1
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Lanz MC, Zhang S, Swaffer MP, Ziv I, Götz LH, Kim J, McCarthy F, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. Nat Struct Mol Biol 2024:10.1038/s41594-024-01353-z. [PMID: 39048803 DOI: 10.1038/s41594-024-01353-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. In the present study, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that the ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in a manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.
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Affiliation(s)
- Michael C Lanz
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA.
| | - Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | | | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Frank McCarthy
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Joshua E Elias
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA.
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2
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Lanz MC, Zhang S, Swaffer MP, Hernández Götz L, McCarty F, Ziv I, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562558. [PMID: 37905015 PMCID: PMC10614910 DOI: 10.1101/2023.10.16.562558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how size influences cell physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be biochemically different. Here, we corroborate these results in mouse hepatocytes and extend our analysis using yeast. We find that size-dependent proteome changes are highly conserved and mostly independent of metabolic state. As eukaryotic cells grow larger, the dilution of the genome elicits a starvation-like proteome phenotype, suggesting that growth in large cells is limited by the genome in a manner analogous to a limiting nutrient. We also demonstrate that the proteomes of replicatively-aged yeast are primarily determined by their large size. Overall, our data suggest that genome concentration is a universal determinant of proteome content in growing cells.
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3
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Minden S, Aniolek M, Noorman H, Takors R. Performing in spite of starvation: How Saccharomyces cerevisiae maintains robust growth when facing famine zones in industrial bioreactors. Microb Biotechnol 2022; 16:148-168. [PMID: 36479922 PMCID: PMC9803336 DOI: 10.1111/1751-7915.14188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 12/13/2022] Open
Abstract
In fed-batch operated industrial bioreactors, glucose-limited feeding is commonly applied for optimal control of cell growth and product formation. Still, microbial cells such as yeasts and bacteria are frequently exposed to glucose starvation conditions in poorly mixed zones or far away from the feedstock inlet point. Despite its commonness, studies mimicking related stimuli are still underrepresented in scale-up/scale-down considerations. This may surprise as the transition from glucose limitation to starvation has the potential to provoke regulatory responses with negative consequences for production performance. In order to shed more light, we performed gene-expression analysis of Saccharomyces cerevisiae grown in intermittently fed chemostat cultures to study the effect of limitation-starvation transitions. The resulting glucose concentration gradient was representative for the commercial scale and compelled cells to tolerate about 76 s with sub-optimal substrate supply. Special attention was paid to the adaptation status of the population by discriminating between first time and repeated entry into the starvation regime. Unprepared cells reacted with a transiently reduced growth rate governed by the general stress response. Yeasts adapted to the dynamic environment by increasing internal growth capacities at the cost of rising maintenance demands by 2.7%. Evidence was found that multiple protein kinase A (PKA) and Snf1-mediated regulatory circuits were initiated and ramped down still keeping the cells in an adapted trade-off between growth optimization and down-regulation of stress response. From this finding, primary engineering guidelines are deduced to optimize both the production host's genetic background and the design of scale-down experiments.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Maria Aniolek
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Henk Noorman
- Royal DSMDelftThe Netherlands,Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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4
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Tan Y, Stein LY, Sauvageau D. The influence of self-cycling fermentation long- and short-cycle schemes on Saccharomyces cerevisiae and Escherichia coli. Sci Rep 2022; 12:13154. [PMID: 35915208 PMCID: PMC9343364 DOI: 10.1038/s41598-022-16831-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Self-cycling fermentation (SCF), a cyclic process in which cells, on average, divide once per cycle, has been shown to lead to whole-culture synchronization and improvements in productivity during bioconversion. Previous studies have shown that the completion of synchronized cell replication sometimes occurs simultaneously with depletion of the limiting nutrient. However, cases in which the end of cell doubling occurred before limiting nutrient exhaustion were also observed. In order to better understand the impact of these patterns on bioprocessing, we investigated the growth of Saccharomyces cerevisiae and Escherichia coli in long- and short-cycle SCF strategies. Three characteristic events were identified during SCF cycles: (1) an optimum in control parameters, (2) the time of completion of synchronized cell division, and (3) the depletion or plateau of the limiting nutrient. Results from this study and literature led to the identification of three potential trends in SCF cycles: (A) co-occurrence of the three key events, (B) cell replication ending prior to the co-occurrence of the other two events, and (C) depletion or plateau of the limiting nutrient occurring later than the co-occurrence of the other two events. Based on these observations, microbial physiological differences were analyzed and a novel definition for SCF is proposed.
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Affiliation(s)
- Yusheng Tan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada.
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5
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A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth. Proc Natl Acad Sci U S A 2020; 117:18869-18879. [PMID: 32675233 DOI: 10.1073/pnas.2002959117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metabolic modeling and machine learning are key components in the emerging next generation of systems and synthetic biology tools, targeting the genotype-phenotype-environment relationship. Rather than being used in isolation, it is becoming clear that their value is maximized when they are combined. However, the potential of integrating these two frameworks for omic data augmentation and integration is largely unexplored. We propose, rigorously assess, and compare machine-learning-based data integration techniques, combining gene expression profiles with computationally generated metabolic flux data to predict yeast cell growth. To this end, we create strain-specific metabolic models for 1,143 Saccharomyces cerevisiae mutants and we test 27 machine-learning methods, incorporating state-of-the-art feature selection and multiview learning approaches. We propose a multiview neural network using fluxomic and transcriptomic data, showing that the former increases the predictive accuracy of the latter and reveals functional patterns that are not directly deducible from gene expression alone. We test the proposed neural network on a further 86 strains generated in a different experiment, therefore verifying its robustness to an additional independent dataset. Finally, we show that introducing mechanistic flux features improves the predictions also for knockout strains whose genes were not modeled in the metabolic reconstruction. Our results thus demonstrate that fusing experimental cues with in silico models, based on known biochemistry, can contribute with disjoint information toward biologically informed and interpretable machine learning. Overall, this study provides tools for understanding and manipulating complex phenotypes, increasing both the prediction accuracy and the extent of discernible mechanistic biological insights.
