1
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Lo TW, Choi HJ, Huang D, Wiggins PA. Noise robustness and metabolic load determine the principles of central dogma regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.20.563172. [PMID: 38826369 PMCID: PMC11142067 DOI: 10.1101/2023.10.20.563172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off between metabolic load and growth robustness. The model predicts novel principles of central dogma regulation: Optimal protein expression levels for many genes are in vast overabundance. Essential genes are transcribed above a lower limit of one message per cell cycle. Gene expression is achieved by load balancing between transcription and translation. We present evidence that each of these novel regulatory principles is observed. These results reveal that robustness and metabolic load determine the global regulatory principles that govern central dogma processes, and these principles have broad implications for cellular function.
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Affiliation(s)
- Teresa W. Lo
- Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - Han James Choi
- Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - Dean Huang
- Department of Physics, University of Washington, Seattle, Washington 98195, USA
| | - Paul A. Wiggins
- Department of Physics, University of Washington, Seattle, Washington 98195, USA
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
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2
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Bosch B, DeJesus MA, Schnappinger D, Rock JM. Weak links: Advancing target-based drug discovery by identifying the most vulnerable targets. Ann N Y Acad Sci 2024; 1535:10-19. [PMID: 38595325 DOI: 10.1111/nyas.15139] [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: 04/11/2024]
Abstract
Mycobacterium tuberculosis remains the most common infectious killer worldwide despite decades of antitubercular drug development. Effectively controlling the tuberculosis (TB) pandemic will require innovation in drug discovery. In this review, we provide a brief overview of the two main approaches to discovering new TB drugs-phenotypic screens and target-based drug discovery-and outline some of the limitations of each method. We then explore recent advances in genetic tools that aim to overcome some of these limitations. In particular, we highlight a novel metric to prioritize essential targets, termed vulnerability. Stratifying targets based on their vulnerability presents new opportunities for future target-based drug discovery campaigns.
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Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
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3
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Siddiq MA, Duveau F, Wittkopp PJ. Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589130. [PMID: 38659876 PMCID: PMC11042213 DOI: 10.1101/2024.04.12.589130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Phenotypic evolution is shaped by interactions between organisms and their environments. The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. To better understand this dual role of the environment in the production and selection of phenotypic variation, we empirically determined and compared the genotype-phenotype-fitness relationship for mutant strains of the budding yeast Saccharomyces cerevisiae in four environments. Specifically, we measured how mutations in the promoter of the metabolic gene TDH3 modified its expression level and affected its growth on media with four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Genetic variants with similar effects on TDH3 expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. The set of mutants we examined also allowed us to compare the effects of mutations disrupting binding sites for key transcriptional regulators and the TATA box, which is part of the core promoter sequence. Mutations disrupting the binding sites for the transcription factors had more variable effects on expression among environments than mutations disrupting the TATA box, yet mutations with the most environmentally variable effects on fitness were located in the TATA box. This observation suggests that mutations affecting different molecular mechanisms are likely to contribute unequally to regulatory sequence evolution in changing environments.
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Affiliation(s)
- Mohammad A. Siddiq
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
- Authors contributed equally to this work
| | - Fabien Duveau
- Department of Ecology and Evolutionary Biology, University of Michigan
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon, Université de Lyon, France
- Authors contributed equally to this work
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
- Department of Ecology and Evolutionary Biology, University of Michigan
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4
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Domingo J, Minaeva M, Morris JA, Ziosi M, Sanjana NE, Lappalainen T. Non-linear transcriptional responses to gradual modulation of transcription factor dosage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582837. [PMID: 38464330 PMCID: PMC10925300 DOI: 10.1101/2024.03.01.582837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Genomic loci associated with common traits and diseases are typically non-coding and likely impact gene expression, sometimes coinciding with rare loss-of-function variants in the target gene. However, our understanding of how gradual changes in gene dosage affect molecular, cellular, and organismal traits is currently limited. To address this gap, we induced gradual changes in gene expression of four genes using CRISPR activation and inactivation. Downstream transcriptional consequences of dosage modulation of three master trans-regulators associated with blood cell traits (GFI1B, NFE2, and MYB) were examined using targeted single-cell multimodal sequencing. We showed that guide tiling around the TSS is the most effective way to modulate cis gene expression across a wide range of fold-changes, with further effects from chromatin accessibility and histone marks that differ between the inhibition and activation systems. Our single-cell data allowed us to precisely detect subtle to large gene expression changes in dozens of trans genes, revealing that many responses to dosage changes of these three TFs are non-linear, including non-monotonic behaviours, even when constraining the fold-changes of the master regulators to a copy number gain or loss. We found that the dosage properties are linked to gene constraint and that some of these non-linear responses are enriched for disease and GWAS genes. Overall, our study provides a straightforward and scalable method to precisely modulate gene expression and gain insights into its downstream consequences at high resolution.
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Affiliation(s)
| | - Mariia Minaeva
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - John A Morris
- New York Genome Center, New York, NY 10013, USA
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Neville E Sanjana
- New York Genome Center, New York, NY 10013, USA
- Department of Biology, New York University, New York, NY 10003, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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5
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Baghdassarian HM, Lewis NE. Resource allocation in mammalian systems. Biotechnol Adv 2024; 71:108305. [PMID: 38215956 PMCID: PMC11182366 DOI: 10.1016/j.biotechadv.2023.108305] [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: 08/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
Cells execute biological functions to support phenotypes such as growth, migration, and secretion. Complementarily, each function of a cell has resource costs that constrain phenotype. Resource allocation by a cell allows it to manage these costs and optimize their phenotypes. In fact, the management of resource constraints (e.g., nutrient availability, bioenergetic capacity, and macromolecular machinery production) shape activity and ultimately impact phenotype. In mammalian systems, quantification of resource allocation provides important insights into higher-order multicellular functions; it shapes intercellular interactions and relays environmental cues for tissues to coordinate individual cells to overcome resource constraints and achieve population-level behavior. Furthermore, these constraints, objectives, and phenotypes are context-dependent, with cells adapting their behavior according to their microenvironment, resulting in distinct steady-states. This review will highlight the biological insights gained from probing resource allocation in mammalian cells and tissues.
