabolic signals partially mediate these activity changes. Our study reveals a new aspect of TORC1 and PKA signaling, which will be important for understanding growth regulation during the cell cycle.
Collapse
Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Luc-Alban P E Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Yulan B van Oppen
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Marije Been
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| |
Collapse
|
8
|
Information theory entering soils and tissues. Cell Syst 2022; 13:511-513. [PMID: 35863325 DOI: 10.1016/j.cels.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
For a long time, application of information theory for characterizing biological signaling fidelity was limited to "telegraph-like" situations, copying the classical scenario for which it was developed. A study published in this issue of Cell Systems applies this powerful framework to several distinct cases of dynamic signal sensing in complex geometries.
Collapse
|
9
|
Ying T, Alexander H. Quantifying information of intracellular signaling: progress with machine learning. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:10.1088/1361-6633/ac7a4a. [PMID: 35724636 PMCID: PMC9507437 DOI: 10.1088/1361-6633/ac7a4a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Cells convey information about their extracellular environment to their core functional machineries. Studying the capacity of intracellular signaling pathways to transmit information addresses fundamental questions about living systems. Here, we review how information-theoretic approaches have been used to quantify information transmission by signaling pathways that are functionally pleiotropic and subject to molecular stochasticity. We describe how recent advances in machine learning have been leveraged to address the challenges of complex temporal trajectory datasets and how these have contributed to our understanding of how cells employ temporal coding to appropriately adapt to environmental perturbations.
Collapse
Affiliation(s)
- Tang Ying
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- International Academic Center of Complex Systems, Beijing Normal University, Zhuhai 519087, China
| | - Hoffmann Alexander
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
10
|
Achar SR, Bourassa FXP, Rademaker TJ, Lee A, Kondo T, Salazar-Cavazos E, Davies JS, Taylor N, François P, Altan-Bonnet G. Universal antigen encoding of T cell activation from high-dimensional cytokine dynamics. Science 2022; 376:880-884. [PMID: 35587980 DOI: 10.1126/science.abl5311] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Systems immunology lacks a framework with which to derive theoretical understanding from high-dimensional datasets. We combined a robotic platform with machine learning to experimentally measure and theoretically model CD8+ T cell activation. High-dimensional cytokine dynamics could be compressed onto a low-dimensional latent space in an antigen-specific manner (so-called "antigen encoding"). We used antigen encoding to model and reconstruct patterns of T cell immune activation. The model delineated six classes of antigens eliciting distinct T cell responses. We generalized antigen encoding to multiple immune settings, including drug perturbations and activation of chimeric antigen receptor T cells. Such universal antigen encoding for T cell activation may enable further modeling of immune responses and their rational manipulation to optimize immunotherapies.
Collapse
Affiliation(s)
- Sooraj R Achar
- Immunodynamics Group, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Angela Lee
- Immunodynamics Group, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Taisuke Kondo
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Emanuel Salazar-Cavazos
- Immunodynamics Group, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - John S Davies
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Paul François
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| |
Collapse
|
11
|
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression. Cell Syst 2022; 13:353-364.e6. [PMID: 35298924 DOI: 10.1016/j.cels.2022.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 11/18/2021] [Accepted: 02/17/2022] [Indexed: 12/27/2022]
Abstract
Cells live in constantly changing environments and employ dynamic signaling pathways to transduce information about the signals they encounter. However, the mechanisms by which dynamic signals are decoded into appropriate gene expression patterns remain poorly understood. Here, we devise networked optogenetic pathways that achieve dynamic signal processing functions that recapitulate cellular information processing. Exploiting light-responsive transcriptional regulators with differing response kinetics, we build a falling edge pulse detector and show that this circuit can be employed to demultiplex dynamically encoded signals. We combine this demultiplexer with dCas9-based gene networks to construct pulsatile signal filters and decoders. Applying information theory, we show that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state. Finally, we use dynamic multiplexing for precise multidimensional regulation of a heterologous metabolic pathway. Our results elucidate design principles of dynamic information processing and provide original synthetic systems capable of decoding complex signals for biotechnological applications.
Collapse
|
12
|
Argüello-Miranda O, Marchand AJ, Kennedy T, Russo MAX, Noh J. Cell cycle-independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry. J Cell Biol 2022; 221:212720. [PMID: 34694336 PMCID: PMC8548912 DOI: 10.1083/jcb.202103171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/27/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cellular quiescence is a nonproliferative state required for cell survival under stress and during development. In most quiescent cells, proliferation is stopped in a reversible state of low Cdk1 kinase activity; in many organisms, however, quiescent states with high-Cdk1 activity can also be established through still uncharacterized stress or developmental mechanisms. Here, we used a microfluidics approach coupled to phenotypic classification by machine learning to identify stress pathways associated with starvation-triggered high-Cdk1 quiescent states in Saccharomyces cerevisiae. We found that low- and high-Cdk1 quiescent states shared a core of stress-associated processes, such as autophagy, protein aggregation, and mitochondrial up-regulation, but differed in the nuclear accumulation of the stress transcription factors Xbp1, Gln3, and Sfp1. The decision between low- or high-Cdk1 quiescence was controlled by cell cycle-independent accumulation of Xbp1, which acted as a time-delayed integrator of the duration of stress stimuli. Our results show how cell cycle-independent stress-activated factors promote cellular quiescence outside G1/G0.