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6
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Chagoyen M, Poyatos JF. Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program. PLoS Comput Biol 2019; 15:e1007353. [PMID: 31527866 PMCID: PMC6764696 DOI: 10.1371/journal.pcbi.1007353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 09/27/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
Environmental or genetic perturbations lead to gene expression changes. While most analyses of these changes emphasize the presence of qualitative differences on just a few genes, we now know that changes are widespread. This large-scale variation has been linked to the exclusive influence of a global transcriptional program determined by the new physiological state of the cell. However, given the sophistication of eukaryotic regulation, we expect to have a complex architecture of specific control affecting this program. Here, we examine this architecture. Using data of Saccharomyces cerevisiae expression in different nutrient conditions, we first propose a five-sector genome partition, which integrates earlier models of resource allocation, as a framework to examine the deviations from the global control. In this scheme, we recognize invariant genes, whose regulation is dominated by physiology, specific genes, which substantially depart from it, and two additional classes that contain the frequently assumed growth-dependent genes. Whereas the invariant class shows a considerable absence of specific regulation, the rest is enriched by regulation at the level of transcription factors (TFs) and epigenetic modulators. We nevertheless find markedly different strategies in how these classes deviate. On the one hand, there are TFs that act in a unique way between partition constituents, and on the other, the action of chromatin modifiers is significantly diverse. The balance between regulatory strategies ultimately modulates the action of the general transcription machinery and therefore limits the possibility of establishing a unifying program of expression change at a genomic scale. How can we understand expression changes observed as a result of environmental or genetic perturbations? This issue has been conventionally answered by examining small groups of genes whose expression becomes qualitatively altered after these perturbations. But this approach is too simplistic, as we now know that extensive variation is typically observed. To explain this variation, recent works proposed a model in which genome-wide changes are explained by the action of a general program of transcription. Our manuscript reasons that given the complexity of eukaryotic transcriptional control, a unifying program of regulation cannot be achievable. Instead, we propose within an integrated framework of resource allocation that a rich structure of deviations from it exists and that by characterizing these deviations we can fully appreciate large-scale expression change.
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Affiliation(s)
- Mónica Chagoyen
- Computational Systems Biology Group (CNB-CSIC), Madrid, Spain
- * E-mail: (MC); (JFP)
| | - Juan F. Poyatos
- Logic of Genomic Systems Laboratory (CNB-CSIC), Madrid, Spain
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
- * E-mail: (MC); (JFP)
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7
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Liu FY, Lo SC, Shu CC. The Reaction of Dimerization by Itself Reduces the Noise Intensity of the Protein Monomer. Sci Rep 2019; 9:3405. [PMID: 30833660 PMCID: PMC6399348 DOI: 10.1038/s41598-019-39611-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/29/2019] [Indexed: 12/22/2022] Open
Abstract
Because of the small particle number of intracellular species participating in genetic circuits, stochastic fluctuations are inevitable. This intracellular noise is detrimental to precise regulation. To maintain the proper function of a cell, some natural motifs attenuate the noise at the protein level. In many biological systems, the protein monomer is used as a regulator, but the protein dimer also exists. In the present study, we demonstrated that the dimerization reaction reduces the noise intensity of the protein monomer. Compared with two common noise-buffering motifs, the incoherent feedforward loop (FFL) and negative feedback control, the coefficient of variation (COV) in the case of dimerization was 25% less. Furthermore, we examined a system with direct interaction between proteins and other ligands. Both the incoherent FFL and negative feedback control failed to buffer the noise, but the dimerization was effective. Remarkably, the formation of only one protein dimer was sufficient to cause a 7.5% reduction in the COV.
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Affiliation(s)
- Feng-You Liu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan R.O.C
| | - Shih-Chiang Lo
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan R.O.C
| | - Che-Chi Shu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan R.O.C..
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8
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Lo SC, Liu FY, Jhang WS, Shu CC. The Insight into Protein-Ligand Interactions, a Novel Way of Buffering Protein Noise in Gene Expression. J Comput Biol 2018; 26:86-95. [PMID: 30204477 DOI: 10.1089/cmb.2018.0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Random fluctuations are often considered detrimental in the context of gene regulation. Studies aimed at discovering the noise-buffering strategies are important. In this study, we demonstrated a novel design of attenuating noise at protein-level. The protein-ligand interaction dramatically reduced noise so that the coefficient of variation (COV) became roughly 1/3. Remarkably, in comparison to the other two noise-buffering methods, the negative feedback control and the incoherent feedforward loop, the COV of the target protein in the case of protein-ligand interaction appeared to be less than 1/2 of that of the other two methods. The high correlation of the target protein and the ligand grants the present method great ability to buffer noise. Further, it buffers noise at the stage after translation so it is also capable of attenuating the noise inherited from the process of translation.
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Affiliation(s)
- Shih-Chiang Lo
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan
| | - Feng-You Liu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan
| | - Wun-Sin Jhang
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan
| | - Che-Chi Shu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan
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9
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Kirke J, Kaplan N, Velez S, Jin XL, Vichyavichien P, Zhang XH. Tissue-Preferential Activity and Induction of the Pepper Capsaicin Synthase PUN1 Promoter by Wounding, Heat and Metabolic Pathway Precursor in Tobacco and Tomato Plants. Mol Biotechnol 2018; 60:194-202. [PMID: 29372506 DOI: 10.1007/s12033-018-0060-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A promoter is an essential structural component of a gene that controls its transcription activity in different development stages and in response to various environmental stimuli. Knowledge of promoter functionality in heterologous systems is important in the study of gene regulation and biotechnological application. In order to explore the activity of the pepper capsaicin synthase gene (PUN1) promoter, gene constructs of pPUN1::GUS (for β-glucuronidase) and pPUN1::NtKED (for a tobacco wound-responsive protein) were introduced into tobacco and tomato, respectively, and their activities were examined. Higher levels of GUS staining intensity and transcription were detected in ovary, anther and pollen than other tissues or organs in tobacco plants. Likewise, transgenic tomato fruits had a higher level of pPUN1::NtKED gene expression than the leaf and flower. The PUN1-driven gene expression can be transiently induced by wounding, heat (40 °C) and the capsaicinoid biosynthetic pathway precursor phenylalanine. When compared to the reported pPUN1::GUS-expressing Arabidopsis, the PUN1 promoter exhibited a more similar pattern of activities among pepper, tobacco and tomato, all Solanaceae plants. Our results suggest the potential utility of this tissue-preferential and inducible promoter in other non-pungent Solanaceae plants for research of gene function and regulation as well as in the biotechnological applications.