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Affiliation(s)
- Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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6
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McCain JSP. Mapping combinatorial expression perturbations to growth in Escherichia coli. Cell Syst 2024; 15:106-108. [PMID: 38387440 DOI: 10.1016/j.cels.2024.01.006] [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: 01/21/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
The connection between growth and gene expression has often been considered in a single gene. Repurposing a drug-drug interaction model, the multidimensional effects of several simultaneous gene expression perturbations on growth have been examined in the model bacteria Escherichia coli.
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Affiliation(s)
- J Scott P McCain
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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7
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Otto RM, Turska-Nowak A, Brown PM, Reynolds KA. A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment. Cell Syst 2024; 15:134-148.e7. [PMID: 38340730 PMCID: PMC10885703 DOI: 10.1016/j.cels.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/13/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Quantifying and predicting growth rate phenotype given variation in gene expression and environment is complicated by epistatic interactions and the vast combinatorial space of possible perturbations. We developed an approach for mapping expression-growth rate landscapes that integrates sparsely sampled experimental measurements with an interpretable machine learning model. We used mismatch CRISPRi across pairs and triples of genes to create over 8,000 titrated changes in E. coli gene expression under varied environmental contexts, exploring epistasis in up to 22 distinct environments. Our results show that a pairwise model previously used to describe drug interactions well-described these data. The model yielded interpretable parameters related to pathway architecture and generalized to predict the combined effect of up to four perturbations when trained solely on pairwise perturbation data. We anticipate this approach will be broadly applicable in optimizing bacterial growth conditions, generating pharmacogenomic models, and understanding the fundamental constraints on bacterial gene expression. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Ryan M Otto
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Agata Turska-Nowak
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Philip M Brown
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Kimberly A Reynolds
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA; Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA.
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8
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Kang CK, Kim AR. Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants. iScience 2024; 27:108747. [PMID: 38222110 PMCID: PMC10784702 DOI: 10.1016/j.isci.2023.108747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/29/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024] Open
Abstract
Massively parallel reporter assay measures transcriptional activities of various cis-regulatory modules (CRMs) in a single experiment. We developed a thermodynamic computational model framework that calculates quantitative levels of gene expression directly from regulatory DNA sequences. Using the framework, we investigated the molecular mechanisms of cis-regulatory mutations of a synthetic enhancer that cause abnormal gene expression. We found that, in a human cell line, competitive binding between family transcription factors (TFs) with slightly different binding preferences significantly increases the accuracy of recapitulating the transcriptional effects of thousands of single- or multi-mutations. We also discovered that even if various harmful mutations occurred in an activator binding site, CRM could stably maintain or even increase gene expression through a certain form of competitive binding between family TFs. These findings enhance understanding the effect of SNPs and indels on CRMs and would help building robust custom-designed CRMs for biologics production and gene therapy.
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Affiliation(s)
- Chan-Koo Kang
- School of Life Science, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Department of Advanced Convergence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
| | - Ah-Ram Kim
- School of Life Science, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Department of Advanced Convergence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Applied Artificial Intelligence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
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9
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Frumkin I, Laub MT. Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways. Nat Ecol Evol 2023; 7:2067-2079. [PMID: 37945946 PMCID: PMC10697842 DOI: 10.1038/s41559-023-02224-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Abstract
Cellular novelty can emerge when non-functional loci become functional genes in a process termed de novo gene birth. But how proteins with random amino acid sequences beneficially integrate into existing cellular pathways remains poorly understood. We screened ~108 genes, generated from random nucleotide sequences and devoid of homology to natural genes, for their ability to rescue growth arrest of Escherichia coli cells producing the ribonuclease toxin MazF. We identified ~2,000 genes that could promote growth, probably by reducing transcription from the promoter driving toxin expression. Additionally, one random protein, named Random antitoxin of MazF (RamF), modulated protein homeostasis by interacting with chaperones, leading to MazF proteolysis and a consequent loss of its toxicity. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for how de novo gene birth can produce functional proteins that effectively benefit cells evolving under stress.
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Affiliation(s)
- Idan Frumkin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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10
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Renganaath K, Albert FW. Trans -eQTL hotspots shape complex traits by modulating cellular states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567054. [PMID: 38014174 PMCID: PMC10680915 DOI: 10.1101/2023.11.14.567054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces cerevisiae . We discovered thousands of genetic correlations between gene expression and growth, suggesting functional connections. Local regulatory variation was a minor source of these genetic correlations. Instead, genetic correlations tended to arise from multiple independent trans -acting regulatory loci. Trans -acting hotspots that affect the expression of numerous genes accounted for particularly large fractions of genetic growth variation and of genetic correlations between gene expression and growth. Genes with genetic correlations were enriched for similar biological processes across traits, but with heterogeneous direction of effect. Our results reveal how trans -acting regulatory hotspots shape complex traits by altering cellular states.