Collapse
Affiliation(s)
- Orlando Argüello-Miranda
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ashley J Marchand
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Taylor Kennedy
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX
| | - Marielle A X Russo
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| |
Collapse
|
13
|
Mattingly HH, Kamino K, Machta BB, Emonet T. Escherichia coli chemotaxis is information limited. NATURE PHYSICS 2021; 17:1426-1431. [PMID: 35035514 PMCID: PMC8758097 DOI: 10.1038/s41567-021-01380-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/10/2021] [Indexed: 05/08/2023]
Abstract
Organisms acquire and use information from their environment to guide their behaviour. However, it is unclear whether this information quantitatively limits their behavioural performance. Here, we relate information to the ability of Escherichia coli to navigate up chemical gradients, the behaviour known as chemotaxis. First, we derive a theoretical limit on the speed with which cells climb gradients, given the rate at which they acquire information. Next, we measure cells' gradient-climbing speeds and the rate of information acquisition by their chemotaxis signaling pathway. We find that E. coli make behavioural decisions with much less than the one bit required to determine whether they are swimming up-gradient. Some of this information is irrelevant to gradient climbing, and some is lost in communication to behaviour. Despite these limitations, E. coli climb gradients at speeds within a factor of two of the theoretical bound. Thus, information can limit the performance of an organism, and sensory-motor pathways may have evolved to efficiently use information acquired from the environment.
Collapse
Affiliation(s)
- H H Mattingly
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - K Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - B B Machta
- Department of Physics, Yale University
- Systems Biology Institute, West Campus, Yale University
| | - T Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
- Department of Physics, Yale University
| |
Collapse
|
14
|
Jalihal AP, Kraikivski P, Murali TM, Tyson JJ. Modeling and analysis of the macronutrient signaling network in budding yeast. Mol Biol Cell 2021; 32:ar20. [PMID: 34495680 PMCID: PMC8693975 DOI: 10.1091/mbc.e20-02-0117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Adaptive modulation of the global cellular growth state of unicellular organisms is crucial for their survival in fluctuating nutrient environments. Because these organisms must be able to respond reliably to ever varying and unpredictable nutritional conditions, their nutrient signaling networks must have a certain inbuilt robustness. In eukaryotes, such as the budding yeast Saccharomyces cerevisiae, distinct nutrient signals are relayed by specific plasma membrane receptors to signal transduction pathways that are interconnected in complex information-processing networks, which have been well characterized. However, the complexity of the signaling network confounds the interpretation of the overall regulatory "logic" of the control system. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling network in budding yeast, focusing on early temporal responses to carbon and nitrogen signaling. We build a computational model of this network to reconcile literature-curated quantitative experimental data with our proposed molecular mechanism. We evaluate the robustness of our estimates of the model's kinetic parameter values. We test the model by comparing predictions made in mutant strains with qualitative experimental observations made in the same strains. Finally, we use the model to predict nutrient-responsive transcription factor activities in a number of mutant strains undergoing complex nutrient shifts.
Collapse
Affiliation(s)
- Amogh P Jalihal
- Genetics, Bioinformatics, and Computational Biology PhD Program
| | - Pavel Kraikivski
- Division of Systems Biology, Academy of Integrated Science, Virginia Tech, Blacksburg, VA 24061
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061
| | - John J Tyson
- Division of Systems Biology, Academy of Integrated Science, Virginia Tech, Blacksburg, VA 24061.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061
| |
Collapse
|
15
|
Hsu IS, Strome B, Lash E, Robbins N, Cowen LE, Moses AM. A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PLoS Genet 2021; 17:e1009629. [PMID: 34506483 PMCID: PMC8457507 DOI: 10.1371/journal.pgen.1009629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/22/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Stochastic signaling dynamics expand living cells' information processing capabilities. An increasing number of studies report that regulators encode information in their pulsatile dynamics. The evolutionary mechanisms that lead to complex signaling dynamics remain uncharacterized, perhaps because key interactions of signaling proteins are encoded in intrinsically disordered regions (IDRs), whose evolution is difficult to analyze. Here we focused on the IDR that controls the stochastic pulsing dynamics of Crz1, a transcription factor in fungi downstream of the widely conserved calcium signaling pathway. We find that Crz1 IDRs from anciently diverged fungi can all respond transiently to calcium stress; however, only Crz1 IDRs from the Saccharomyces clade support pulsatility, encode extra information, and rescue fitness in competition assays, while the Crz1 IDRs from distantly related fungi do none of the three. On the other hand, we find that Crz1 pulsing is conserved in the distantly related fungi, consistent with the evolutionary model of stabilizing selection on the signaling phenotype. Further, we show that a calcineurin docking site in a specific part of the IDRs appears to be sufficient for pulsing and show evidence for a beneficial increase in the relative calcineurin affinity of this docking site. We propose that evolutionary flexibility of functionally divergent IDRs underlies the conservation of stochastic signaling by stabilizing selection.