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Affiliation(s)
- Justin Kirke
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Noah Kaplan
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Stephanie Velez
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Xiao-Lu Jin
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Paveena Vichyavichien
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Xing-Hai Zhang
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA.
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10
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Abstract
Although any genotype–phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analyzing ∼500 yeast quantitative traits, we reveal a basic “supervisor–worker” gene architecture underlying a trait. Supervisors are often identified by “perturbational” approaches (such as gene deletion), whereas workers, which usually show small and statistically insignificant deletion effects, are tracked primarily by “observational” approaches that examine the correlation between gene activity and trait value across a number of conditions. Accordingly, supervisors provide most of the genetic understandings of the trait whereas workers provide rich mechanistic understandings. Further analyses suggest that most observed supervisor–worker interactions may evolve largely neutrally, resulting in pervasive between-worker epistasis that suppresses the tractability of workers. In contrast, a fraction of supervisors are recruited/maintained by natural selection to build worker co-expression, boosting the tractability of workers. Thus, by revealing a supervisor–worker gene architecture underlying complex traits, the opposite roles of natural selection versus neutral drift in shaping the gene architecture, and the complementary strengths of the perturbational and observational research strategies in characterizing the gene architecture, this study may lay a new conceptual foundation for understanding the molecular basis of complex traits.
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Affiliation(s)
- Han Chen
- State Key Laboratory of Bio-control, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chung-I Wu
- State Key Laboratory of Bio-control, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Xionglei He
- State Key Laboratory of Bio-control, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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11
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de Jong H, Casagranda S, Giordano N, Cinquemani E, Ropers D, Geiselmann J, Gouzé JL. Mathematical modelling of microbes: metabolism, gene expression and growth. J R Soc Interface 2017; 14:20170502. [PMID: 29187637 PMCID: PMC5721159 DOI: 10.1098/rsif.2017.0502] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 11/12/2022] Open
Abstract
The growth of microorganisms involves the conversion of nutrients in the environment into biomass, mostly proteins and other macromolecules. This conversion is accomplished by networks of biochemical reactions cutting across cellular functions, such as metabolism, gene expression, transport and signalling. Mathematical modelling is a powerful tool for gaining an understanding of the functioning of this large and complex system and the role played by individual constituents and mechanisms. This requires models of microbial growth that provide an integrated view of the reaction networks and bridge the scale from individual reactions to the growth of a population. In this review, we derive a general framework for the kinetic modelling of microbial growth from basic hypotheses about the underlying reaction systems. Moreover, we show that several families of approximate models presented in the literature, notably flux balance models and coarse-grained whole-cell models, can be derived with the help of additional simplifying hypotheses. This perspective clearly brings out how apparently quite different modelling approaches are related on a deeper level, and suggests directions for further research.
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Affiliation(s)
| | - Stefano Casagranda
- University Côte d'Azur, Inria, INRA, CNRS, UPMC University Paris 06, BIOCORE team, Sophia-Antipolis, France
| | - Nils Giordano
- University Grenoble-Alpes, Inria, Grenoble, France
- University Grenoble-Alpes, CNRS, LIPhy, Grenoble, France
| | | | | | - Johannes Geiselmann
- University Grenoble-Alpes, Inria, Grenoble, France
- University Grenoble-Alpes, CNRS, LIPhy, Grenoble, France
| | - Jean-Luc Gouzé
- University Côte d'Azur, Inria, INRA, CNRS, UPMC University Paris 06, BIOCORE team, Sophia-Antipolis, France
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12
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Annunziata F, Matyjaszkiewicz A, Fiore G, Grierson CS, Marucci L, di Bernardo M, Savery NJ. An Orthogonal Multi-input Integration System to Control Gene Expression in Escherichia coli. ACS Synth Biol 2017; 6:1816-1824. [PMID: 28723080 DOI: 10.1021/acssynbio.7b00109] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many biotechnological applications, it is useful for gene expression to be regulated by multiple signals, as this allows the programming of complex behavior. Here we implement, in Escherichia coli, a system that compares the concentration of two signal molecules, and tunes GFP expression proportionally to their relative abundance. The computation is performed via molecular titration between an orthogonal σ factor and its cognate anti-σ factor. We use mathematical modeling and experiments to show that the computation system is predictable and able to adapt GFP expression dynamically to a wide range of combinations of the two signals, and our model qualitatively captures most of these behaviors. We also demonstrate in silico the practical applicability of the system as a reference-comparator, which compares an intrinsic signal (reflecting the state of the system) with an extrinsic signal (reflecting the desired reference state) in a multicellular feedback control strategy.