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11
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Bruggeman FJ, Teusink B, Steuer R. Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models. Bioessays 2023; 45:e2300015. [PMID: 37559168 DOI: 10.1002/bies.202300015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023]
Abstract
Microbial systems biology has made enormous advances in relating microbial physiology to the underlying biochemistry and molecular biology. By meticulously studying model microorganisms, in particular Escherichia coli and Saccharomyces cerevisiae, increasingly comprehensive computational models predict metabolic fluxes, protein expression, and growth. The modeling rationale is that cells are constrained by a limited pool of resources that they allocate optimally to maximize fitness. As a consequence, the expression of particular proteins is at the expense of others, causing trade-offs between cellular objectives such as instantaneous growth, stress tolerance, and capacity to adapt to new environments. While current computational models are remarkably predictive for E. coli and S. cerevisiae when grown in laboratory environments, this may not hold for other growth conditions and other microorganisms. In this contribution, we therefore discuss the relationship between the instantaneous growth rate, limited resources, and long-term fitness. We discuss uses and limitations of current computational models, in particular for rapidly changing and adverse environments, and propose to classify microbial growth strategies based on Grimes's CSR framework.
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Affiliation(s)
- Frank J Bruggeman
- Systems Biology Lab/AIMMS, VU University, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Biology Lab/AIMMS, VU University, Amsterdam, The Netherlands
| | - Ralf Steuer
- Institute for Theoretical Biology (ITB), Institute for Biology, Humboldt-University of Berlin, Berlin, Germany
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12
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Xie X, Sun X, Wang Y, Lehner B, Li X. Dominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles. Nat Commun 2023; 14:5551. [PMID: 37689712 PMCID: PMC10492795 DOI: 10.1038/s41467-023-41188-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/25/2023] [Indexed: 09/11/2023] Open
Abstract
An important challenge in genetics, evolution and biotechnology is to understand and predict how mutations combine to alter phenotypes, including molecular activities, fitness and disease. In diploids, mutations in a gene can combine on the same chromosome or on different chromosomes as a "heteroallelic combination". However, a direct comparison of the extent, sign, and stability of the genetic interactions between variants within and between alleles is lacking. Here we use thermodynamic models of protein folding and ligand-binding to show that interactions between mutations within and between alleles are expected in even very simple biophysical systems. Protein folding alone generates within-allele interactions and a single molecular interaction is sufficient to cause between-allele interactions and dominance. These interactions change differently, quantitatively and qualitatively as a system becomes more complex. Altering the concentration of a ligand can, for example, switch alleles from dominant to recessive. Our results show that intra-molecular epistasis and dominance should be widely expected in even the simplest biological systems but also reinforce the view that they are plastic system properties and so a formidable challenge to predict. Accurate prediction of both intra-molecular epistasis and dominance will require either detailed mechanistic understanding and experimental parameterization or brute-force measurement and learning.
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Affiliation(s)
- Xuan Xie
- Zhejiang University - University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400, P. R. China
| | - Xia Sun
- Zhejiang University - University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400, P. R. China
- Deanery of Biomedical Sciences, College of Medicine & Veterinary Medicine, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Yuheng Wang
- Zhejiang University - University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400, P. R. China
- Deanery of Biomedical Sciences, College of Medicine & Veterinary Medicine, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Ben Lehner
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain.
- ICREA, Pg. Luis Companys 23, Barcelona, 08010, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton, Cambridge, CB10 1SA, UK.
| | - Xianghua Li
- Zhejiang University - University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400, P. R. China.
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton, Cambridge, CB10 1SA, UK.
- Deanery of Biomedical Sciences, College of Medicine & Veterinary Medicine, University of Edinburgh, Edinburgh, EH8 9XD, UK.
- Biomedical and Health Translational Centre of Zhejiang Province, Haizhou East Road 718, Haining, 314400, P. R. China.
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13
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Torres A, Cockerell S, Phillips M, Balázsi G, Ghosh K. MaxCal can infer models from coupled stochastic trajectories of gene expression and cell division. Biophys J 2023; 122:2623-2635. [PMID: 37218129 PMCID: PMC10397576 DOI: 10.1016/j.bpj.2023.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023] Open
Abstract
Gene expression is inherently noisy due to small numbers of proteins and nucleic acids inside a cell. Likewise, cell division is stochastic, particularly when tracking at the level of a single cell. The two can be coupled when gene expression affects the rate of cell division. Single-cell time-lapse experiments can measure both fluctuations by simultaneously recording protein levels inside a cell and its stochastic division. These information-rich noisy trajectory data sets can be harnessed to learn about the underlying molecular and cellular details that are often not known a priori. A critical question is: How can we infer a model given data where fluctuations at two levels-gene expression and cell division-are intricately convoluted? We show the principle of maximum caliber (MaxCal)-integrated within a Bayesian framework-can be used to infer several cellular and molecular details (division rates, protein production, and degradation rates) from these coupled stochastic trajectories (CSTs). We demonstrate this proof of concept using synthetic data generated from a known model. An additional challenge in data analysis is that trajectories are often not in protein numbers, but in noisy fluorescence that depends on protein number in a probabilistic manner. We again show that MaxCal can infer important molecular and cellular rates even when data are in fluorescence, another example of CST with three confounding factors-gene expression noise, cell division noise, and fluorescence distortion-all coupled. Our approach will provide guidance to build models in synthetic biology experiments as well as general biological systems where examples of CSTs are abundant.
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Affiliation(s)
- Andrew Torres
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Spencer Cockerell
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Gábor Balázsi
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Kingshuk Ghosh
- Molecular and Cellular Biophysics, University of Denver, Denver, Colorado; Department of Physics and Astronomy, University of Denver, Denver, Colorado.
