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Wu R, Kong L, Liu F. Regulation of biofilm gene expression by DNA replication in Bacillus subtilis. J Cell Mol Med 2024; 28:e18481. [PMID: 38899542 PMCID: PMC11187747 DOI: 10.1111/jcmm.18481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Bacillus subtilis relies on biofilms for survival in harsh environments. Extracellular polymeric substance (EPS) is a crucial component of biofilms, yet the dynamics of EPS production in single cells remain elusive. To unveil the modulation of EPS synthesis, we built a minimal network model comprising the SinI-SinR-SlrR module, Spo0A, and EPS. Stochastic simulations revealed that antagonistic interplay between SinI and SinR enables EPS production in bursts. SlrR widens these bursts and increases their frequency by stabilizing SinR-SlrR complexes and depleting free SinR. DNA replication and chromosomal positioning of key genes dictate pulsatile changes in the slrR:sinR gene dosage ratio (gr) and Spo0A-P levels, each promoting EPS production in distinct phases of the cell cycle. As the cell cycle lengthens with nutrient stress, the duty cycle of gr pulsing decreases, whereas the amplitude of Spo0A-P pulses elevates. This coordinated response facilitates keeping a constant proportion of EPS-secreting cells within colonies across diverse nutrient conditions. Our results suggest that bacteria may 'encode' eps expression through strategic chromosomal organization. This work illuminates how stochastic protein interactions, gene copy number imbalance, and cell-cycle dynamics orchestrate EPS synthesis, offering a deeper understanding of biofilm formation.
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Affiliation(s)
- Renjie Wu
- National Laboratory of Solid State Microstructures, Department of Physics, Collaborative Innovation Center of Advanced Microstructures and Institute for Brain SciencesNanjing UniversityNanjingP. R. China
| | - Ling‐Xing Kong
- National Laboratory of Solid State Microstructures, Department of Physics, Collaborative Innovation Center of Advanced Microstructures and Institute for Brain SciencesNanjing UniversityNanjingP. R. China
| | - Feng Liu
- National Laboratory of Solid State Microstructures, Department of Physics, Collaborative Innovation Center of Advanced Microstructures and Institute for Brain SciencesNanjing UniversityNanjingP. R. China
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2
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Mehdizadeh Gohari I, Edwards AN, McBride SM, McClane BA. The impact of orphan histidine kinases and phosphotransfer proteins on the regulation of clostridial sporulation initiation. mBio 2024; 15:e0224823. [PMID: 38477571 PMCID: PMC11210211 DOI: 10.1128/mbio.02248-23] [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] [Indexed: 03/14/2024] Open
Abstract
Sporulation is an important feature of the clostridial life cycle, facilitating survival of these bacteria in harsh environments, contributing to disease transmission for pathogenic species, and sharing common early steps that are also involved in regulating industrially important solvent production by some non-pathogenic species. Initial genomics studies suggested that Clostridia lack the classical phosphorelay that phosphorylates Spo0A and initiates sporulation in Bacillus, leading to the hypothesis that sporulation in Clostridia universally begins when Spo0A is phosphorylated by orphan histidine kinases (OHKs). However, components of the classical Bacillus phosphorelay were recently identified in some Clostridia. Similar Bacillus phosphorelay components have not yet been found in the pathogenic Clostridia or the solventogenic Clostridia of industrial importance. For some of those Clostridia lacking a classical phosphorelay, the involvement of OHKs in sporulation initiation has received support from genetic studies demonstrating the involvement of several apparent OHKs in their sporulation. In addition, several clostridial OHKs directly phosphorylate Spo0A in vitro. Interestingly, there is considerable protein domain diversity among the sporulation-associated OHKs in Clostridia. Further adding to the emergent complexity of sporulation initiation in Clostridia, several candidate OHK phosphotransfer proteins that were OHK candidates were shown to function as phosphatases that reduce sporulation in some Clostridia. The mounting evidence indicates that no single pathway explains sporulation initiation in all Clostridia and supports the need for further study to fully understand the unexpected and biologically fascinating mechanistic diversity of this important process among these medically and industrially important bacteria.
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Affiliation(s)
- Iman Mehdizadeh Gohari
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Bruce A. McClane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Karaki T, Sunaga A, Takahashi Y, Asai K. Artificial activation of both σ H and Spo0A in Bacillus subtilis enforced initiation of spore development at the vegetatively growing phase. J GEN APPL MICROBIOL 2024; 69:215-228. [PMID: 37380492 DOI: 10.2323/jgam.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
When Bacillus subtilis cells face environmental deterioration, such as exhaustion of nutrients and an increase in cell density, they form spores. It is known that phosphorylation of Spo0A and activation of σH are key events at the initiation of sporulation. However, the initiation of sporulation is an extremely complicated process, and the relationship between these two events remains to be elucidated. To determine the minimum requirements for triggering sporulation initiation, we attempted to induce cell sporulation at the log phase, regardless of nutrients and cell density. In rich media such as Luria-Bertani (LB) medium, the cells of B. subtilis do not sporulate efficiently, possibly because of excess nutrition. When the amount of xylose in the LB medium was limited, σH -dependent transcription of the strain, in which sigA was under the control of the xylose-inducible promoter, was induced, and the frequency of sporulation was elevated according to the decreased level of σA. We also employed a fusion of sad67, which codes for an active form of Spo0A, and the IPTG-inducible promoter. The combination of lowered σA expression and activated Spo0A allowed the cells in the log phase to stop growing and rush into spore development. This observation of enforced initiation of sporulation in the mutant strain was detected even in the presence of the wild-type strain, suggesting that only intracellular events initiate and fulfill spore development regardless of extracellular conditions. Under natural sporulation conditions, the amount of σA did not change drastically throughout growth. Mechanisms that sequester σA from the core RNA polymerase and help σH to become active exist, but this has not yet been elucidated.