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Affiliation(s)
- Fabio Annunziata
- School
of Biochemistry, University of Bristol, BS8 1TD, Bristol, U.K
- BrisSynBio, Bristol, BS8 1TQ, U.K
| | - Antoni Matyjaszkiewicz
- Department
of Engineering Mathematics, University of Bristol, BS8 1UB, Bristol, U.K
- BrisSynBio, Bristol, BS8 1TQ, U.K
| | - Gianfranco Fiore
- Department
of Engineering Mathematics, University of Bristol, BS8 1UB, Bristol, U.K
- BrisSynBio, Bristol, BS8 1TQ, U.K
| | - Claire S. Grierson
- School
of Biological Sciences, University of Bristol, BS8 1UH, Bristol, U.K
- BrisSynBio, Bristol, BS8 1TQ, U.K
| | - Lucia Marucci
- Department
of Engineering Mathematics, University of Bristol, BS8 1UB, Bristol, U.K
- BrisSynBio, Bristol, BS8 1TQ, U.K
| | - Mario di Bernardo
- Department
of Engineering Mathematics, University of Bristol, BS8 1UB, Bristol, U.K
- Department
of Electrical Engineering and Information Technology, University of Naples Federico II, 80125, Naples, Italy
- BrisSynBio, Bristol, BS8 1TQ, U.K
| | - Nigel J. Savery
- School
of Biochemistry, University of Bristol, BS8 1TD, Bristol, U.K
- BrisSynBio, Bristol, BS8 1TQ, U.K
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13
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Diao J, Charlebois DA, Nevozhay D, Bódi Z, Pál C, Balázsi G. Efflux Pump Control Alters Synthetic Gene Circuit Function. ACS Synth Biol 2016; 5:619-31. [PMID: 27111147 DOI: 10.1021/acssynbio.5b00154] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Synthetic biology aims to design new biological systems for predefined purposes, such as the controlled secretion of biofuels, pharmaceuticals, or other chemicals. Synthetic gene circuits regulating an efflux pump from the ATP-binding cassette (ABC) protein family could achieve this. However, ABC efflux pumps can also drive out intracellular inducer molecules that control the gene circuits. This will introduce an implicit feedback that could alter gene circuit function in ways that are poorly understood. Here, we used two synthetic gene circuits inducible by tetracycline family molecules to regulate the expression of a yeast ABC pump (Pdr5p) that pumps out the inducer. Pdr5p altered the dose-responses of the original gene circuits substantially in Saccharomyces cerevisiae. While one aspect of the change could be attributed to the efflux pumping function of Pdr5p, another aspect remained unexplained. Quantitative modeling indicated that reduced regulator gene expression in addition to efflux pump function could fully explain the altered dose-responses. These predictions were validated experimentally. Overall, we highlight how efflux pumps can alter gene circuit dynamics and demonstrate the utility of mathematical modeling in understanding synthetic gene circuit function in new circumstances.
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Affiliation(s)
- Junchen Diao
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Unit 950, 7435 Fannin Street, Houston, Texas 77054, United States
| | - Daniel A. Charlebois
- The Louis and Beatrice Laufer Center for Physical & Quantitative Biology, Stony Brook University, 115C Laufer Center, Z-5252, Stony Brook, New York 11794, United States
| | - Dmitry Nevozhay
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Unit 950, 7435 Fannin Street, Houston, Texas 77054, United States
- School of
Biomedicine, Far Eastern Federal University, 8 Sukhanova Street, Vladivostok, 690950, Russia
| | - Zoltán Bódi
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., H-6726 Szeged, Hungary
| | - Csaba Pál
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62., H-6726 Szeged, Hungary
| | - Gábor Balázsi
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Unit 950, 7435 Fannin Street, Houston, Texas 77054, United States
- The Louis and Beatrice Laufer Center for Physical & Quantitative Biology, Stony Brook University, 115C Laufer Center, Z-5252, Stony Brook, New York 11794, United States
- Department of Biomedical Engineering, Z-5281, Stony Brook University, Stony Brook, New York 11794, United States
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14
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Mori M, Hwa T, Martin OC, De Martino A, Marinari E. Constrained Allocation Flux Balance Analysis. PLoS Comput Biol 2016; 12:e1004913. [PMID: 27355325 PMCID: PMC4927118 DOI: 10.1371/journal.pcbi.1004913] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/11/2016] [Indexed: 12/01/2022] Open
Abstract
New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an “ensemble averaging” procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws. The intracellular protein levels of exponentially growing bacteria are known to vary strongly with growth conditions, as described by quantitative “growth laws”. This work introduces a computational genome-scale framework (Constrained Allocation Flux Balance Analysis, CAFBA) which incorporates growth laws into canonical Flux Balance Analysis. Upon introducing 3 parameters based on established growth laws for E. coli, CAFBA accurately reproduces empirical results on the growth-rate dependent rate of carbon overflow and growth yield, and generates testable predictions about cellular energetic strategies and protein expression levels. CAFBA therefore provides a simple, quantitative approach to balancing the trade-off between growth and its associated biosynthetic costs at genome-scale, without the burden of tuning many inaccessible parameters.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Fisica, Sapienza Università di Roma, Rome, Italy
- Departamento de Bioquímica y Biología Molecular I, Universidad Complutense de Madrid, Madrid, Spain
- Department of Physics, University of California at San Diego, La Jolla, California, United States of America
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, California, United States of America
- Institute for Theoretical Studies, ETH Zurich, Switzerland
| | - Olivier C. Martin
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Andrea De Martino
- Dipartimento di Fisica, Sapienza Università di Roma, Rome, Italy
- Soft and Living Matter Lab, Istituto di Nanotecnologia (CNR-NANOTEC), Consiglio Nazionale delle Ricerche, Rome, Italy
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Human Genetics Foundation, Turin, Italy
- * E-mail:
| | - Enzo Marinari
- Dipartimento di Fisica, Sapienza Università di Roma, Rome, Italy
- Soft and Living Matter Lab, Istituto di Nanotecnologia (CNR-NANOTEC), Consiglio Nazionale delle Ricerche, Rome, Italy
- INFN, Sezione di Roma 1, Rome, Italy
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15
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Bren A, Park JO, Towbin BD, Dekel E, Rabinowitz JD, Alon U. Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP. Sci Rep 2016; 6:24834. [PMID: 27109914 PMCID: PMC4843011 DOI: 10.1038/srep24834] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
Abstract
In most conditions, glucose is the best carbon source for E. coli: it provides faster growth than other sugars, and is consumed first in sugar mixtures. Here we identify conditions in which E. coli strains grow slower on glucose than on other sugars, namely when a single amino acid (arginine, glutamate, or proline) is the sole nitrogen source. In sugar mixtures with these nitrogen sources, E. coli still consumes glucose first, but grows faster rather than slower after exhausting glucose, generating a reversed diauxic shift. We trace this counterintuitive behavior to a metabolic imbalance: levels of TCA-cycle metabolites including α-ketoglutarate are high, and levels of the key regulatory molecule cAMP are low. Growth rates were increased by experimentally increasing cAMP levels, either by adding external cAMP, by genetically perturbing the cAMP circuit or by inhibition of glucose uptake. Thus, the cAMP control circuitry seems to have a ‘bug’ that leads to slow growth under what may be an environmentally rare condition.