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14
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Wan Y, Cohen J, Szenk M, Farquhar KS, Coraci D, Krzysztoń R, Azukas J, Van Nest N, Smashnov A, Chern YJ, De Martino D, Nguyen LC, Bien H, Bravo-Cordero JJ, Chan CH, Rosner MR, Balázsi G. Nonmonotone invasion landscape by noise-aware control of metastasis activator levels. Nat Chem Biol 2023; 19:887-899. [PMID: 37231268 PMCID: PMC10299915 DOI: 10.1038/s41589-023-01344-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/18/2023] [Indexed: 05/27/2023]
Abstract
A major pharmacological assumption is that lowering disease-promoting protein levels is generally beneficial. For example, inhibiting metastasis activator BACH1 is proposed to decrease cancer metastases. Testing such assumptions requires approaches to measure disease phenotypes while precisely adjusting disease-promoting protein levels. Here we developed a two-step strategy to integrate protein-level tuning, noise-aware synthetic gene circuits into a well-defined human genomic safe harbor locus. Unexpectedly, engineered MDA-MB-231 metastatic human breast cancer cells become more, then less and then more invasive as we tune BACH1 levels up, irrespective of the native BACH1. BACH1 expression shifts in invading cells, and expression of BACH1's transcriptional targets confirm BACH1's nonmonotone phenotypic and regulatory effects. Thus, chemical inhibition of BACH1 could have unwanted effects on invasion. Additionally, BACH1's expression variability aids invasion at high BACH1 expression. Overall, precisely engineered, noise-aware protein-level control is necessary and important to unravel disease effects of genes to improve clinical drug efficacy.
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Affiliation(s)
- Yiming Wan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Joseph Cohen
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Mariola Szenk
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Kevin S Farquhar
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Damiano Coraci
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rafał Krzysztoń
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Joshua Azukas
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
| | - Nicholas Van Nest
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Alex Smashnov
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Yi-Jye Chern
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Daniela De Martino
- Department of Medicine, Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Long Chi Nguyen
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Harold Bien
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Jose Javier Bravo-Cordero
- Department of Medicine, Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chia-Hsin Chan
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Marsha Rich Rosner
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Gábor Balázsi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA.
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15
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Müller J, Bollenbach T. Quantitative approaches to study phenotypic effects of large-scale genetic perturbations. Curr Opin Microbiol 2023; 74:102333. [PMID: 37276805 DOI: 10.1016/j.mib.2023.102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/30/2023] [Accepted: 05/08/2023] [Indexed: 06/07/2023]
Abstract
How microbes interact with their environment and how the complex interplay of their genes enables them to survive and thrive under stress is a fundamental question in microbial system biology, which is also important from a public health perspective. Large-scale studies of gene-gene, gene-drug, and drug-drug interactions have proven to be powerful tools for elucidating gene function and functional modules in the cell. Approaches that systematically quantify phenotypes in libraries of microbial strains with genome-wide genetic perturbations are crucial for progress in this area. Here, we review recent advances in this field, and point out applications to the study of gene-drug interactions. We highlight newly developed techniques for the rapid generation of genome-wide mutant libraries and the high-throughput measurement of more complex phenotypes and other observables, such as cell morphology or thermal stability of the proteome.
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Affiliation(s)
- Janina Müller
- Institute for Biological Physics, University of Cologne, 50931 Cologne, Germany
| | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, 50931 Cologne, Germany; Center for Data and Simulation Science, University of Cologne, 50931 Cologne, Germany.
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16
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Aubé S, Nielly-Thibault L, Landry CR. Evolutionary trade-off and mutational bias could favor transcriptional over translational divergence within paralog pairs. PLoS Genet 2023; 19:e1010756. [PMID: 37235586 DOI: 10.1371/journal.pgen.1010756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
How changes in the different steps of protein synthesis-transcription, translation and degradation-contribute to differences of protein abundance among genes is not fully understood. There is however accumulating evidence that transcriptional divergence might have a prominent role. Here, we show that yeast paralogous genes are more divergent in transcription than in translation. We explore two causal mechanisms for this predominance of transcriptional divergence: an evolutionary trade-off between the precision and economy of gene expression and a larger mutational target size for transcription. Performing simulations within a minimal model of post-duplication evolution, we find that both mechanisms are consistent with the observed divergence patterns. We also investigate how additional properties of the effects of mutations on gene expression, such as their asymmetry and correlation across levels of regulation, can shape the evolution of paralogs. Our results highlight the importance of fully characterizing the distributions of mutational effects on transcription and translation. They also show how general trade-offs in cellular processes and mutation bias can have far-reaching evolutionary impacts.