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Affiliation(s)
- Tomomitsu Karaki
- Area of Biochemistry and Molecular Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University
| | - Ai Sunaga
- Area of Biochemistry and Molecular Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University
| | - Yasuhiro Takahashi
- Area of Biochemistry and Molecular Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University
| | - Kei Asai
- Area of Biochemistry and Molecular Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture
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4
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Dannenberg S, Penning J, Simm A, Klumpp S. The motility-matrix production switch in Bacillus subtilis-a modeling perspective. J Bacteriol 2024; 206:e0004723. [PMID: 38088582 PMCID: PMC10810213 DOI: 10.1128/jb.00047-23] [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: 08/22/2023] [Accepted: 11/09/2023] [Indexed: 01/26/2024] Open
Abstract
Phenotype switching can be triggered by external stimuli and by intrinsic stochasticity. Here, we focus on the motility-matrix production switch in Bacillus subtilis. We use modeling to describe the SinR-SlrR bistable switch and its regulation by SinI and to distinguish different sources of stochasticity. Our simulations indicate that intrinsic fluctuations in the synthesis of SinI are insufficient to drive spontaneous switching and suggest that switching is triggered by upstream noise from the Spo0A phosphorelay. IMPORTANCE The switch from motility to matrix production is the first step toward biofilm formation and, thus, to multicellular behavior in Bacillus subtilis. The transition is governed by a bistable switch based on the interplay of the regulators SinR and SlrR, while SinI transmits upstream signals to that switch. Quantitative modeling can be used to study the switching dynamics. Here, we build such a model step by step to describe the dynamics of the switch and its regulation and to study how spontaneous switching is triggered by upstream noise from the Spo0A phosphorelay.
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Affiliation(s)
- Simon Dannenberg
- University of Göttingen, Institute for the Dynamics of Complex Systems, Göttingen, Germany
| | - Jonas Penning
- University of Göttingen, Institute for the Dynamics of Complex Systems, Göttingen, Germany
| | - Alexander Simm
- University of Göttingen, Institute for the Dynamics of Complex Systems, Göttingen, Germany
| | - Stefan Klumpp
- University of Göttingen, Institute for the Dynamics of Complex Systems, Göttingen, Germany
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5
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Marathe A, Zarazúa-Osorio B, Srivastava P, Fujita M. The master regulator for entry into sporulation in Bacillus subtilis becomes a mother cell-specific transcription factor for forespore engulfment. Mol Microbiol 2023; 120:439-461. [PMID: 37485800 DOI: 10.1111/mmi.15132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The Spo0A transcription factor is activated by phosphorylation in starving Bacillus subtilis cells. The activated Spo0A (Spo0A~P) regulates genes controlling entry into sporulation and appears to control mother-cell-specific gene expression after asymmetric division, but the latter remains elusive. Here, we found that Spo0A~P directly binds to three conserved DNA sequences (0A1-3) in the promoter region of the mother cell-specific lytic transglycosylase gene spoIID, which is transcribed by σE -RNA polymerase (RNAP) and negatively controlled by the SpoIIID transcription factor and required for forespore engulfment. Systematic mutagenesis of the 0A boxes revealed that the 0A1 and 0A2 boxes located upstream of the promoter positively control the transcription of spoIID. In contrast, the 0A3 box located downstream of the promoter negatively controls the transcription of spoIID. The mutated SpoIIID binding site located between the -35 and -10 promoter elements causes increased expression of spoIID and reduced sporulation. When the mutations of 0A1, 0A2, and IIID sites are combined, sporulation is restored. Collectively, our data suggest that the mother cell-specific spoIID expression is precisely controlled by the coordination of three factors, Spo0A~P, SpoIIID, and σE -RNAP, for proper sporulation. The conservation of this mechanism across spore-forming species was discussed.
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Affiliation(s)
- Anuradha Marathe
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Priyanka Srivastava
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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6
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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.
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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
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7
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Abstract
The universally conserved protein elongation factor P (EF-P) facilitates translation at amino acids that form peptide bonds with low efficiency, particularly polyproline tracts. Despite its wide conservation, it is not essential in most bacteria and its physiological role remains unclear. Here, we show that EF-P affects the process of sporulation initiation in the bacterium Bacillus subtilis. We observe that the lack of EF-P delays expression of sporulation-specific genes. Using ribosome profiling, we observe that expression of spo0A, encoding a transcription factor that functions as the master regulator of sporulation, is lower in a Δefp strain than the wild type. Ectopic expression of Spo0A rescues the sporulation initiation phenotype, indicating that reduced spo0A expression explains the sporulation defect in Δefp cells. Since Spo0A is the earliest sporulation transcription factor, these data suggest that sporulation initiation can be delayed when protein synthesis is impaired. IMPORTANCE Elongation factor P (EF-P) is a universally conserved translation factor that prevents ribosome stalling at amino acids that form peptide bonds with low efficiency, particularly polyproline tracts. Phenotypes associated with EF-P deletion are pleiotropic, and the mechanistic basis underlying many of these phenotypes is unclear. Here, we show that the absence of EF-P affects the ability of B. subtilis to initiate sporulation by preventing normal expression of Spo0A, the key transcriptional regulator of this process. These data illustrate a mechanism that accounts for the sporulation delay and further suggest that cells are capable of sensing translation stress before committing to sporulation.