Collapse
Affiliation(s)
- Ian S. Hsu
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Bob Strome
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Emma Lash
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alan M. Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- * E-mail:
| |
Collapse
|
16
|
Chen K, Rong N, Wang S, Luo C. A novel two-layer-integrated microfluidic device for high-throughput yeast proteomic dynamics analysis at the single-cell level. Integr Biol (Camb) 2021; 12:241-249. [PMID: 32995887 DOI: 10.1093/intbio/zyaa018] [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: 04/20/2020] [Revised: 08/12/2020] [Accepted: 08/31/2020] [Indexed: 11/14/2022]
Abstract
Current microfluidic methods for studying multicell strains (e.g., m-types) with multienvironments (e.g., n-types) require large numbers of inlets/outlets (m*n), a complicated procedure or expensive machinery. Here, we developed a novel two-layer-integrated method to combine different PDMS microchannel layers with different functions into one chip by a PDMS through-hole array, which improved the design of a PDMS-based microfluidic system. Using this method, we succeeded in converting 2 × m × n inlets/outlets into m + n inlets/outlets and reduced the time cost of loading processing (from m × n to m) of the device for studying multicell strains (e.g., m-types) in varied multitemporal environments (i.e., n-types). Using this device, the dynamic behavior of the cell-stress-response proteins was studied when the glucose concentration decreased from 2% to a series of lower concentrations. Our device could also be widely used in high-throughput studies of various stress responses, and the new concept of a multilayer-integrated fabrication method could greatly improve the design of PDMS-based microfluidic systems.
Collapse
Affiliation(s)
- Kaiyue Chen
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Shujing Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| |
Collapse
|
17
|
Wada T, Hironaka KI, Wataya M, Fujii M, Eto M, Uda S, Hoshino D, Kunida K, Inoue H, Kubota H, Takizawa T, Karasawa Y, Nakatomi H, Saito N, Hamaguchi H, Furuichi Y, Manabe Y, Fujii NL, Kuroda S. Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise. Cell Rep 2021; 32:108051. [PMID: 32877665 DOI: 10.1016/j.celrep.2020.108051] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/22/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
Cell-to-cell variability in signal transduction in biological systems is often considered noise. However, intercellular variation (i.e., cell-to-cell variability) has the potential to enable individual cells to encode different information. Here, we show that intercellular variation increases information transmission of skeletal muscle. We analyze the responses of multiple cultured myotubes or isolated skeletal muscle fibers as a multiple-cell channel composed of single-cell channels. We find that the multiple-cell channel, which incorporates intercellular variation as information, not noise, transmitted more information in the presence of intercellular variation than in the absence according to the "response diversity effect," increasing in the gradualness of dose response by summing the cell-to-cell variable dose responses. We quantify the information transmission of human facial muscle contraction during intraoperative neurophysiological monitoring and find that information transmission of muscle contraction is comparable to that of a multiple-cell channel. Thus, our data indicate that intercellular variation can increase the information capacity of tissues.
Collapse
Affiliation(s)
- Takumi Wada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ken-Ichi Hironaka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mitsutaka Wataya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masashi Fujii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Miki Eto
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinsuke Uda
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Hoshino
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Katsuyuki Kunida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Haruki Inoue
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tsuguto Takizawa
- Department of Neurosurgery, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yasuaki Karasawa
- Department of Neurosurgery, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan; Department of Rehabilitation, University of Tokyo Hospital, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Hirofumi Nakatomi
- Department of Neurosurgery, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Hiroki Hamaguchi
- Department of Health Promotion Sciences, Graduate School of Human Health Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Yasuro Furuichi
- Department of Health Promotion Sciences, Graduate School of Human Health Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Yasuko Manabe
- Department of Health Promotion Sciences, Graduate School of Human Health Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Nobuharu L Fujii
- Department of Health Promotion Sciences, Graduate School of Human Health Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| |
Collapse
|
18
|
Wu Y, Wu J, Deng M, Lin Y. Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs. Nat Commun 2021; 12:3145. [PMID: 34035307 PMCID: PMC8149833 DOI: 10.1038/s41467-021-23425-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
Recent single-cell studies have revealed that yeast stress response involves transcription factors that are activated in pulses. However, it remains unclear whether and how these dynamic transcription factors temporally interact to regulate stress survival. Here we show that budding yeast cells can exploit the temporal relationship between paralogous general stress regulators, Msn2 and Msn4, during stress response. We find that individual pulses of Msn2 and Msn4 are largely redundant, and cells can enhance the expression of their shared targets by increasing their temporal divergence. Thus, functional redundancy between these two paralogs is modulated in a dynamic manner to confer fitness advantages for yeast cells, which might feed back to promote the preservation of their redundancy. This evolutionary implication is supported by evidence from Msn2/Msn4 orthologs and analyses of other transcription factor paralogs. Together, we show a cell fate control mechanism through temporal redundancy modulation in yeast, which may represent an evolutionarily important strategy for maintaining functional redundancy between gene duplicates.