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Affiliation(s)
- Simon Aubé
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Québec, Canada
- Centre de Recherche en Données Massives, Université Laval, Québec, Québec, Canada
| | - Lou Nielly-Thibault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Québec, Canada
- Centre de Recherche en Données Massives, Université Laval, Québec, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Québec, Canada
- Centre de Recherche en Données Massives, Université Laval, Québec, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
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17
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Daalman WKG, Sweep E, Laan L. A tractable physical model for the yeast polarity predicts epistasis and fitness. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220044. [PMID: 37004720 PMCID: PMC10067261 DOI: 10.1098/rstb.2022.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Accurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where mechanistic information is abundant. We coarse-grain molecular interactions into a so-called mesotype, which we combine with gene expression noise into a physical cell cycle model. First, we show with computer simulations that the mesotype allows validation of the most current biochemical polarity models by quantitatively matching doubling times. Second, the mesotype elucidates epistasis emergence as exemplified by evaluating the predicted mutational effect of key polarity protein Bem1p when combined with known interactors or under different growth conditions. This example also illustrates how unlikely evolutionary trajectories can become more accessible. The tractability of our biophysically justifiable approach inspires a road-map towards bottom-up modelling complementary to statistical inferences. This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
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Affiliation(s)
| | - Els Sweep
- Department of Bionanoscience, TU Delft, 2629 HZ Delft, The Netherlands
| | - Liedewij Laan
- Department of Bionanoscience, TU Delft, 2629 HZ Delft, The Netherlands
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18
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Radford F, Rinehart J, Isaacs FJ. Mapping the in vivo fitness landscape of a tethered ribosome. SCIENCE ADVANCES 2023; 9:eade8934. [PMID: 37115918 PMCID: PMC10146877 DOI: 10.1126/sciadv.ade8934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fitness landscapes are models of the sequence space of a genetic element that map how each sequence corresponds to its activity and can be used to guide laboratory evolution. The ribosome is a macromolecular machine that is essential for protein synthesis in all organisms. Because of the prevalence of dominant lethal mutations, a comprehensive fitness landscape of the ribosomal peptidyl transfer center (PTC) has not yet been attained. Here, we develop a method to functionally map an orthogonal tethered ribosome (oRiboT), which permits complete mutagenesis of nucleotides located in the PTC and the resulting epistatic interactions. We found that most nucleotides studied showed flexibility to mutation, and identified epistatic interactions between them, which compensate for deleterious mutations. This work provides a basis for a deeper understanding of ribosome function and malleability and could be used to inform design of engineered ribosomes with applications to synthesize next-generation biomaterials and therapeutics.
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Affiliation(s)
- Felix Radford
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Corresponding author.
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19
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Pompei S, Cosentino Lagomarsino M. A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains. Proc Natl Acad Sci U S A 2023; 120:e2211687120. [PMID: 37018197 PMCID: PMC10104565 DOI: 10.1073/pnas.2211687120] [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: 07/07/2022] [Accepted: 02/19/2023] [Indexed: 04/06/2023] Open
Abstract
The early development of aneuploidy from an accidental chromosome missegregation shows contrasting effects. On the one hand, it is associated with significant cellular stress and decreased fitness. On the other hand, it often carries a beneficial effect and provides a quick (but typically transient) solution to external stress. These apparently controversial trends emerge in several experimental contexts, particularly in the presence of duplicated chromosomes. However, we lack a mathematical evolutionary modeling framework that comprehensively captures these trends from the mutational dynamics and the trade-offs involved in the early stages of aneuploidy. Here, focusing on chromosome gains, we address this point by introducing a fitness model where a fitness cost of chromosome duplications is contrasted by a fitness advantage from the dosage of specific genes. The model successfully captures the experimentally measured probability of emergence of extra chromosomes in a laboratory evolution setup. Additionally, using phenotypic data collected in rich media, we explored the fitness landscape, finding evidence supporting the existence of a per-gene cost of extra chromosomes. Finally, we show that the substitution dynamics of our model, evaluated in the empirical fitness landscape, explains the relative abundance of duplicated chromosomes observed in yeast population genomics data. These findings lay a firm framework for the understanding of the establishment of newly duplicated chromosomes, providing testable quantitative predictions for future observations.
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Affiliation(s)
- Simone Pompei
- IFOM ETS (Ente del Terzo Settore) - The AIRC (Associazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology, Milano20139, Italy
| | - Marco Cosentino Lagomarsino
- IFOM ETS (Ente del Terzo Settore) - The AIRC (Associazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology, Milano20139, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, Milano20133, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Milano, Milano20133, Italy
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20
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Riachy L, Ferrand T, Chasserot-Golaz S, Galas L, Alexandre S, Montero-Hadjadje M. Advanced Imaging Approaches to Reveal Molecular Mechanisms Governing Neuroendocrine Secretion. Neuroendocrinology 2023; 113:107-119. [PMID: 34915491 DOI: 10.1159/000521457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/19/2022]
Abstract
Identification of the molecular mechanisms governing neuroendocrine secretion and resulting intercellular communication is one of the great challenges of cell biology to better understand organism physiology and neurosecretion disruption-related pathologies such as hypertension, neurodegenerative, or metabolic diseases. To visualize molecule distribution and dynamics at the nanoscale, many imaging approaches have been developed and are still emerging. In this review, we provide an overview of the pioneering studies using transmission electron microscopy, atomic force microscopy, total internal reflection microscopy, and super-resolution microscopy in neuroendocrine cells to visualize molecular mechanisms driving neurosecretion processes, including exocytosis and associated fusion pores, endocytosis and associated recycling vesicles, and protein-protein or protein-lipid interactions. Furthermore, the potential and the challenges of these different advanced imaging approaches for application in the study of neuroendocrine cell biology are discussed, aiming to guide researchers to select the best approach for their specific purpose around the crucial but not yet fully understood neurosecretion process.
