1
|
Loman TE, Ma Y, Ilin V, Gowda S, Korsbo N, Yewale N, Rackauckas C, Isaacson SA. Catalyst: Fast and flexible modeling of reaction networks. PLoS Comput Biol 2023; 19:e1011530. [PMID: 37851697 PMCID: PMC10584191 DOI: 10.1371/journal.pcbi.1011530] [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: 06/03/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
We introduce Catalyst.jl, a flexible and feature-filled Julia library for modeling and high-performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating stochastic chemical kinetics (jump process), chemical Langevin equation (stochastic differential equation), and reaction rate equation (ordinary differential equation) representations for CRNs. Through comprehensive benchmarks, we demonstrate that Catalyst simulation runtimes are often one to two orders of magnitude faster than other popular tools. More broadly, Catalyst acts as both a domain-specific language and an intermediate representation for symbolically encoding CRN models as Julia-native objects. This enables a pipeline of symbolically specifying, analyzing, and modifying CRNs; converting Catalyst models to symbolic representations of concrete mathematical models; and generating compiled code for numerical solvers. Leveraging ModelingToolkit.jl and Symbolics.jl, Catalyst models can be analyzed, simplified, and compiled into optimized representations for use in numerical solvers. Finally, we demonstrate Catalyst's broad extensibility and composability by highlighting how it can compose with a variety of Julia libraries, and how existing open-source biological modeling projects have extended its intermediate representation.
Collapse
Affiliation(s)
- Torkel E. Loman
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Computer Science and AI Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yingbo Ma
- JuliaHub, Cambridge, Massachusetts, United States of America
| | - Vasily Ilin
- Department of Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Shashi Gowda
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Niklas Korsbo
- Pumas-AI, Baltimore, Maryland, United States of America
| | - Nikhil Yewale
- Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai, India
| | - Chris Rackauckas
- Computer Science and AI Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- JuliaHub, Cambridge, Massachusetts, United States of America
- Pumas-AI, Baltimore, Maryland, United States of America
| | - Samuel A. Isaacson
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
| |
Collapse
|
2
|
Loman TE, Locke JCW. The σB alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics. PLoS Comput Biol 2023; 19:e1011265. [PMID: 37540712 PMCID: PMC10431680 DOI: 10.1371/journal.pcbi.1011265] [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: 10/10/2022] [Revised: 08/16/2023] [Accepted: 06/12/2023] [Indexed: 08/06/2023] Open
Abstract
Single-cell approaches are revealing a high degree of heterogeneity, or noise, in gene expression in isogenic bacteria. How gene circuits modulate this noise in gene expression to generate robust output dynamics is unclear. Here we use the Bacillus subtilis alternative sigma factor σB as a model system for understanding the role of noise in generating circuit output dynamics. σB controls the general stress response in B. subtilis and is activated by a range of energy and environmental stresses. Recent single-cell studies have revealed that the circuit can generate two distinct outputs, stochastic pulsing and a single pulse response, but the conditions under which each response is generated are under debate. We implement a stochastic mathematical model of the σB circuit to investigate this and find that the system's core circuit can generate both response types. This is despite one response (stochastic pulsing) being stochastic in nature, and the other (single response pulse) being deterministic. We demonstrate that the main determinant for whichever response is generated is the degree with which the input pathway activates the core circuit, although the noise properties of the input pathway also biases the system towards one or the other type of output. Thus, our work shows how stochastic modelling can reveal the mechanisms behind non-intuitive gene circuit output dynamics.