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Affiliation(s)
- Anat Bren
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
| | - Junyoung O Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Benjamin D Towbin
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
| | - Erez Dekel
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Uri Alon
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
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16
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Chávez S, García-Martínez J, Delgado-Ramos L, Pérez-Ortín JE. The importance of controlling mRNA turnover during cell proliferation. Curr Genet 2016; 62:701-710. [PMID: 27007479 DOI: 10.1007/s00294-016-0594-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/13/2022]
Abstract
Microbial gene expression depends not only on specific regulatory mechanisms, but also on cellular growth because important global parameters, such as abundance of mRNAs and ribosomes, could be growth rate dependent. Understanding these global effects is necessary to quantitatively judge gene regulation. In the last few years, transcriptomic works in budding yeast have shown that a large fraction of its genes is coordinately regulated with growth rate. As mRNA levels depend simultaneously on synthesis and degradation rates, those studies were unable to discriminate the respective roles of both arms of the equilibrium process. We recently analyzed 80 different genomic experiments and found a positive and parallel correlation between both RNA polymerase II transcription and mRNA degradation with growth rates. Thus, the total mRNA concentration remains roughly constant. Some gene groups, however, regulate their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulate their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lower mRNA levels by reducing mRNA stability or the transcription rate, respectively. We critically review here these results and analyze them in relation to their possible extrapolation to other organisms and in relation to the new questions they open.
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Affiliation(s)
- Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - José García-Martínez
- Departamento de Genética, Universitat de València, Burjassot, Spain.,ERI Biotecmed, Universitat de València, Burjassot, Spain
| | - Lidia Delgado-Ramos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain. .,ERI Biotecmed, Universitat de València, Burjassot, Spain.
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17
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Baumstark R, Hänzelmann S, Tsuru S, Schaerli Y, Francesconi M, Mancuso FM, Castelo R, Isalan M. The propagation of perturbations in rewired bacterial gene networks. Nat Commun 2015; 6:10105. [PMID: 26670742 DOI: 10.1038/ncomms10105] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/04/2015] [Indexed: 11/09/2022] Open
Abstract
What happens to gene expression when you add new links to a gene regulatory network? To answer this question, we profile 85 network rewirings in E. coli. Here we report that concerted patterns of differential expression propagate from reconnected hub genes. The rewirings link promoter regions to different transcription factor and σ-factor genes, resulting in perturbations that span four orders of magnitude, changing up to ∼ 70% of the transcriptome. Importantly, factor connectivity and promoter activity both associate with perturbation size. Perturbations from related rewirings have more similar transcription profiles and a statistical analysis reveals ∼ 20 underlying states of the system, associating particular gene groups with rewiring constructs. We examine two large clusters (ribosomal and flagellar genes) in detail. These represent alternative global outcomes from different rewirings because of antagonism between these major cell states. This data set of systematically related perturbations enables reverse engineering and discovery of underlying network interactions.
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Affiliation(s)
- Rebecca Baumstark
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Sonja Hänzelmann
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Saburo Tsuru
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yolanda Schaerli
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Mirko Francesconi
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Francesco M Mancuso
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Genomics Cancer Group, Vall d 'Hebron Institute of Oncology (VHIO), Carrer Natzaret 15-17, 08035 Barcelona, Spain
| | - Robert Castelo
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Mark Isalan
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain.,Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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18
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Izard J, Gomez Balderas CDC, Ropers D, Lacour S, Song X, Yang Y, Lindner AB, Geiselmann J, de Jong H. A synthetic growth switch based on controlled expression of RNA polymerase. Mol Syst Biol 2015; 11:840. [PMID: 26596932 PMCID: PMC4670729 DOI: 10.15252/msb.20156382] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The ability to control growth is essential for fundamental studies of bacterial physiology and biotechnological applications. We have engineered an Escherichia coli strain in which the transcription of a key component of the gene expression machinery, RNA polymerase, is under the control of an inducible promoter. By changing the inducer concentration in the medium, we can adjust the RNA polymerase concentration and thereby switch bacterial growth between zero and the maximal growth rate supported by the medium. We show that our synthetic growth switch functions in a medium-independent and reversible way, and we provide evidence that the switching phenotype arises from the ultrasensitive response of the growth rate to the concentration of RNA polymerase. We present an application of the growth switch in which both the wild-type E. coli strain and our modified strain are endowed with the capacity to produce glycerol when growing on glucose. Cells in which growth has been switched off continue to be metabolically active and harness the energy gain to produce glycerol at a twofold higher yield than in cells with natural control of RNA polymerase expression. Remarkably, without any further optimization, the improved yield is close to the theoretical maximum computed from a flux balance model of E. coli metabolism. The proposed synthetic growth switch is a promising tool for gaining a better understanding of bacterial physiology and for applications in synthetic biology and biotechnology.