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8
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The Slowdown of Growth Rate Controls the Single-Cell Distribution of Biofilm Matrix Production via an SinI-SinR-SlrR Network. mSystems 2023; 8:e0062222. [PMID: 36786593 PMCID: PMC10134886 DOI: 10.1128/msystems.00622-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
In Bacillus subtilis, master regulator Spo0A controls several cell-differentiation pathways. Under moderate starvation, phosphorylated Spo0A (Spo0A~P) induces biofilm formation by indirectly activating genes controlling matrix production in a subpopulation of cells via an SinI-SinR-SlrR network. Under severe starvation, Spo0A~P induces sporulation by directly and indirectly regulating sporulation gene expression. However, what determines the heterogeneity of individual cell fates is not fully understood. In particular, it is still unclear why, despite being controlled by a single master regulator, biofilm matrix production and sporulation seem mutually exclusive on a single-cell level. In this work, with mathematical modeling, we showed that the fluctuations in the growth rate and the intrinsic noise amplified by the bistability in the SinI-SinR-SlrR network could explain the single-cell distribution of matrix production. Moreover, we predicted an incoherent feed-forward loop; the decrease in the cellular growth rate first activates matrix production by increasing in Spo0A phosphorylation level but then represses it via changing the relative concentrations of SinR and SlrR. Experimental data provide evidence to support model predictions. In particular, we demonstrate how the degree to which matrix production and sporulation appear mutually exclusive is affected by genetic perturbations. IMPORTANCE The mechanisms of cell-fate decisions are fundamental to our understanding of multicellular organisms and bacterial communities. However, even for the best-studied model systems we still lack a complete picture of how phenotypic heterogeneity of genetically identical cells is controlled. Here, using B. subtilis as a model system, we employ a combination of mathematical modeling and experiments to explain the population-level dynamics and single-cell level heterogeneity of matrix gene expression. The results demonstrate how the two cell fates, biofilm matrix production and sporulation, can appear mutually exclusive without explicitly inhibiting one another. Such a mechanism could be used in a wide range of other biological systems.
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Arjes HA, Gui H, Porter R, Atolia E, Peters JM, Gross C, Kearns DB, Huang KC. Fatty Acid Synthesis Knockdown Promotes Biofilm Wrinkling and Inhibits Sporulation in Bacillus subtilis. mBio 2022; 13:e0138822. [PMID: 36069446 PMCID: PMC9600695 DOI: 10.1128/mbio.01388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/05/2022] [Indexed: 02/05/2023] Open
Abstract
Many bacterial species typically live in complex three-dimensional biofilms, yet much remains unknown about differences in essential processes between nonbiofilm and biofilm lifestyles. Here, we created a CRISPR interference (CRISPRi) library of knockdown strains covering all known essential genes in the biofilm-forming Bacillus subtilis strain NCIB 3610 and investigated growth, biofilm colony wrinkling, and sporulation phenotypes of the knockdown library. First, we showed that gene essentiality is largely conserved between liquid and surface growth and between two media. Second, we quantified biofilm colony wrinkling using a custom image analysis algorithm and found that fatty acid synthesis and DNA gyrase knockdown strains exhibited increased wrinkling independent of biofilm matrix gene expression. Third, we designed a high-throughput screen to quantify sporulation efficiency after essential gene knockdown; we found that partial knockdowns of essential genes remained competent for sporulation in a sporulation-inducing medium, but knockdown of essential genes involved in fatty acid synthesis exhibited reduced sporulation efficiency in LB, a medium with generally lower levels of sporulation. We conclude that a subset of essential genes are particularly important for biofilm structure and sporulation/germination and suggest a previously unappreciated and multifaceted role for fatty acid synthesis in bacterial lifestyles and developmental processes. IMPORTANCE For many bacteria, life typically involves growth in dense, three-dimensional communities called biofilms that contain cells with differentiated roles held together by extracellular matrix. To examine how essential gene function varies between vegetative growth and the developmental states of biofilm formation and sporulation, we created and screened a comprehensive library of strains using CRISPRi to knockdown expression of each essential gene in the biofilm-capable Bacillus subtilis strain 3610. High-throughput assays and computational algorithms identified a subset of essential genes involved in biofilm wrinkling and sporulation and indicated that fatty acid synthesis plays important and multifaceted roles in bacterial development.
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Affiliation(s)
- Heidi A. Arjes
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Haiwen Gui
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Rachel Porter
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
| | - Esha Atolia
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Carol Gross
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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10
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Dynamic gene expression and growth underlie cell-to-cell heterogeneity in Escherichia coli stress response. Proc Natl Acad Sci U S A 2022; 119:e2115032119. [PMID: 35344432 PMCID: PMC9168488 DOI: 10.1073/pnas.2115032119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Individual bacteria that share identical genomes and growth environments can display substantial cell-to-cell differences in expression of stress-response genes and single-cell growth rates. This phenotypic heterogeneity can impact the survival of single cells facing sudden stress. However, the windows of time that cells spend in vulnerable or tolerant states are often unknown. We quantify the temporal expression of a suite of stress-response reporters, while simultaneously monitoring growth. We observe pulsatile expression across genes with a range of stress-response functions, finding that single-cell growth rates are often anticorrelated with reporter levels. These dynamic phenotypic differences have a concrete link to function, in which individual cells undergoing a pulse of elevated expression and slow growth are predisposed to survive antibiotic exposure. Cell-to-cell heterogeneity in gene expression and growth can have critical functional consequences, such as determining whether individual bacteria survive or die following stress. Although phenotypic variability is well documented, the dynamics that underlie it are often unknown. This information is important because dramatically different outcomes can arise from gradual versus rapid changes in expression and growth. Using single-cell time-lapse microscopy, we measured the temporal expression of a suite of stress-response reporters in Escherichia coli, while simultaneously monitoring growth rate. In conditions without stress, we found several examples of pulsatile expression. Single-cell growth rates were often anticorrelated with reporter levels, with changes in growth preceding changes in expression. These dynamics have functional consequences, which we demonstrate by measuring survival after challenging cells with the antibiotic ciprofloxacin. Our results suggest that fluctuations in both gene expression and growth dynamics in stress-response networks have direct consequences on survival.