Collapse
Affiliation(s)
- Torkel E. Loman
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - James C. W. Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
3
|
Vohradsky J. Quantitative Aspect of Bacillus subtilis σB Regulatory Network-A Computational Simulation. BIOLOGY 2022; 11:biology11121729. [PMID: 36552239 PMCID: PMC9775250 DOI: 10.3390/biology11121729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/07/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022]
Abstract
Bacillus subtilis is a model organism used to study molecular processes in prokaryotic cells. Sigma factor B, which associates with RNA polymerase, is one of the transcriptional regulators involved in the cell's response to environmental stress. This study addresses the key question of how the levels of free SigB, which acts as the actual regulator of gene expression, are controlled. A set of chemical equations describing the network controlling the levels of free SigB was designed, leading to a set of differential equations quantifying the dynamics of the network. Utilizing a microarray-measured gene expression time series then allowed the simulation of the kinetic behavior of the network in real conditions and investigation of the role of phosphatases RsbU/RsbP transmitting the environmental signal and controlling the amounts of free SigB. Moreover, the role of kinetic constants controlling the formation of the molecular complexes, which consequently influence the amount of free SigB, was investigated. The simulation showed that although the total amount of sigma B is relatively high in the unstressed population, the amount of free SigB, which actually controls its regulon, is quite low. The simulation also allowed determination of the proportion of all the network members that were free or bound in complexes. While previously the qualitative features of B. subtilis SigB have been studied in detail, the kinetics of the network have mostly been ignored. In summary, the computational results based on experimental data provide a quantitative insight into the functioning of the SigB-dependent circuit and provide a roadmap for its further exploration in this industrially important bacterium.
Collapse
Affiliation(s)
- Jiri Vohradsky
- Laboratory of Bioinformatics, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| |
Collapse
|
4
|
Zorzan I, Del Favero S, Giaretta A, Manganelli R, Di Camillo B, Schenato L. Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response. BMC Bioinformatics 2021; 22:558. [PMID: 34798803 PMCID: PMC8605609 DOI: 10.1186/s12859-021-04372-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/11/2021] [Indexed: 12/19/2022] Open
Abstract
Background The ability to rapidly adapt to adverse environmental conditions represents the key of success of many pathogens and, in particular, of Mycobacterium tuberculosis. Upon exposition to heat shock, antibiotics or other sources of stress, appropriate responses in terms of genes transcription and proteins activity are activated leading part of a genetically identical bacterial population to express a different phenotype, namely to develop persistence. When the stress response network is mathematically described by an ordinary differential equations model, development of persistence in the bacterial population is associated with bistability of the model, since different emerging phenotypes are represented by different stable steady states. Results In this work, we develop a mathematical model of SigE stress response network that incorporates interactions not considered in mathematical models currently available in the literature. We provide, through involved analytical computations, accurate approximations of the system’s nullclines, and exploit the obtained expressions to determine, in a reliable though computationally efficient way, the number of equilibrium points of the system. Conclusions Theoretical analysis and perturbation experiments point out the crucial role played by the degradation pathway involving RseA, the anti-sigma factor of SigE, for coexistence of two stable equilibria and the emergence of bistability. Our results also indicate that a fine control on RseA concentration is a necessary requirement in order for the system to exhibit bistability. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04372-5.
Collapse
Affiliation(s)
- Irene Zorzan
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.
| | - Simone Del Favero
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Alberto Giaretta
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.,Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro (Padova), Italy
| | - Luca Schenato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| |
Collapse
|
5
|
Schwall CP, Loman TE, Martins BMC, Cortijo S, Villava C, Kusmartsev V, Livesey T, Saez T, Locke JCW. Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit. Mol Syst Biol 2021; 17:e9832. [PMID: 34286912 PMCID: PMC8287880 DOI: 10.15252/msb.20209832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.
Collapse
Affiliation(s)
| | | | - Bruno M C Martins
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | | | | | - Toby Livesey
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Teresa Saez
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | | |
Collapse
|
6
|
Park J, Dies M, Lin Y, Hormoz S, Smith-Unna SE, Quinodoz S, Hernández-Jiménez MJ, Garcia-Ojalvo J, Locke JCW, Elowitz MB. Molecular Time Sharing through Dynamic Pulsing in Single Cells. Cell Syst 2018; 6:216-229.e15. [PMID: 29454936 PMCID: PMC6070344 DOI: 10.1016/j.cels.2018.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 09/04/2017] [Accepted: 01/10/2018] [Indexed: 11/19/2022]
Abstract
In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ~1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.
Collapse
Affiliation(s)
- Jin Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marta Dies
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; Department of Physics and Nuclear Engineering, Universitat Politecnica de Catalunya, 08222 Terrassa, Spain; Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Yihan Lin
- Center for Quantitative Biology, and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Sahand Hormoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Sofia Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
| | - James C W Locke
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Microsoft Research, Cambridge, UK.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|