Collapse
Affiliation(s)
- Yan Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Jiaqi Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Minghua Deng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
- Center for Statistical Science, Peking University, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
19
|
Murugan A, Husain K, Rust MJ, Hepler C, Bass J, Pietsch JMJ, Swain PS, Jena SG, Toettcher JE, Chakraborty AK, Sprenger KG, Mora T, Walczak AM, Rivoire O, Wang S, Wood KB, Skanata A, Kussell E, Ranganathan R, Shih HY, Goldenfeld N. Roadmap on biology in time varying environments. Phys Biol 2021; 18:10.1088/1478-3975/abde8d. [PMID: 33477124 PMCID: PMC8652373 DOI: 10.1088/1478-3975/abde8d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/21/2021] [Indexed: 02/02/2023]
Abstract
Biological organisms experience constantly changing environments, from sudden changes in physiology brought about by feeding, to the regular rising and setting of the Sun, to ecological changes over evolutionary timescales. Living organisms have evolved to thrive in this changing world but the general principles by which organisms shape and are shaped by time varying environments remain elusive. Our understanding is particularly poor in the intermediate regime with no separation of timescales, where the environment changes on the same timescale as the physiological or evolutionary response. Experiments to systematically characterize the response to dynamic environments are challenging since such environments are inherently high dimensional. This roadmap deals with the unique role played by time varying environments in biological phenomena across scales, from physiology to evolution, seeking to emphasize the commonalities and the challenges faced in this emerging area of research.
Collapse
Affiliation(s)
- Arvind Murugan
- James Franck Institute, Department of Physics, University of Chicago, Chicago, IL 60637, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Kabir Husain
- James Franck Institute, Department of Physics, University of Chicago, Chicago, IL 60637, United States of America
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, United States of America,Department of Physics, University of Chicago, Chicago, IL 60637, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Chelsea Hepler
- Department of Medicine, Feinberg School of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University, Chicago, IL 60611, United States of America
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University, Chicago, IL 60611, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Julian M J Pietsch
- SynthSys: Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Peter S Swain
- SynthSys: Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Siddhartha G Jena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States of America
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America,Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America,Ragon Institute of the Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Kayla G Sprenger
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America,Ragon Institute of the Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, United States of America
| | - T Mora
- Laboratoire de physique, Ecole normale supérieure, CNRS, PSL Research University, Paris, France
| | - A M Walczak
- Laboratoire de physique, Ecole normale supérieure, CNRS, PSL Research University, Paris, France
| | - O Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Shenshen Wang
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Kevin B Wood
- Departments of Biophysics and Physics, University of Michigan, Ann Arbor, MI 48109-1055, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Antun Skanata
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, Rm. 206, New York, NY 10003, United States of America
| | - Edo Kussell
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, Rm. 206, New York, NY 10003, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Rama Ranganathan
- Center for Physics of Evolving Systems, Biochemistry & Molecular Biology, and the Pritzker School for Molecular Engineering, University of Chicago, Chicago IL 60637, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| | - Hong-Yan Shih
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States of America,Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Nigel Goldenfeld
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States of America,Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States of America,Author to whom any correspondence should be addressed. , , , , , , , , , , and
| |
Collapse
|
20
|
Tang Y, Adelaja A, Ye FXF, Deeds E, Wollman R, Hoffmann A. Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nat Commun 2021; 12:1272. [PMID: 33627672 PMCID: PMC7904837 DOI: 10.1038/s41467-021-21562-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023] Open
Abstract
Cellular responses to environmental changes are encoded in the complex temporal patterns of signaling proteins. However, quantifying the accumulation of information over time to direct cellular decision-making remains an unsolved challenge. This is, in part, due to the combinatorial explosion of possible configurations that need to be evaluated for information in time-course measurements. Here, we develop a quantitative framework, based on inferred trajectory probabilities, to calculate the mutual information encoded in signaling dynamics while accounting for cell-cell variability. We use it to understand NFκB transcriptional dynamics in response to different immune threats, and reveal that some threats are distinguished faster than others. Our analyses also suggest specific temporal phases during which information distinguishing threats becomes available to immune response genes; one specific phase could be mapped to the functionality of the IκBα negative feedback circuit. The framework is generally applicable to single-cell time series measurements, and enables understanding how temporal regulatory codes transmit information over time.
Collapse
Affiliation(s)
- Ying Tang
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Adewunmi Adelaja
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Felix X-F Ye
- Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA
| | - Eric Deeds
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Roy Wollman
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA.
| |
Collapse
|
21
|
Abstract
Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?