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11
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Bacillus subtilis Histidine Kinase KinC Activates Biofilm Formation by Controlling Heterogeneity of Single-Cell Responses. mBio 2022; 13:e0169421. [PMID: 35012345 PMCID: PMC8749435 DOI: 10.1128/mbio.01694-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Bacillus subtilis, biofilm and sporulation pathways are both controlled by a master regulator, Spo0A, which is activated by phosphorylation via a phosphorelay-a cascade of phosphotransfer reactions commencing with autophosphorylation of histidine kinases KinA, KinB, KinC, KinD, and KinE. However, it is unclear how the kinases, despite acting via the same regulator, Spo0A, differentially regulate downstream pathways, i.e., how KinA mainly activates sporulation genes and KinC mainly activates biofilm genes. In this work, we found that KinC also downregulates sporulation genes, suggesting that KinC has a negative effect on Spo0A activity. To explain this effect, with a mathematical model of the phosphorelay, we revealed that unlike KinA, which always activates Spo0A, KinC has distinct effects on Spo0A at different growth stages: during fast growth, KinC acts as a phosphate source and activates Spo0A, whereas during slow growth, KinC becomes a phosphate sink and contributes to decreasing Spo0A activity. However, under these conditions, KinC can still increase the population-mean biofilm matrix production activity. In a population, individual cells grow at different rates, and KinC would increase the Spo0A activity in the fast-growing cells but reduce the Spo0A activity in the slow-growing cells. This mechanism reduces single-cell heterogeneity of Spo0A activity, thereby increasing the fraction of cells that activate biofilm matrix production. Thus, KinC activates biofilm formation by controlling the fraction of cells activating biofilm gene expression. IMPORTANCE In many bacterial and eukaryotic systems, multiple cell fate decisions are activated by a single master regulator. Typically, the activities of the regulators are controlled posttranslationally in response to different environmental stimuli. The mechanisms underlying the ability of these regulators to control multiple outcomes are not understood in many systems. By investigating the regulation of Bacillus subtilis master regulator Spo0A, we show that sensor kinases can use a novel mechanism to control cell fate decisions. By acting as a phosphate source or sink, kinases can interact with one another and provide accurate regulation of the phosphorylation level. Moreover, this mechanism affects the cell-to-cell heterogeneity of the transcription factor activity and eventually determines the fraction of different cell types in the population. These results demonstrate the importance of intercellular heterogeneity for understanding the effects of genetic perturbations on cell fate decisions. Such effects can be applicable to a wide range of cellular systems.
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12
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Siddiqui SH, Park J, Kang D, Khan M, Shim K. Cortisol differentially affects the viability and myogenesis of mono- and co-cultured porcine gluteal muscles satellite cells and fibroblasts. Tissue Cell 2021; 73:101615. [PMID: 34419738 DOI: 10.1016/j.tice.2021.101615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 12/19/2022]
Abstract
Cortisol is a ubiquitously expressed stress hormone. In this study, we investigated the effects of exogenous cortisol on porcine gluteal muscles primary cultured satellite cells and fibroblasts. Satellite cells and fibroblasts were mono-or co-cultured, and cells in each type of culture were categorized into the control and cortisol-treated (treatment) groups. We selected 28 μmol mL-1 cortisol for treatment based on their efficacy. Cortisol treatment reduced viability of monocultured satellite cells and fibroblasts. In both monocultured and co-cultured cells, the nucleus in the treatment group was damaged than that control group. Moreover, the total cell cycle duration was shorter in the treatment group than the control group. PAX-7 expression was upregulated in the control group of co-cultured satellite cells and fibroblasts than those remaining groups. Moreover, MyoD expression was downregulated in the cortisol treated group of both mono-and co-cultured satellite cells compared with that in the control group. In co-cultured fibroblasts, MyoD and MyoG expression was upregulated than those remaining groups. The Cyto-C expression was upregulated in the treatment group compared to the control mono-and co-cultured both cells. These results suggest that the selected experimental dose of cortisol reduced cell viability and myogenesis-related gene expression in the monoculture compared to that in the co-culture of satellite cells and fibroblasts.
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Affiliation(s)
- Sharif Hasan Siddiqui
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Jinryong Park
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Darae Kang
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Mousumee Khan
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University, Jeonju, 54907, Republic of Korea
| | - Kwanseob Shim
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
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13
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Barreto HC, Cordeiro TN, Henriques AO, Gordo I. Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate. Sci Rep 2020; 10:18886. [PMID: 33144634 PMCID: PMC7642357 DOI: 10.1038/s41598-020-76017-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
Most model bacteria have been domesticated in laboratory conditions. Yet, the tempo with which a natural isolate diverges from its ancestral phenotype under domestication to a novel laboratory environment is poorly understood. Such knowledge, however is essential to understanding the rate of evolution, the time scale over which a natural isolate can be propagated without loss of its natural adaptive traits, and the reliability of experimental results across labs. Using experimental evolution, phenotypic assays, and whole-genome sequencing, we show that within a week of propagation in a common laboratory environment, a natural isolate of Bacillus subtilis acquires mutations that cause changes in a multitude of traits. A single adaptive mutational step in the gene coding for the transcriptional regulator DegU impairs a DegU-dependent positive autoregulatory loop and leads to loss of robust biofilm architecture, impaired swarming motility, reduced secretion of exoproteases, and to changes in the dynamics of sporulation across environments. Importantly, domestication also resulted in improved survival when the bacteria face pressure from cells of the innate immune system. These results show that degU is a target for mutations during domestication and underscores the importance of performing careful and extremely short-term propagations of natural isolates to conserve the traits encoded in their original genomes.