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Affiliation(s)
- Jérôme Izard
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique (CNRS UMR 5588), Saint Martin d'Hères, France INRIA, Grenoble - Rhône-Alpes research center, Saint Ismier, France
| | - Cindy D C Gomez Balderas
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique (CNRS UMR 5588), Saint Martin d'Hères, France INRIA, Grenoble - Rhône-Alpes research center, Saint Ismier, France
| | - Delphine Ropers
- INRIA, Grenoble - Rhône-Alpes research center, Saint Ismier, France
| | - Stephan Lacour
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique (CNRS UMR 5588), Saint Martin d'Hères, France INRIA, Grenoble - Rhône-Alpes research center, Saint Ismier, France
| | - Xiaohu Song
- Center for Research and Interdisciplinarity, INSERM U1001, Medicine Faculty, Site Cochin Port-Royal, University Paris Descartes, Paris, France
| | - Yifan Yang
- Center for Research and Interdisciplinarity, INSERM U1001, Medicine Faculty, Site Cochin Port-Royal, University Paris Descartes, Paris, France
| | - Ariel B Lindner
- Center for Research and Interdisciplinarity, INSERM U1001, Medicine Faculty, Site Cochin Port-Royal, University Paris Descartes, Paris, France
| | - Johannes Geiselmann
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique (CNRS UMR 5588), Saint Martin d'Hères, France INRIA, Grenoble - Rhône-Alpes research center, Saint Ismier, France
| | - Hidde de Jong
- INRIA, Grenoble - Rhône-Alpes research center, Saint Ismier, France
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19
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Schmidt-Glenewinkel H, Barkai N. Loss of growth homeostasis by genetic decoupling of cell division from biomass growth: implication for size control mechanisms. Mol Syst Biol 2014; 10:769. [PMID: 25538138 PMCID: PMC4300492 DOI: 10.15252/msb.20145513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Growing cells adjust their division time with biomass accumulation to maintain growth homeostasis. Size control mechanisms, such as the size checkpoint, provide an inherent coupling of growth and division by gating certain cell cycle transitions based on cell size. We describe genetic manipulations that decouple cell division from cell size, leading to the loss of growth homeostasis, with cells becoming progressively smaller or progressively larger until arresting. This was achieved by modulating glucose influx independently of external glucose. Division rate followed glucose influx, while volume growth was largely defined by external glucose. Therefore, the coordination of size and division observed in wild-type cells reflects tuning of two parallel processes, which is only refined by an inherent feedback-dependent coupling. We present a class of size control models explaining the observed breakdowns of growth homeostasis.
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Affiliation(s)
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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20
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Optimal control analysis of the dynamic growth behavior of microorganisms. Math Biosci 2014; 258:57-67. [PMID: 25223235 DOI: 10.1016/j.mbs.2014.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 11/22/2022]
Abstract
Understanding the growth behavior of microorganisms using modeling and optimization techniques is an active area of research in the fields of biochemical engineering and systems biology. In this paper, we propose a general modeling framework, based on Monod model, to model the growth of microorganisms. Utilizing the general framework, we formulate an optimal control problem with the objective of maximizing a long-term cellular goal and solve it analytically under various constraints for the growth of microorganisms in a two substrate batch environment. We investigate the relation between long term and short term cellular goals and show that the objective of maximizing cellular concentration at a fixed final time is equivalent to maximization of instantaneous growth rate. We then establish the mathematical connection between the generalized framework and optimal and cybernetic modeling frameworks and derive generalized governing dynamic equations for optimal and cybernetic models. We finally illustrate the influence of various constraints in the cybernetic modeling framework on the optimal growth behavior of microorganisms by solving several dynamic optimization problems using genetic algorithms.
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21
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San Román M, Cancela H, Acerenza L. Source and regulation of flux variability in Escherichia coli. BMC SYSTEMS BIOLOGY 2014; 8:67. [PMID: 24927772 PMCID: PMC4074586 DOI: 10.1186/1752-0509-8-67] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/05/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Metabolic responses are essential for the adaptation of microorganisms to changing environmental conditions. The repertoire of flux responses that the metabolic network can display in different external conditions may be quantified applying flux variability analysis to genome-scale metabolic reconstructions. RESULTS A procedure is developed to classify and quantify the sources of flux variability. We apply the procedure to the latest Escherichia coli metabolic reconstruction, in glucose minimal medium, with an additional constraint to account for the mechanism coordinating carbon and nitrogen utilization mediated by α-ketoglutarate. Flux variability can be decomposed into three components: internal, external and growth variability. Unexpectedly, growth variability is the only significant component of flux variability in the physiological ranges of glucose, oxygen and ammonia uptake rates. To obtain substantial increases in metabolic flexibility, E. coli must decrease growth rate to suboptimal values. This growth-flexibility trade-off gives a straightforward interpretation to recent work showing that most overall cell-to-cell flux variability in a population of E. coli can be attained sampling a small number of enzymes most likely to constrain cell growth. Importantly, it provides an explanation for the global reorganization occurring in metabolic networks during adaptations to environmental challenges. The calculations were repeated with a pathogenic strain and an old reconstruction of the commensal strain, having less than 50% of the reactions of the latest reconstruction, obtaining the same general conclusions. CONCLUSIONS In E. coli growing on glucose, growth variability is the only significant component of flux variability for all physiological conditions explored. Increasing flux variability requires reducing growth to suboptimal values. The growth-flexibility trade-off operates in physiological and evolutionary adaptations, and provides an explanation for the global reorganization occurring during adaptations to environmental challenges. The results obtained do not rely on the knowledge of kinetic and regulatory details of the system and are highly robust to incomplete or incorrect knowledge of the reaction network.
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Affiliation(s)
| | | | - Luis Acerenza
- Systems Biology Laboratory, Faculty of Sciences, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay.
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22
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Abstract
Beyond fuelling cellular activities with building blocks and energy, metabolism also integrates environmental conditions into intracellular signals. The underlying regulatory network is complex and multifaceted: it ranges from slow interactions, such as changing gene expression, to rapid ones, such as the modulation of protein activity via post-translational modification or the allosteric binding of small molecules. In this Review, we outline the coordination of common metabolic tasks, including nutrient uptake, central metabolism, the generation of energy, the supply of amino acids and protein synthesis. Increasingly, a set of key metabolites is recognized to control individual regulatory circuits, which carry out specific functions of information input and regulatory output. Such a modular view of microbial metabolism facilitates an intuitive understanding of the molecular mechanisms that underlie cellular decision making.
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23
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Keren L, Zackay O, Lotan-Pompan M, Barenholz U, Dekel E, Sasson V, Aidelberg G, Bren A, Zeevi D, Weinberger A, Alon U, Milo R, Segal E. Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol 2013; 9:701. [PMID: 24169404 PMCID: PMC3817408 DOI: 10.1038/msb.2013.59] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/27/2013] [Indexed: 12/20/2022] Open
Abstract
Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ~900 S. cerevisiae and ~1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60-90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation-promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome-wide expression profiles across conditions. We present a parameter-free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.