Collapse
Affiliation(s)
- Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, AT-3400 Klosterneuburg, Austria
| | - Thomas Gregor
- Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, FR-75015 Paris, France
| |
Collapse
|
22
|
Patel DS, Diana G, Entchev EV, Zhan M, Lu H, Ch'ng Q. A Multicellular Network Mechanism for Temperature-Robust Food Sensing. Cell Rep 2020; 33:108521. [PMID: 33357442 PMCID: PMC7773553 DOI: 10.1016/j.celrep.2020.108521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/16/2020] [Accepted: 11/24/2020] [Indexed: 11/23/2022] Open
Abstract
Responsiveness to external cues is a hallmark of biological systems. In complex environments, it is crucial for organisms to remain responsive to specific inputs even as other internal or external factors fluctuate. Here, we show how the nematode Caenorhabditis elegans can discriminate between different food levels to modulate its lifespan despite temperature perturbations. This end-to-end robustness from environment to physiology is mediated by food-sensing neurons that communicate via transforming growth factor β (TGF-β) and serotonin signals to form a multicellular gene network. Specific regulations in this network change sign with temperature to maintain similar food responsiveness in the lifespan output. In contrast to robustness of stereotyped outputs, our findings uncover a more complex robustness process involving the higher order function of discrimination in food responsiveness. This process involves rewiring a multicellular network to compensate for temperature and provides a basis for understanding gene-environment interactions. Together, our findings unveil sensory computations that integrate environmental cues to govern physiology. C. elegans’ ability to modulate lifespan in response to food is robust to temperature Robustness requires TGF-β and serotonin signaling in a neuronal network Specific regulations in the neuronal network change sign with temperature Temperature-dependent regulations compensate for temperature
Collapse
Affiliation(s)
- Dhaval S Patel
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA
| | - Giovanni Diana
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Eugeni V Entchev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Mei Zhan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA
| | - QueeLim Ch'ng
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
| |
Collapse
|
23
|
Mouton SN, Thaller DJ, Crane MM, Rempel IL, Terpstra OT, Steen A, Kaeberlein M, Lusk CP, Boersma AJ, Veenhoff LM. A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast. eLife 2020; 9:e54707. [PMID: 32990592 PMCID: PMC7556870 DOI: 10.7554/elife.54707] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/28/2020] [Indexed: 01/03/2023] Open
Abstract
Cellular aging is a multifactorial process that is characterized by a decline in homeostatic capacity, best described at the molecular level. Physicochemical properties such as pH and macromolecular crowding are essential to all molecular processes in cells and require maintenance. Whether a drift in physicochemical properties contributes to the overall decline of homeostasis in aging is not known. Here, we show that the cytosol of yeast cells acidifies modestly in early aging and sharply after senescence. Using a macromolecular crowding sensor optimized for long-term FRET measurements, we show that crowding is rather stable and that the stability of crowding is a stronger predictor for lifespan than the absolute crowding levels. Additionally, in aged cells, we observe drastic changes in organellar volume, leading to crowding on the micrometer scale, which we term organellar crowding. Our measurements provide an initial framework of physicochemical parameters of replicatively aged yeast cells.
Collapse
Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - David J Thaller
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | - Matthew M Crane
- Department of Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - Irina L Rempel
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Owen T Terpstra
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Matt Kaeberlein
- Department of Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | | | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| |
Collapse
|
24
|
Chen K, Shen W, Zhang Z, Xiong F, Ouyang Q, Luo C. Age-dependent decline in stress response capacity revealed by proteins dynamics analysis. Sci Rep 2020; 10:15211. [PMID: 32939000 PMCID: PMC7494919 DOI: 10.1038/s41598-020-72167-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
The aging process is regarded as the progressive loss of physiological integrity, leading to impaired biological functions and the increased vulnerability to death. Among various biological functions, stress response capacity enables cells to alter gene expression patterns and survive when facing internal and external stresses. Here, we explored changes in stress response capacity during the replicative aging of Saccharomyces cerevisiae. To this end, we used a high-throughput microfluidic device to deliver intermittent pulses of osmotic stress and tracked the dynamic changes in the production of downstream stress-responsive proteins, in a large number of individual aging cells. Cells showed a gradual decline in stress response capacity of these osmotic-related downstream proteins during the aging process after the first 5 generations. Among the downstream stress-responsive genes and unrelated genes tested, the residual level of response capacity of Trehalose-6-Phosphate Synthase (TPS2) showed the best correlation with the cell remaining lifespan. By monitor dynamics of the upstream transcription factors and mRNA of Tps2, it was suggested that the decline in downstream stress response capacity was caused by the decline of translational rate of these proteins during aging.
Collapse
Affiliation(s)
- Kaiyue Chen
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wenting Shen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zhiwen Zhang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Fangzheng Xiong
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China. .,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
25
|
Hay J, Troup E, Clark I, Pietsch J, Zieliński T, Millar A. PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO. Wellcome Open Res 2020; 5:96. [PMID: 32766455 PMCID: PMC7388197 DOI: 10.12688/wellcomeopenres.15853.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2020] [Indexed: 11/20/2022] Open
Abstract
Tools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and publication according to open research principles. We present
PyOmeroUpload, a Python toolkit for automatically extracting metadata from experiment logs and text files, processing images and uploading these payloads to OMERO servers to create fully annotated, multidimensional datasets. The toolkit comes packaged in portable, platform-independent Docker images that enable users to deploy and run the utilities easily, regardless of Operating System constraints. A selection of use cases is provided, illustrating the primary capabilities and flexibility offered with the toolkit, along with a discussion of limitations and potential future extensions.