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Affiliation(s)
- Hugo C Barreto
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago N Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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14
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Gauvry E, Mathot AG, Couvert O, Leguérinel I, Coroller L. Effects of temperature, pH and water activity on the growth and the sporulation abilities of Bacillus subtilis BSB1. Int J Food Microbiol 2020; 337:108915. [PMID: 33152569 DOI: 10.1016/j.ijfoodmicro.2020.108915] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 07/15/2020] [Accepted: 10/04/2020] [Indexed: 11/27/2022]
Abstract
Spore-forming bacteria are implicated in cases of food spoilage or food poisoning. In their sporulated form, they are resistant to physical and chemical treatments applied in the food industry and can persist throughout the food chain. The sporulation leads to an increase in the concentration of resistant forms in final products or food processing equipment. In order to identify sporulation environments in the food industry, it is necessary to be able to predict bacterial sporulation according to environmental factors. As sporulation occurs after bacterial growth, a kinetic model of growth-sporulation was used to describe the evolution of vegetative cells and spores through time. The effects of temperature, pH and water activity on the growth and the sporulation abilities of Bacillus subtilis BSB1 were modelled. The values of the growth boundaries were used as inputs to predict these effects. The good description of the sporulation kinetics by growth parameters suggests that the impact of the studied environmental factors is the same on both physiological process. Suboptimal conditions for growth delay the appearance of the first spores, and spores appear more synchronously in suboptimal conditions for growth. The developed model was also applicable to describe the growth and sporulation curves in changing temperature and pH conditions over time.
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Affiliation(s)
- Emilie Gauvry
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Anne-Gabrielle Mathot
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Olivier Couvert
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Ivan Leguérinel
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Louis Coroller
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France.
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15
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Tu Z, R. Abhyankar W, N. Swarge B, van der Wel N, Kramer G, Brul S, J. de Koning L. Artificial Sporulation Induction (ASI) by kinA Overexpression Affects the Proteomes and Properties of Bacillus subtilis Spores. Int J Mol Sci 2020; 21:ijms21124315. [PMID: 32560401 PMCID: PMC7352945 DOI: 10.3390/ijms21124315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/07/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
To facilitate more accurate spore proteomic analysis, the current study focuses on inducing homogeneous sporulation by overexpressing kinA and assesses the effect of synchronized sporulation initiation on spore resistance, structures, the germination behavior at single-spore level and the proteome. The results indicate that, in our set up, the sporulation by overexpressing kinA can generate a spore yield of 70% within 8 h. The procedure increases spore wet heat resistance and thickness of the spore coat and cortex layers, whilst delaying the time to spore phase-darkening and burst after addition of germinant. The proteome analysis reveals that the upregulated proteins in the kinA induced spores, compared to spores without kinA induction, as well as the 'wildtype' spores, are mostly involved in spore formation. The downregulated proteins mostly belong to the categories of coping with stress, carbon and nitrogen metabolism, as well as the regulation of sporulation. Thus, while kinA overexpression enhances synchronicity in sporulation initiation, it also has profound effects on the central equilibrium of spore formation and spore germination, through modulation of the spore molecular composition and stress resistance physiology.
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Affiliation(s)
- Zhiwei Tu
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Wishwas R. Abhyankar
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Bhagyashree N. Swarge
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Nicole van der Wel
- Department of Medical Biology, Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, 1100 DD Amsterdam, The Netherlands;
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Correspondence: ; Tel.: +31-20-525-7079 (ext. 6970)
| | - Leo J. de Koning
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
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16
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Castillo-Hair SM, Baerman EA, Fujita M, Igoshin OA, Tabor JJ. Optogenetic control of Bacillus subtilis gene expression. Nat Commun 2019; 10:3099. [PMID: 31308373 PMCID: PMC6629627 DOI: 10.1038/s41467-019-10906-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/07/2019] [Indexed: 01/27/2023] Open
Abstract
The Gram-positive bacterium Bacillus subtilis exhibits complex spatial and temporal gene expression signals. Although optogenetic tools are ideal for studying such processes, none has been engineered for this organism. Here, we port a cyanobacterial light sensor pathway comprising the green/red photoreversible two-component system CcaSR, two metabolic enzymes for production of the chromophore phycocyanobilin (PCB), and an output promoter to control transcription of a gene of interest into B. subtilis. Following an initial non-functional design, we optimize expression of pathway genes, enhance PCB production via a translational fusion of the biosynthetic enzymes, engineer a strong chimeric output promoter, and increase dynamic range with a miniaturized photosensor kinase. Our final design exhibits over 70-fold activation and rapid response dynamics, making it well-suited to studying a wide range of gene regulatory processes. In addition, the synthetic biology methods we develop to port this pathway should make B. subtilis easier to engineer in the future.
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Affiliation(s)
| | - Elliot A Baerman
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd., Houston, TX, 77004, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
- Center for Theoretical Biophysics, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX, 77005, USA.
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA.