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Affiliation(s)
- Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ora Zackay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Barenholz
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Erez Dekel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Vered Sasson
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Aidelberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Danny Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Milo
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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24
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Slavov N, Botstein D. Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression. Mol Biol Cell 2012; 24:157-68. [PMID: 23135997 PMCID: PMC3541962 DOI: 10.1091/mbc.e12-09-0670] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nutrition and the growth rate of a cell are two interacting factors with pervasive physiological effects. Our experiments decouple these factors and demonstrate the role of a growth rate signal, independent of the actual rate of biomass increase, on gene regulation, the cell division cycle, and the switch to a respiro-fermentative metabolism. To survive and proliferate, cells need to coordinate their metabolism, gene expression, and cell division. To understand this coordination and the consequences of its failure, we uncoupled biomass synthesis from nutrient signaling by growing, in chemostats, yeast auxotrophs for histidine, lysine, or uracil in excess of natural nutrients (i.e., sources of carbon, nitrogen, sulfur, and phosphorus), such that their growth rates (GRs) were regulated by the availability of their auxotrophic requirements. The physiological and transcriptional responses to GR changes of these cultures differed markedly from the respective responses of prototrophs whose growth-rate is regulated by the availability of natural nutrients. The data for all auxotrophs at all GRs recapitulated the features of aerobic glycolysis, fermentation despite high oxygen levels in the growth media. In addition, we discovered wide bimodal distributions of cell sizes, indicating a decoupling between the cell division cycle (CDC) and biomass production. The aerobic glycolysis was reflected in a general signature of anaerobic growth, including substantial reduction in the expression levels of mitochondrial and tricarboxylic acid genes. We also found that the magnitude of the transcriptional growth-rate response (GRR) in the auxotrophs is only 40–50% of the magnitude in prototrophs. Furthermore, the auxotrophic cultures express autophagy genes at substantially lower levels, which likely contributes to their lower viability. Our observations suggest that a GR signal, which is a function of the abundance of essential natural nutrients, regulates fermentation/respiration, the GRR, and the CDC.
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Affiliation(s)
- Nikolai Slavov
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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25
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Beg QK, Zampieri M, Klitgord N, Collins SB, Altafini C, Serres MH, Segrè D. Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Res 2012; 40:7132-49. [PMID: 22638572 PMCID: PMC3424579 DOI: 10.1093/nar/gks467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
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Affiliation(s)
- Qasim K Beg
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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26
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Levy S, Kafri M, Carmi M, Barkai N. The competitive advantage of a dual-transporter system. Science 2012; 334:1408-12. [PMID: 22158820 DOI: 10.1126/science.1207154] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cells use transporters of different affinities to regulate nutrient influx. When nutrients are depleted, low-affinity transporters are replaced by high-affinity ones. High-affinity transporters are helpful when concentrations of nutrients are low, but the advantage of reducing their abundance when nutrients are abundant is less clear. When we eliminated such reduced production of the Saccharomyces cerevisiae high-affinity transporters for phosphate and zinc, the elapsed time from the initiation of the starvation program until the lack of nutrients limited growth was shortened, and recovery from starvation was delayed. The latter phenotype was rescued by constitutive activation of the starvation program. Dual-transporter systems appear to prolong preparation for starvation and to facilitate subsequent recovery, which may optimize sensing of nutrient depletion by integrating internal and external information about nutrient availability.
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Affiliation(s)
- Sagi Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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27
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Growth rate-dependent control in Enterococcus faecalis: effects on the transcriptome and proteome, and strong regulation of lactate dehydrogenase. Appl Environ Microbiol 2011; 78:170-6. [PMID: 22038603 DOI: 10.1128/aem.06604-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecalis V583 was grown in a glucose-limited chemostat at three different growth rates (0.05, 0.15, and 0.4 h⁻¹). The fermentation pattern changed with growth rate, from a mostly homolactic profile at a high growth rate to a fermentation dominated by formate, acetate, and ethanol production at a low growth rate. A number of amino acids were consumed at the lower growth rates but not by fast-growing cells. The change in metabolic profile was caused mainly by decreased flux through lactate dehydrogenase. The transcription of ldh-1, encoding the principal lactate dehydrogenase, showed very strong growth rate dependence and differed by three orders of magnitude between the highest and the lowest growth rates. Despite the increase in ldh-1 transcript, the content of the Ldh-1 protein was the same under all conditions. Using microarrays and quantitative PCR, the levels of 227 gene transcripts were found to be affected by the growth rate, and 56 differentially expressed proteins were found by proteomic analyses. Few genes or proteins showed a growth rate-dependent increase or decrease in expression across the whole range of conditions, and many showed a maximum or minimum at the middle growth rate (i.e., 0.15 h⁻¹). For many gene products, a discrepancy between transcriptomic and proteomic data were seen, indicating posttranscriptional regulation of expression.
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Bollenbach T, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Mol Cell 2011; 42:413-25. [PMID: 21596308 DOI: 10.1016/j.molcel.2011.04.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/08/2011] [Accepted: 03/18/2011] [Indexed: 11/30/2022]
Abstract
Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations.