PyOmeroUpload is available from:
https://github.com/SynthSys/pyOmeroUpload.
Collapse
Affiliation(s)
- Johnny Hay
- EPCC, University of Edinburgh, Edinburgh, EH9 3FD, UK.,SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Eilidh Troup
- EPCC, University of Edinburgh, Edinburgh, EH9 3FD, UK.,SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Ivan Clark
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Julian Pietsch
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Tomasz Zieliński
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Andrew Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK
| |
Collapse
|
26
|
Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H. Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Syst 2020; 11:336-353.e24. [PMID: 32898473 PMCID: PMC7648432 DOI: 10.1016/j.cels.2020.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/08/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023]
Abstract
Gene expression is thought to be affected not only by the concentration of transcription factors (TFs) but also the dynamics of their nuclear translocation. Testing this hypothesis requires direct control of TF dynamics. Here, we engineer CLASP, an optogenetic tool for rapid and tunable translocation of a TF of interest. Using CLASP fused to Crz1, we observe that, for the same integrated concentration of nuclear TF over time, changing input dynamics changes target gene expression: pulsatile inputs yield higher expression than continuous inputs, or vice versa, depending on the target gene. Computational modeling reveals that a dose-response saturating at low TF input can yield higher gene expression for pulsatile versus continuous input, and that multi-state promoter activation can yield the opposite behavior. Our integrated tool development and modeling approach characterize promoter responses to Crz1 nuclear translocation dynamics, extracting quantitative features that may help explain the differential expression of target genes. CLASP is a modular optogenetic strategy to control the nuclear localization of transcription factors (TFs) and elicit gene expression from their cognate promoters. CLASP control of Crz1 nuclear localization, coupled with computational modeling, revealed how promoters can differentially decode dynamic transcription factor signals. The integrated strategy of CLASP development and modeling presents a generalized approach to causally investigate the transcriptional consequences of dynamic TF nuclear shuttling.
Collapse
Affiliation(s)
- Susan Y Chen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lindsey C Osimiri
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA
| | - Michael Chevalier
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor H Nguyen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew H Ng
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacob Stewart-Ornstein
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lauren T Neves
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
27
|
Maity A, Wollman R. Information transmission from NFkB signaling dynamics to gene expression. PLoS Comput Biol 2020; 16:e1008011. [PMID: 32797040 PMCID: PMC7478807 DOI: 10.1371/journal.pcbi.1008011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/08/2020] [Accepted: 06/02/2020] [Indexed: 02/06/2023] Open
Abstract
The dynamic signal encoding paradigm suggests that information flows from the extracellular environment into specific signaling patterns (encoding) that are then read by downstream effectors to control cellular behavior. Previous work empirically quantified the information content of dynamic signaling patterns. However, whether this information can be faithfully transmitted to the gene expression level is unclear. Here we used NFkB signaling as a model to understand the accuracy of information transmission from signaling dynamics into gene expression. Using a detailed mathematical model, we simulated realistic NFkB signaling patterns with different degrees of variability. The NFkB patterns were used as an input to a simple gene expression model. Analysis of information transmission between ligand and NFkB and ligand and gene expression allows us to determine information loss in transmission between receptors to dynamic signaling patterns and between signaling dynamics to gene expression. Information loss could occur due to biochemical noise or due to a lack of specificity. We found that noise-free gene expression has very little information loss suggesting that gene expression can preserve specificity in NFkB patterns. As expected, the addition of noise to the gene expression model results in information loss. Interestingly, this effect can be mitigated by a specific choice of parameters that can substantially reduce information loss due to biochemical noise during gene expression. Overall our results show that the cellular capacity for information transmission from dynamic signaling patterns to gene expression can be high enough to preserve ligand specificity and thereby the accuracy of cellular response to environmental cues.