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17
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Differentiation of Vegetative Cells into Spores: a Kinetic Model Applied to Bacillus subtilis. Appl Environ Microbiol 2019; 85:AEM.00322-19. [PMID: 30902849 DOI: 10.1128/aem.00322-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/10/2019] [Indexed: 01/28/2023] Open
Abstract
Spore-forming bacteria are natural contaminants of food raw materials, and sporulation can occur in many environments from farm to fork. In order to characterize and to predict spore formation over time, we developed a model that describes both the kinetics of growth and the differentiation of vegetative cells into spores. The model is based on a classical growth model and enables description of the kinetics of sporulation with the addition of three parameters specific to sporulation. Two parameters are related to the probability of each vegetative cell to commit to sporulation and to form a spore, and the last one is related to the time needed to form a spore once the cell is committed to sporulation. The goodness of fit of this growth-sporulation model was assessed using growth-sporulation kinetics at various temperatures in laboratory medium or in whey for Bacillus subtilis, Bacillus cereus, and Bacillus licheniformis The model accurately describes the kinetics in these different conditions, with a mean error lower than 0.78 log10 CFU/ml for the growth and 1.08 log10 CFU/ml for the sporulation. The biological meaning of the parameters was validated with a derivative strain of Bacillus subtilis 168 which produces green fluorescent protein at the initiation of sporulation. This model provides physiological information on the spore formation and on the temporal abilities of vegetative cells to differentiate into spores and reveals the heterogeneity of spore formation during and after growth.IMPORTANCE The growth-sporulation model describes the progressive transition from vegetative cells to spores with sporulation parameters describing the sporulation potential of each vegetative cell. Consequently, the model constitutes an interesting tool to assess the sporulation potential of a bacterial population over time with accurate parameters such as the time needed to obtain one resistant spore and the probability of sporulation. Further, this model can be used to assess these data under various environmental conditions in order to better identify the conditions favorable for sporulation regarding the time to obtain the first spore and/or the concentrations of spores which could be reached during a food process.
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18
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Patange O, Schwall C, Jones M, Villava C, Griffith DA, Phillips A, Locke JCW. Escherichia coli can survive stress by noisy growth modulation. Nat Commun 2018; 9:5333. [PMID: 30559445 PMCID: PMC6297224 DOI: 10.1038/s41467-018-07702-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/13/2018] [Indexed: 12/31/2022] Open
Abstract
Gene expression can be noisy, as can the growth of single cells. Such cell-to-cell variation has been implicated in survival strategies for bacterial populations. However, it remains unclear how single cells couple gene expression with growth to implement these strategies. Here, we show how noisy expression of a key stress-response regulator, RpoS, allows E. coli to modulate its growth dynamics to survive future adverse environments. We reveal a dynamic positive feedback loop between RpoS and growth rate that produces multi-generation RpoS pulses. We do so experimentally using single-cell, time-lapse microscopy and microfluidics and theoretically with a stochastic model. Next, we demonstrate that E. coli prepares for sudden stress by entering prolonged periods of slow growth mediated by RpoS. This dynamic phenotype is captured by the RpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability. Noisy gene expression leading to phenotypic variability can help organisms to survive in changing environments. Here, Patange et al. show that noisy expression of a stress response regulator, RpoS, allows E. coli cells to modulate their growth rates to survive future adverse environments.
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Affiliation(s)
- Om Patange
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Christian Schwall
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Matt Jones
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Casandra Villava
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | | | | | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK. .,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK. .,Microsoft Research, Cambridge, CB1 2FB, UK.
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19
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Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion. Proc Natl Acad Sci U S A 2018; 115:4288-4293. [PMID: 29610314 DOI: 10.1073/pnas.1706920115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell fate determination is typically regulated by biological networks, yet increasing evidences suggest that cell-cell communication and environmental stresses play crucial roles in the behavior of a cell population. A recent microfluidic experiment showed that the metabolic codependence of two cell populations generates a collective oscillatory dynamic during the expansion of a Bacillus subtilis biofilm. We develop a modeling framework for the spatiotemporal dynamics of the associated metabolic circuit for cells in a colony. We elucidate the role of metabolite diffusion and the need of two distinct cell populations to observe oscillations. Uniquely, this description captures the onset and thereafter stable oscillatory dynamics during expansion and predicts the existence of damping oscillations under various environmental conditions. This modeling scheme provides insights to understand how cells integrate the information from external signaling and cell-cell communication to determine the optimal survival strategy and/or maximize cell fitness in a multicellular system.
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20
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Abstract
The ability of bacterial cells to adjust their gene expression program in response to environmental perturbation is often critical for their survival. Recent experimental advances allowing us to quantitatively record gene expression dynamics in single cells and in populations coupled with mathematical modeling enable mechanistic understanding on how these responses are shaped by the underlying regulatory networks. Here, we review how the combination of local and global factors affect dynamical responses of gene regulatory networks. Our goal is to discuss the general principles that allow extrapolation from a few model bacteria to less understood microbes. We emphasize that, in addition to well-studied effects of network architecture, network dynamics are shaped by global pleiotropic effects and cell physiology.