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Affiliation(s)
- Tobias Bollenbach
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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Alberghina L, Mavelli G, Drovandi G, Palumbo P, Pessina S, Tripodi F, Coccetti P, Vanoni M. Cell growth and cell cycle in Saccharomyces cerevisiae: basic regulatory design and protein-protein interaction network. Biotechnol Adv 2011; 30:52-72. [PMID: 21821114 DOI: 10.1016/j.biotechadv.2011.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/23/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
Abstract
In this review we summarize the major connections between cell growth and cell cycle in the model eukaryote Saccharomyces cerevisiae. In S. cerevisiae regulation of cell cycle progression is achieved predominantly during a narrow interval in the late G1 phase known as START (Pringle and Hartwell, 1981). At START a yeast cell integrates environmental and internal signals (such as nutrient availability, presence of pheromone, attainment of a critical size, status of the metabolic machinery) and decides whether to enter a new cell cycle or to undertake an alternative developmental program. Several signaling pathways, that act to connect the nutritional status to cellular actions, are briefly outlined. A Growth & Cycle interaction network has been manually curated. More than one fifth of the edges within the Growth & Cycle network connect Growth and Cycle proteins, indicating a strong interconnection between the processes of cell growth and cell cycle. The backbone of the Growth & Cycle network is composed of middle-degree nodes suggesting that it shares some properties with HOT networks. The development of multi-scale modeling and simulation analysis will help to elucidate relevant central features of growth and cycle as well as to identify their system-level properties. Confident collaborative efforts involving different expertises will allow to construct consensus, integrated models effectively linking the processes of cell growth and cell cycle, ultimately contributing to shed more light also on diseases in which an altered proliferation ability is observed, such as cancer.
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Affiliation(s)
- Lilia Alberghina
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy.
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30
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Scott M, Hwa T. Bacterial growth laws and their applications. Curr Opin Biotechnol 2011; 22:559-65. [PMID: 21592775 DOI: 10.1016/j.copbio.2011.04.014] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 03/24/2011] [Accepted: 04/20/2011] [Indexed: 11/28/2022]
Abstract
Quantitative empirical relationships between cell composition and growth rate played an important role in the early days of microbiology. Gradually, the focus of the field began to shift from growth physiology to the ever more elaborate molecular mechanisms of regulation employed by the organisms. Advances in systems biology and biotechnology have renewed interest in the physiology of the cell as a whole. Furthermore, gene expression is known to be intimately coupled to the growth state of the cell. Here, we review recent efforts in characterizing such couplings, particularly the quantitative phenomenological approaches exploiting bacterial 'growth laws.' These approaches point toward underlying design principles that can guide the predictive manipulation of cell behavior in the absence of molecular details.
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Affiliation(s)
- Matthew Scott
- Department of Applied Mathematics, University of Waterloo, 200 University Ave. W., Waterloo, Ontario N2L 3G1, Canada.
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31
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Pelechano V, Pérez-Ortín JE. There is a steady-state transcriptome in exponentially growing yeast cells. Yeast 2010; 27:413-22. [PMID: 20301094 DOI: 10.1002/yea.1768] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The growth of yeast cells in batches in glucose-based media is a standard condition in most yeast laboratories. Most gene expression experiments are done by taking this condition as a reference. Presumably, cells are in a stable physiological condition that can be easily reproduced in other laboratories. With this assumption, however, it is necessary to consider that the average amount of the mRNAs per cell for most genes does not change during exponential growth. That is to say, there is a steady-state condition for the transcriptome. However, this has not been rigorously demonstrated to date. In this work we take several cell samples during the exponential phase growth to perform a kinetic study using the genomic run-on (GRO) technique, which allows simultaneous measurement of the amount of mRNA and transcription rate variation at the genomic level. We show here that the steady-state condition is fulfilled for almost all the genes during most exponential growth in yeast extract-peptone-dextrose medium (YPD) and, therefore, that simultaneous measures of the transcription rates and the amounts of mRNA can be used for indirect mRNA stability calculations. With this kinetic approach, we were also able to determine the relative influence of the transcription rate and the mRNA stability changes for the mRNA variation for those genes that deviate from the steady state.
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Affiliation(s)
- Vicent Pelechano
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, Spain
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32
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Busti S, Coccetti P, Alberghina L, Vanoni M. Glucose signaling-mediated coordination of cell growth and cell cycle in Saccharomyces cerevisiae. SENSORS 2010; 10:6195-240. [PMID: 22219709 PMCID: PMC3247754 DOI: 10.3390/s100606195] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 05/26/2010] [Accepted: 05/27/2010] [Indexed: 01/05/2023]
Abstract
Besides being the favorite carbon and energy source for the budding yeast Sacchromyces cerevisiae, glucose can act as a signaling molecule to regulate multiple aspects of yeast physiology. Yeast cells have evolved several mechanisms for monitoring the level of glucose in their habitat and respond quickly to frequent changes in the sugar availability in the environment: the cAMP/PKA pathways (with its two branches comprising Ras and the Gpr1/Gpa2 module), the Rgt2/Snf3-Rgt1 pathway and the main repression pathway involving the kinase Snf1. The cAMP/PKA pathway plays the prominent role in responding to changes in glucose availability and initiating the signaling processes that promote cell growth and division. Snf1 (the yeast homologous to mammalian AMP-activated protein kinase) is primarily required for the adaptation of yeast cell to glucose limitation and for growth on alternative carbon source, but it is also involved in the cellular response to various environmental stresses. The Rgt2/Snf3-Rgt1 pathway regulates the expression of genes required for glucose uptake. Many interconnections exist between the diverse glucose sensing systems, which enables yeast cells to fine tune cell growth, cell cycle and their coordination in response to nutritional changes.
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Affiliation(s)
- Stefano Busti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy.
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33
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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34
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A unifying view of 21st century systems biology. FEBS Lett 2010; 583:3891-4. [PMID: 19913537 DOI: 10.1016/j.febslet.2009.11.024] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 11/10/2009] [Accepted: 11/10/2009] [Indexed: 11/21/2022]
Abstract
The idea that multi-scale dynamic complex systems formed by interacting macromolecules and metabolites, cells, organs and organisms underlie some of the most fundamental aspects of life was proposed by a few visionaries half a century ago. We are witnessing a powerful resurgence of this idea made possible by the availability of nearly complete genome sequences, ever improving gene annotations and interactome network maps, the development of sophisticated informatic and imaging tools, and importantly, the use of engineering and physics concepts such as control and graph theory. Alongside four other fundamental "great ideas" as suggested by Sir Paul Nurse, namely, the gene, the cell, the role of chemistry in biological processes, and evolution by natural selection, systems-level understanding of "What is Life" may materialize as one of the major ideas of biology.
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