Collapse
Affiliation(s)
- Alok Maity
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Roy Wollman
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
- Departments of Integrative Biology and Physiology and Chemistry and Biochemistry, University of California UCLA, California, United States of America
- * E-mail:
| |
Collapse
|
28
|
Stultz LK, Hunsucker A, Middleton S, Grovenstein E, O'Leary J, Blatt E, Miller M, Mobley J, Hanson PK. Proteomic analysis of the S. cerevisiae response to the anticancer ruthenium complex KP1019. Metallomics 2020; 12:876-890. [PMID: 32329475 PMCID: PMC7362344 DOI: 10.1039/d0mt00008f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Like platinum-based chemotherapeutics, the anticancer ruthenium complex indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(iii)], or KP1019, damages DNA, induces apoptosis, and causes tumor regression in animal models. Unlike platinum-based drugs, KP1019 showed no dose-limiting toxicity in a phase I clinical trial. Despite these advances, the mechanism(s) and target(s) of KP1019 remain unclear. For example, the drug may damage DNA directly or by causing oxidative stress. Likewise, KP1019 binds cytosolic proteins, suggesting DNA is not the sole target. Here we use the budding yeast Saccharomyces cerevisiae as a model in a proteomic study of the cellular response to KP1019. Mapping protein level changes onto metabolic pathways revealed patterns consistent with elevated synthesis and/or cycling of the antioxidant glutathione, suggesting KP1019 induces oxidative stress. This result was supported by increased fluorescence of the redox-sensitive dye DCFH-DA and increased KP1019 sensitivity of yeast lacking Yap1, a master regulator of the oxidative stress response. In addition to oxidative and DNA stress, bioinformatic analysis revealed drug-dependent increases in proteins involved ribosome biogenesis, translation, and protein (re)folding. Consistent with proteotoxic effects, KP1019 increased expression of a heat-shock element (HSE) lacZ reporter. KP1019 pre-treatment also sensitized yeast to oxaliplatin, paralleling prior research showing that cancer cell lines with elevated levels of translation machinery are hypersensitive to oxaliplatin. Combined, these data suggest that one of KP1019's many targets may be protein metabolism, which opens up intriguing possibilities for combination therapy.
Collapse
Affiliation(s)
- Laura K Stultz
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Alexandra Hunsucker
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Sydney Middleton
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Evan Grovenstein
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Jacob O'Leary
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Eliot Blatt
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Mary Miller
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - James Mobley
- Department of Surgery, University of Alabama at Birmingham, School of Medicine, Birmingham, AL 35294, USA
| | - Pamela K Hanson
- Department of Biology, Furman University, Greenville, SC 29613, USA.
| |
Collapse
|
29
|
Hay J, Troup E, Clark I, Pietsch J, Zieliński T, Millar A. PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO. Wellcome Open Res 2020; 5:96. [DOI: 10.12688/wellcomeopenres.15853.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 11/20/2022] Open
Abstract
Tools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and publication according to open research principles. We present PyOmeroUpload, a Python toolkit for automatically extracting metadata from experiment logs and text files, processing images and uploading these payloads to OMERO servers to create fully annotated, multidimensional datasets. The toolkit comes packaged in portable, platform-independent Docker images that enable users to deploy and run the utilities easily, regardless of Operating System constraints. A selection of use cases is provided, illustrating the primary capabilities and flexibility offered with the toolkit, along with a discussion of limitations and potential future extensions. PyOmeroUpload is available from: https://github.com/SynthSys/pyOmeroUpload.
Collapse
|
30
|
Binary Expression Enhances Reliability of Messaging in Gene Networks. ENTROPY 2020; 22:e22040479. [PMID: 33286254 PMCID: PMC7516962 DOI: 10.3390/e22040479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 01/31/2023]
Abstract
The promoter state of a gene and its expression levels are modulated by the amounts of transcription factors interacting with its regulatory regions. Hence, one may interpret a gene network as a communicating system in which the state of the promoter of a gene (the source) is communicated by the amounts of transcription factors that it expresses (the message) to modulate the state of the promoter and expression levels of another gene (the receptor). The reliability of the gene network dynamics can be quantified by Shannon's entropy of the message and the mutual information between the message and the promoter state. Here we consider a stochastic model for a binary gene and use its exact steady state solutions to calculate the entropy and mutual information. We show that a slow switching promoter with long and equally standing ON and OFF states maximizes the mutual information and reduces entropy. That is a binary gene expression regime generating a high variance message governed by a bimodal probability distribution with peaks of the same height. Our results indicate that Shannon's theory can be a powerful framework for understanding how bursty gene expression conciliates with the striking spatio-temporal precision exhibited in pattern formation of developing organisms.