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Affiliation(s)
- David L Shis
- Department of Biosciences, Rice University, Houston, Texas 77005, USA;
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, USA; .,Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Oleg A Igoshin
- Department of Biosciences, Rice University, Houston, Texas 77005, USA; .,Department of Bioengineering, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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21
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Russell JR, Cabeen MT, Wiggins PA, Paulsson J, Losick R. Noise in a phosphorelay drives stochastic entry into sporulation in Bacillus subtilis. EMBO J 2017; 36:2856-2869. [PMID: 28838935 DOI: 10.15252/embj.201796988] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/17/2017] [Accepted: 08/01/2017] [Indexed: 11/09/2022] Open
Abstract
Entry into sporulation in Bacillus subtilis is governed by a phosphorelay in which phosphoryl groups from a histidine kinase are successively transferred via relay proteins to the response regulator Spo0A. Spo0A~P, in turn, sets in motion events that lead to asymmetric division and activation of the cell-specific transcription factor σF, a hallmark for entry into sporulation. Here, we have used a microfluidics-based platform to investigate the activation of Spo0A and σF in individual cells held under constant, sporulation-inducing conditions. The principal conclusions were that: (i) activation of σF occurs with an approximately constant probability after adaptation to conditions of nutrient limitation; (ii) activation of σF is tightly correlated with, and preceded by, Spo0A~P reaching a high threshold level; (iii) activation of Spo0A takes place abruptly just prior to asymmetric division; and (iv) the primary source of noise in the activation of Spo0A is the phosphorelay. We propose that cells exhibit a constant probability of attaining a high threshold level of Spo0A~P due to fluctuations in the flux of phosphoryl groups through the phosphorelay.
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Affiliation(s)
- Jonathan R Russell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Matthew T Cabeen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Paul A Wiggins
- Departments of Physics, Bioengineering and Microbiology, University of Washington, Seattle, WA, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
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22
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Shao B, Yuan H, Zhang R, Wang X, Zhang S, Ouyang Q, Hao N, Luo C. Reconstructing the regulatory circuit of cell fate determination in yeast mating response. PLoS Comput Biol 2017; 13:e1005671. [PMID: 28742153 PMCID: PMC5546706 DOI: 10.1371/journal.pcbi.1005671] [Citation(s) in RCA: 5] [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: 03/28/2017] [Revised: 08/07/2017] [Accepted: 07/09/2017] [Indexed: 12/22/2022] Open
Abstract
Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes. However, retrieving biological insights from large-scale protein dynamics data remains a challenging task. Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and developed integrated experimental and computational approaches to analyze the proteomic dynamics during the process of cell fate determination. When exposed to a high dose of mating pheromone, the yeast cell undergoes growth arrest and forms a shmoo-like morphology; however, at intermediate doses, chemotropic elongated growth is initialized. To understand the gene regulatory networks that control this differentiation switch, we employed a high-throughput microfluidic imaging system that allows real-time and simultaneous measurements of cell growth and protein expression. Using kinetic modeling of protein dynamics, we classified the stimulus-dependent changes in protein abundance into two sources: global changes due to physiological alterations and gene-specific changes. A quantitative framework was proposed to decouple gene-specific regulatory modes from the growth-dependent global modulation of protein abundance. Based on the temporal patterns of gene-specific regulation, we established the network architectures underlying distinct cell fates using a reverse engineering method and uncovered the dose-dependent rewiring of gene regulatory network during mating differentiation. Furthermore, our results suggested a potential crosstalk between the pheromone response pathway and the target of rapamycin (TOR)-regulated ribosomal biogenesis pathway, which might underlie a cell differentiation switch in yeast mating response. In summary, our modeling approach addresses the distinct impacts of the global and gene-specific regulation on the control of protein dynamics and provides new insights into the mechanisms of cell fate determination. We anticipate that our integrated experimental and modeling strategies could be widely applicable to other biological systems. A systematic characterization of the proteomic changes during the process of cell differentiation is critical for understanding the underlying molecular mechanisms. However, protein expression can be largely affected by changes in cell physiological state, which hampers the detection of regulatory interactions. Here we proposed an integrated experimental and computational framework to reconstruct regulatory circuits in mating differentiation of budding yeast Saccharomyces cerevisiae, in which distinct cell fates are triggered by alteration in pheromone concentration. A modeling approach was developed to decouple gene-specific regulation from growth-dependent global regulation of protein expression, allowing us to reverse engineering the gene regulatory circuits underlying distinct cell fates. Our work highlights the importance of model-based analysis of proteomic data and delivers new insight into dose-dependent differentiation behavior of budding yeast.
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Affiliation(s)
- Bin Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Haiyu Yuan
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Rongfei Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xuan Wang
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Shuwen Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (CL); (NH)
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
- * E-mail: (CL); (NH)
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23
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Nordholt N, van Heerden J, Kort R, Bruggeman FJ. Effects of growth rate and promoter activity on single-cell protein expression. Sci Rep 2017; 7:6299. [PMID: 28740089 PMCID: PMC5524720 DOI: 10.1038/s41598-017-05871-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/05/2017] [Indexed: 12/01/2022] Open
Abstract
Protein expression in a single cell depends on its global physiological state. Moreover, genetically-identical cells exhibit variability (noise) in protein expression, arising from the stochastic nature of biochemical processes, cell growth and division. While it is well understood how cellular growth rate influences mean protein expression, little is known about the relationship between growth rate and noise in protein expression. Here we quantify this relationship in Bacillus subtilis by a novel combination of experiments and theory. We measure the effects of promoter activity and growth rate on the expression of a fluorescent protein in single cells. We disentangle the observed protein expression noise into protein-specific and systemic contributions, using theory and variance decomposition. We find that noise in protein expression depends solely on mean expression levels, regardless of whether expression is set by promoter activity or growth rate, and that noise increases linearly with growth rate. Our results can aid studies of (synthetic) gene circuits of single cells and their condition dependence.
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Affiliation(s)
- Niclas Nordholt
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1087, NL1081, HV, Amsterdam, The Netherlands
| | - Johan van Heerden
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1087, NL1081, HV, Amsterdam, The Netherlands
| | - Remco Kort
- Molecular Cell Physiology, AIMMS, VU Amsterdam, De Boelelaan 1087, NL1081, HV, Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1087, NL1081, HV, Amsterdam, The Netherlands.