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Affiliation(s)
- Lina Riachy
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Thomas Ferrand
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Sylvette Chasserot-Golaz
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Strasbourg University, Strasbourg, France
| | - Ludovic Galas
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Stéphane Alexandre
- Polymères, Biopolymères, Surfaces Laboratory, CNRS, Normandie University, UNIROUEN, UMR 6270, Rouen, France
| | - Maité Montero-Hadjadje
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
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21
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Mechanisms of regulatory evolution in yeast. Curr Opin Genet Dev 2022; 77:101998. [PMID: 36220001 PMCID: PMC10117219 DOI: 10.1016/j.gde.2022.101998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
Studies of regulatory variation in yeast - at the level of new mutations, polymorphisms within a species, and divergence between species - have provided great insight into the molecular and evolutionary processes responsible for the evolution of gene expression in eukaryotes. The increasing ease with which yeast genomes can be manipulated and expression quantified in a high-throughput manner has recently accelerated mechanistic studies of cis- and trans-regulatory variation at multiple evolutionary timescales. These studies have, for example, identified differences in the properties of cis- and trans-acting mutations that affect their evolutionary fate, experimentally characterized the molecular mechanisms through which cis- and trans-regulatory variants act, and illustrated how regulatory networks can diverge between species with or without changes in gene expression.
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22
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Bédard C, Cisneros AF, Jordan D, Landry CR. Correlation between protein abundance and sequence conservation: what do recent experiments say? Curr Opin Genet Dev 2022; 77:101984. [PMID: 36162152 DOI: 10.1016/j.gde.2022.101984] [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: 06/23/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 01/27/2023]
Abstract
Cells evolve in a space of parameter values set by physical and chemical forces. These constraints create associations among cellular properties. A particularly strong association is the negative correlation between the rate of evolution of proteins and their abundance in the cell. Highly expressed proteins evolve slower than lowly expressed ones. Multiple hypotheses have been put forward to explain this relationship, including, for instance, the requirement for higher mRNA stability, misfolding avoidance, and misinteraction avoidance for highly expressed proteins. Here, we review some of these hypotheses, their predictions, and how they are supported to finally discuss recent experiments that have been performed to test these predictions.
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Affiliation(s)
- Camille Bédard
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada. https://twitter.com/@CamilleBed17
| | - Angel F Cisneros
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada. https://twitter.com/@AngelFCC119
| | - David Jordan
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada. https://twitter.com/@DavidJordan1997
| | - Christian R Landry
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada; Centre de Recherche sur les Données Massives, Université Laval, G1V 0A6, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada.
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23
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Srivastava M, Payne JL. On the incongruence of genotype-phenotype and fitness landscapes. PLoS Comput Biol 2022; 18:e1010524. [PMID: 36121840 PMCID: PMC9521842 DOI: 10.1371/journal.pcbi.1010524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/29/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
The mapping from genotype to phenotype to fitness typically involves multiple nonlinearities that can transform the effects of mutations. For example, mutations may contribute additively to a phenotype, but their effects on fitness may combine non-additively because selection favors a low or intermediate value of that phenotype. This can cause incongruence between the topographical properties of a fitness landscape and its underlying genotype-phenotype landscape. Yet, genotype-phenotype landscapes are often used as a proxy for fitness landscapes to study the dynamics and predictability of evolution. Here, we use theoretical models and empirical data on transcription factor-DNA interactions to systematically study the incongruence of genotype-phenotype and fitness landscapes when selection favors a low or intermediate phenotypic value. Using the theoretical models, we prove a number of fundamental results. For example, selection for low or intermediate phenotypic values does not change simple sign epistasis into reciprocal sign epistasis, implying that genotype-phenotype landscapes with only simple sign epistasis motifs will always give rise to single-peaked fitness landscapes under such selection. More broadly, we show that such selection tends to create fitness landscapes that are more rugged than the underlying genotype-phenotype landscape, but this increased ruggedness typically does not frustrate adaptive evolution because the local adaptive peaks in the fitness landscape tend to be nearly as tall as the global peak. Many of these results carry forward to the empirical genotype-phenotype landscapes, which may help to explain why low- and intermediate-affinity transcription factor-DNA interactions are so prevalent in eukaryotic gene regulation. How do mutations change phenotypic traits and organismal fitness? This question is often addressed in the context of a classic metaphor of evolutionary theory—the fitness landscape. A fitness landscape is akin to a physical landscape, in which genotypes define spatial coordinates, and fitness defines the elevation of each coordinate. Evolution then acts like a hill-climbing process, in which populations ascend fitness peaks as a consequence of mutation and selection. It is becoming increasingly common to construct such landscapes using experimental data from high-throughput sequencing technologies and phenotypic assays, in systems such as macromolecules and gene regulatory circuits. Although these landscapes are typically defined by molecular phenotypes, and are therefore more appropriately referred to as genotype-phenotype landscapes, they are often used to study evolutionary dynamics. This requires the assumption that the molecular phenotype is a reasonable proxy for fitness, which need not be the case. For example, selection may favor a low or intermediate phenotypic value, causing incongruence between a fitness landscape and its underlying genotype-phenotype landscape. Here, we study such incongruence using a diversity of theoretical models and experimental data from gene regulatory systems. We regularly find incongruence, in that fitness landscapes tend to comprise more peaks than their underlying genotype-phenotype landscapes. However, using evolutionary simulations, we show that this increased ruggedness need not impede adaptation.
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Affiliation(s)
- Malvika Srivastava
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
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24
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Moschner C, Wedd C, Bakshi S. The context matrix: Navigating biological complexity for advanced biodesign. Front Bioeng Biotechnol 2022; 10:954707. [PMID: 36082163 PMCID: PMC9445834 DOI: 10.3389/fbioe.2022.954707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/29/2022] [Indexed: 12/05/2022] Open
Abstract
Synthetic biology offers many solutions in healthcare, production, sensing and agriculture. However, the ability to rationally engineer synthetic biosystems with predictable and robust functionality remains a challenge. A major reason is the complex interplay between the synthetic genetic construct, its host, and the environment. Each of these contexts contains a number of input factors which together can create unpredictable behaviours in the engineered biosystem. It has become apparent that for the accurate assessment of these contextual effects a more holistic approach to design and characterisation is required. In this perspective article, we present the context matrix, a conceptual framework to categorise and explore these contexts and their net effect on the designed synthetic biosystem. We propose the use and community-development of the context matrix as an aid for experimental design that simplifies navigation through the complex design space in synthetic biology.