Collapse
|
31
|
Convergence between Regulation of Carbon Utilization and Catabolic Repression in Xanthophyllomyces dendrorhous. mSphere 2020; 5:5/2/e00065-20. [PMID: 32238568 PMCID: PMC7113583 DOI: 10.1128/msphere.00065-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthophyllomyces dendrorhous is a carotenogenic yeast with a singular metabolic capacity to produce astaxanthin, a valuable antioxidant pigment. This yeast can assimilate several carbon sources and sustain fermentation even under aerobic conditions. Since astaxanthin biosynthesis is affected by the carbon source, the study of carotenogenesis regulatory mechanisms is key for improving astaxanthin yield in X. dendrorhous This study aimed to elucidate the regulation of the metabolism of different carbon sources and the phenomenon of catabolic repression in this yeast. To this end, protein and transcript levels were quantified by iTRAQ (isobaric tags for relative and absolute quantification) and transcriptomic sequencing (RNA-seq) in the wild-type strain under conditions of glucose, maltose, or succinate treatment and in the mutant strains for genes MIG1, CYC8, and TUP1 under conditions of glucose treatment. Alternative carbon sources such as maltose and succinate affected the relative abundances of 14% of the wild-type proteins, which were mainly grouped into the carbohydrate metabolism category, with the glycolysis/gluconeogenesis and citrate cycle pathways being the most highly represented pathways. Each mutant strain showed significant proteomic profile changes, affecting approximately 2% of the total proteins identified, compared to the wild-type strain under glucose treatment conditions. Similarly to the results seen with the alternative carbon sources, the changes in the mutant strains mainly affected carbohydrate metabolism, with glycolysis/gluconeogenesis and the pentose phosphate and citrate cycle pathways being the most highly represented pathways. Our results showed convergence between carbon assimilation and catabolic repression in the strains studied. Interestingly, indications of cooperative, opposing, and overlapping processes during catabolic regulation were found. We also identified target proteins of the regulatory processes, reinforcing the likelihood of catabolic repression at the posttranscriptional level.IMPORTANCE The conditions affecting catabolic regulation in X. dendrorhous are complex and suggest the presence of an alternative mechanism of regulation. The repressors Mig1, Cyc8, and Tup1 are essential elements for the regulation of the use of glucose and other carbon sources. All play different roles but, depending on the growth conditions, can work in convergent, synergistic, and complementary ways to use carbon sources and to regulate other targets for yeast metabolism. Our results reinforced the belief that further studies in X. dendrorhous are needed to clarify a specific regulatory mechanism at the domain level of the repressors as well as its relationship with those of other metabolic repressors, i.e., the stress response, to elucidate carotenogenic regulation at the transcriptomic and proteomic levels in this yeast.
Collapse
|
32
|
Tottori T, Fujii M, Kuroda S. Robustness against additional noise in cellular information transmission. Phys Rev E 2019; 100:042403. [PMID: 31770940 DOI: 10.1103/physreve.100.042403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Indexed: 06/10/2023]
Abstract
Fluctuations in intracellular reactions (intrinsic noise) reduce the information transmitted from an extracellular input to a cellular response. However, recent studies have demonstrated that the decrease in the transmitted information with respect to extracellular input fluctuations (extrinsic noise) is smaller when the intrinsic noise is larger. Therefore, it has been suggested that robustness against extrinsic noise increases with the level of the intrinsic noise. We call this phenomenon intrinsic noise-induced robustness (INIR). As previous studies on this phenomenon have focused on complex biochemical reactions, the relation between INIR and the input-output of a system is unclear. Moreover, the mechanism of INIR remains elusive. In this paper, we address these questions by analyzing simple models. We first analyze a model in which the input-output relation is linear. We show that the robustness against extrinsic noise increases with the intrinsic noise, confirming the INIR phenomenon. Moreover, the robustness against the extrinsic noise is more strongly dependent on the intrinsic noise when the variance of the intrinsic noise is larger than that of the input distribution. Next, we analyze a threshold model in which the output depends on whether the input exceeds the threshold. When the threshold is equal to the mean of the input, INIR is realized, but when the threshold is much larger than the mean, the threshold model exhibits stochastic resonance, and INIR is not always apparent. The robustness against extrinsic noise and the transmitted information can be traded off against one another in the linear model and the threshold model without stochastic resonance, whereas they can be simultaneously increased in the threshold model with stochastic resonance.
Collapse
Affiliation(s)
- Takehiro Tottori
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Masashi Fujii
- Department of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8526, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| |
Collapse
|
33
|
Cepeda-Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. PLoS Comput Biol 2019; 15:e1007290. [PMID: 31479447 PMCID: PMC6743786 DOI: 10.1371/journal.pcbi.1007290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 09/13/2019] [Accepted: 07/29/2019] [Indexed: 01/16/2023] Open
Abstract
Across diverse biological systems-ranging from neural networks to intracellular signaling and genetic regulatory networks-the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks.
Collapse
Affiliation(s)
| | - Jakob Ruess
- Inria Saclay – Ile-de-France, F-91120 Palaiseau, France
- Institut Pasteur, F-75015 Paris, France
| | - Gašper Tkačik
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
| |
Collapse
|
34
|
Dose dependent gene expression is dynamically modulated by the history, physiology and age of yeast cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:457-471. [DOI: 10.1016/j.bbagrm.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/14/2022]
|
35
|
Lugagne JB, Dunlop MJ. Cell-machine interfaces for characterizing gene regulatory network dynamics. ACTA ACUST UNITED AC 2019; 14:1-8. [PMID: 31579842 DOI: 10.1016/j.coisb.2019.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Gene regulatory networks and the dynamic responses they produce offer a wealth of information about how biological systems process information about their environment. Recently, researchers interested in dissecting these networks have been outsourcing various parts of their experimental workflow to computers. Here we review how, using microfluidic or optogenetic tools coupled with fluorescence imaging, it is now possible to interface cells and computers. These platforms enable scientists to perform informative dynamic stimulations of genetic pathways and monitor their reaction. It is also possible to close the loop and regulate genes in real time, providing an unprecedented view of how signals propagate through the network. Finally, we outline new tools that can be used within the framework of cell-machine interfaces.
Collapse
Affiliation(s)
- Jean-Baptiste Lugagne
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
| |
Collapse
|