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24
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van Boxtel C, van Heerden JH, Nordholt N, Schmidt P, Bruggeman FJ. Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments. J R Soc Interface 2017; 14:20170141. [PMID: 28701503 PMCID: PMC5550968 DOI: 10.1098/rsif.2017.0141] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/16/2017] [Indexed: 01/08/2023] Open
Abstract
Natural selection has shaped the strategies for survival and growth of microorganisms. The success of microorganisms depends not only on slow evolutionary tuning but also on the ability to adapt to unpredictable changes in their environment. In principle, adaptive strategies range from purely deterministic mechanisms to those that exploit the randomness intrinsic to many cellular and molecular processes. Depending on the environment and selective pressures, particular strategies can lie somewhere along this continuum. In recent years, non-genetic cell-to-cell differences have received a lot of attention, not least because of their potential impact on the ability of microbial populations to survive in dynamic environments. Using several examples, we describe the origins of spontaneous and induced mechanisms of phenotypic adaptation. We identify some of the commonalities of these examples and consider the potential role of chance and constraints in microbial phenotypic adaptation.
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Affiliation(s)
- Coco van Boxtel
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Johan H van Heerden
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Niclas Nordholt
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Phillipp Schmidt
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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25
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Kiehler B, Haggett L, Fujita M. The PAS domains of the major sporulation kinase in Bacillus subtilis play a role in tetramer formation that is essential for the autokinase activity. Microbiologyopen 2017; 6. [PMID: 28449380 PMCID: PMC5552956 DOI: 10.1002/mbo3.481] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/25/2017] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
Sporulation in Bacillus subtilis is induced upon starvation. In a widely accepted model, an N‐terminal “sensor” domain of the major sporulation kinase KinA recognizes a hypothetical starvation signal(s) and autophosphorylates a histidine residue to activate the master regulator Spo0A via a multicomponent phosphorelay. However, to date no confirmed signal has been found. Here, we demonstrated that PAS‐A, the most N‐terminal of the three PAS domains (PAS‐ABC), is dispensable for the activity, contrary to a previous report. Our data indicated that the autokinase activity is dependent on the formation of a functional tetramer, which is mediated by, at least, PAS‐B and PAS‐C. Additionally, we ruled out the previously proposed notion that NAD+/NADH ratio controls KinA activity through the PAS‐A domain by demonstrating that the cofactors show no effects on the kinase activity in vitro. In support of these data, we found that the cofactors exist in approximately 1000‐fold excess of KinA in the cell and the cofactors’ ratio does not change significantly during growth and sporulation, suggesting that changes in the cofactor ratio might not play a role in controlling KinA activity. These data may refute the widely‐held belief that the activity of KinA is regulated in response to an unknown starvation signal(s).
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Affiliation(s)
- Brittany Kiehler
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Lindsey Haggett
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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26
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Narula J, Fujita M, Igoshin OA. Functional requirements of cellular differentiation: lessons from Bacillus subtilis. Curr Opin Microbiol 2016; 34:38-46. [PMID: 27501460 DOI: 10.1016/j.mib.2016.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/11/2016] [Indexed: 01/09/2023]
Abstract
Successful execution of differentiation programs requires cells to assess multitudes of internal and external cues and respond with appropriate gene expression programs. Here, we review how Bacillus subtilis sporulation network deals with these tasks focusing on the lessons generalizable to other systems. With feedforward loops controlling both production and activation of downstream transcriptional regulators, cells achieve ultrasensitive threshold-like responses. The arrangement of sporulation network genes on the chromosome and transcriptional feedback loops allow coordination of sporulation decision with DNA-replication. Furthermore, to assess the starvation conditions without sensing specific metabolites, cells respond to changes in their growth rates with increased activity of sporulation master regulator. These design features of the sporulation network enable cells to robustly decide between vegetative growth and sporulation.
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Affiliation(s)
- Jatin Narula
- Department of Bioengineering and Center for Theoretical Biological Physics, Rice University, United States
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, United States
| | - Oleg A Igoshin
- Department of Bioengineering and Center for Theoretical Biological Physics, Rice University, United States.
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Narula J, Kuchina A, Zhang F, Fujita M, Süel GM, Igoshin OA. Slowdown of growth controls cellular differentiation. Mol Syst Biol 2016; 12:871. [PMID: 27216630 PMCID: PMC5289222 DOI: 10.15252/msb.20156691] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
How can changes in growth rate affect the regulatory networks behavior and the outcomes of cellular differentiation? We address this question by focusing on starvation response in sporulating Bacillus subtilis We show that the activity of sporulation master regulator Spo0A increases with decreasing cellular growth rate. Using a mathematical model of the phosphorelay-the network controlling Spo0A-we predict that this increase in Spo0A activity can be explained by the phosphorelay protein accumulation and lengthening of the period between chromosomal replication events caused by growth slowdown. As a result, only cells growing slower than a certain rate reach threshold Spo0A activity necessary for sporulation. This growth threshold model accurately predicts cell fates and explains the distribution of sporulation deferral times. We confirm our predictions experimentally and show that the concentration rather than activity of phosphorelay proteins is affected by the growth slowdown. We conclude that sensing the growth rates enables cells to indirectly detect starvation without the need for evaluating specific stress signals.
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Affiliation(s)
- Jatin Narula
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Anna Kuchina
- Division of Biological Sciences, UCSD, San Diego, CA, USA
| | - Fang Zhang
- Division of Biological Sciences, UCSD, San Diego, CA, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Gürol M Süel
- Division of Biological Sciences, UCSD, San Diego, CA, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX, USA
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