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25
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Rabbers I, Bruggeman FJ. Escherichia coli
robustly expresses ATP synthase at growth rate‐maximizing concentrations. FEBS J 2022; 289:4925-4934. [PMID: 35175666 PMCID: PMC9544884 DOI: 10.1111/febs.16401] [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: 07/28/2021] [Revised: 12/16/2021] [Accepted: 02/15/2022] [Indexed: 11/30/2022]
Abstract
Fitness‐enhancing adaptations of protein expression and its regulation are an important aspect of bacterial evolution. A key question is whether evolution has led to optimal protein expression that maximizes immediate growth rate (short‐term fitness) in a robust manner (consistently across diverse conditions). Alternatively, they could display suboptimal short‐term fitness, because they cannot do better or because they instead strive for long‐term fitness maximization by, for instance, preparing for future conditions. To address this question, we focus on the ATP‐producing enzyme F1F0 H+‐ATPase, which is an abundant enzyme and ubiquitously expressed across conditions. Its expression is highly regulated and dependent on growth rate and nutrient conditions. For instance, during growth on sugars, when metabolism is overflowing acetate, glycolysis supplies most ATP, while H+‐ATPase is the main source of ATP synthesis during growth on acetate. We tested the optimality of H+‐ATPase expression in Escherichia coli across different nutrient conditions. In all tested conditions, wild‐type E. coli expresses its H+‐ATPase remarkably close (within a few per cent) to optimal concentrations that maximize immediate growth rate. This work indicates that bacteria can indeed achieve robust optimal protein expression for immediate growth‐rate maximization.
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Affiliation(s)
- Iraes Rabbers
- Systems Biology Lab, AIMMS VU University Amsterdam The Netherlands
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26
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Johnson MS, Desai MM. Mutational robustness changes during long-term adaptation in laboratory budding yeast populations. eLife 2022; 11:76491. [PMID: 35880743 PMCID: PMC9355567 DOI: 10.7554/elife.76491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
As an adapting population traverses the fitness landscape, its local neighborhood (i.e., the collection of fitness effects of single-step mutations) can change shape because of interactions with mutations acquired during evolution. These changes to the distribution of fitness effects can affect both the rate of adaptation and the accumulation of deleterious mutations. However, while numerous models of fitness landscapes have been proposed in the literature, empirical data on how this distribution changes during evolution remains limited. In this study, we directly measure how the fitness landscape neighborhood changes during laboratory adaptation. Using a barcode-based mutagenesis system, we measure the fitness effects of 91 specific gene disruption mutations in genetic backgrounds spanning 8000–10,000 generations of evolution in two constant environments. We find that the mean of the distribution of fitness effects decreases in one environment, indicating a reduction in mutational robustness, but does not change in the other. We show that these distribution-level patterns result from differences in the relative frequency of certain patterns of epistasis at the level of individual mutations, including fitness-correlated and idiosyncratic epistasis.
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Affiliation(s)
- Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
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27
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Gene regulation in Escherichia coli is commonly selected for both high plasticity and low noise. Nat Ecol Evol 2022; 6:1165-1179. [PMID: 35726087 DOI: 10.1038/s41559-022-01783-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 05/03/2022] [Indexed: 11/08/2022]
Abstract
Bacteria often respond to dynamically changing environments by regulating gene expression. Despite this regulation being critically important for growth and survival, little is known about how selection shapes gene regulation in natural populations. To better understand the role natural selection plays in shaping bacterial gene regulation, here we compare differences in the regulatory behaviour of naturally segregating promoter variants from Escherichia coli (which have been subject to natural selection) to randomly mutated promoter variants (which have never been exposed to natural selection). We quantify gene expression phenotypes (expression level, plasticity and noise) for hundreds of promoter variants across multiple environments and show that segregating promoter variants are enriched for mutations with minimal effects on expression level. In many promoters, we infer that there is strong selection to maintain high levels of plasticity, and direct selection to decrease or increase cell-to-cell variability in expression. Taken together, these results expand our knowledge of how gene regulation is affected by natural selection and highlight the power of comparing naturally segregating polymorphisms to de novo random mutations to quantify the action of selection.
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28
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Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Nature 2022; 606:725-731. [PMID: 35676473 PMCID: PMC9650438 DOI: 10.1038/s41586-022-04823-w] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/28/2022] [Indexed: 01/12/2023]
Abstract
Synonymous mutations in protein-coding genes do not alter protein sequences and are thus generally presumed to be neutral or nearly neutral1-5. Here, to experimentally verify this presumption, we constructed 8,341 yeast mutants each carrying a synonymous, nonsynonymous or nonsense mutation in one of 21 endogenous genes with diverse functions and expression levels and measured their fitness relative to the wild type in a rich medium. Three-quarters of synonymous mutations resulted in a significant reduction in fitness, and the distribution of fitness effects was overall similar-albeit nonidentical-between synonymous and nonsynonymous mutations. Both synonymous and nonsynonymous mutations frequently disturbed the level of mRNA expression of the mutated gene, and the extent of the disturbance partially predicted the fitness effect. Investigations in additional environments revealed greater across-environment fitness variations for nonsynonymous mutants than for synonymous mutants despite their similar fitness distributions in each environment, suggesting that a smaller proportion of nonsynonymous mutants than synonymous mutants are always non-deleterious in a changing environment to permit fixation, potentially explaining the common observation of substantially lower nonsynonymous than synonymous substitution rates. The strong non-neutrality of most synonymous mutations, if it holds true for other genes and in other organisms, would require re-examination of numerous biological conclusions about mutation, selection, effective population size, divergence time and disease mechanisms that rely on the assumption that synoymous mutations are neutral.
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Hogan AM, Cardona ST. Gradients in gene essentiality reshape antibacterial research. FEMS Microbiol Rev 2022; 46:fuac005. [PMID: 35104846 PMCID: PMC9075587 DOI: 10.1093/femsre/fuac005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.
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Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
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30
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The evolution, evolvability and engineering of gene regulatory DNA. Nature 2022; 603:455-463. [PMID: 35264797 DOI: 10.1038/s41586-022-04506-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Abstract
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal phenotype and fitness1-3. Constructing complete fitness landscapes, in which DNA sequences are mapped to fitness, is a long-standing goal in biology, but has remained elusive because it is challenging to generalize reliably to vast sequence spaces4-6. Here we build sequence-to-expression models that capture fitness landscapes and use them to decipher principles of regulatory evolution. Using millions of randomly sampled promoter DNA sequences and their measured expression levels in the yeast Saccharomyces cerevisiae, we learn deep neural network models that generalize with excellent prediction performance, and enable sequence design for expression engineering. Using our models, we study expression divergence under genetic drift and strong-selection weak-mutation regimes to find that regulatory evolution is rapid and subject to diminishing returns epistasis; that conflicting expression objectives in different environments constrain expression adaptation; and that stabilizing selection on gene expression leads to the moderation of regulatory complexity. We present an approach for using such models to detect signatures of selection on expression from natural variation in regulatory sequences and use it to discover an instance of convergent regulatory evolution. We assess mutational robustness, finding that regulatory mutation effect sizes follow a power law, characterize regulatory evolvability, visualize promoter fitness landscapes, discover evolvability archetypes and illustrate the mutational robustness of natural regulatory sequence populations. Our work provides a general framework for designing regulatory sequences and addressing fundamental questions in regulatory evolution.
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31
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Elsemman IE, Rodriguez Prado A, Grigaitis P, Garcia Albornoz M, Harman V, Holman SW, van Heerden J, Bruggeman FJ, Bisschops MMM, Sonnenschein N, Hubbard S, Beynon R, Daran-Lapujade P, Nielsen J, Teusink B. Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Nat Commun 2022; 13:801. [PMID: 35145105 PMCID: PMC8831649 DOI: 10.1038/s41467-022-28467-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/27/2022] [Indexed: 01/20/2023] Open
Abstract
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation—known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells. Metabolically active organelles compete for cytosolic space and resources during metabolism rewiring. Here, the authors develop a computational model of yeast metabolism and resource allocation to predict condition- and compartment-specific proteome constraints that govern metabolic strategies.
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Affiliation(s)
- Ibrahim E Elsemman
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark.,Department of Information Systems, Faculty of Computers and Information, Assiut University, Assiut, Egypt
| | - Angelica Rodriguez Prado
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Pranas Grigaitis
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Victoria Harman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Stephen W Holman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Johan van Heerden
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mark M M Bisschops
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Nikolaus Sonnenschein
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark
| | - Simon Hubbard
- Division of Evolution & Genomic Sciences, University of Manchester, Manchester, UK
| | - Rob Beynon
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Pascale Daran-Lapujade
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark. .,Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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32
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Bheemireddy S, Srinivasan N. Computational Study on the Dynamics of Mycobacterium Tuberculosis RNA Polymerase Assembly. Methods Mol Biol 2022; 2516:61-79. [PMID: 35922622 DOI: 10.1007/978-1-0716-2413-5_5] [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: 06/15/2023]
Abstract
Gene regulation is an intricate phenomenon involving precise function of many macromolecular complexes. Molecular basis of this phenomenon is highly complex and cannot be fully understood using a single technique. Computational approaches can play a crucial role in overall understanding of functional and mechanistic features of a protein or an assembly. Large amounts of structural data pertaining to these complexes are publicly available. In this project, we took advantage of the availability of the structural information to unravel functional intricacies of Mycobacterium tuberculosis RNA polymerase upon interaction with RbpA. In this article, we discuss how the knowledge on protein structure and dynamics can be exploited to study function using various computational tools and resources. Overall, this article provides an overview of various computational methods which can be efficiently used to understand the role of any protein. We hope especially the nonexperts in the field could benefit from our article.
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Affiliation(s)
- Sneha Bheemireddy
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India.
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33
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Park S, Supek F, Lehner B. Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers. Nat Commun 2021; 12:7051. [PMID: 34862370 PMCID: PMC8642467 DOI: 10.1038/s41467-021-27242-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/09/2021] [Indexed: 11/10/2022] Open
Abstract
The classic two-hit model posits that both alleles of a tumor suppressor gene (TSG) must be inactivated to cause cancer. In contrast, for some oncogenes and haploinsufficient TSGs, a single genetic alteration can suffice to increase tumor fitness. Here, by quantifying the interactions between mutations and copy number alterations (CNAs) across 10,000 tumors, we show that many cancer genes actually switch between acting as one-hit or two-hit drivers. Third order genetic interactions identify the causes of some of these switches in dominance and dosage sensitivity as mutations in other genes in the same biological pathway. The correct genetic model for a gene thus depends on the other mutations in a genome, with a second hit in the same gene or an alteration in a different gene in the same pathway sometimes representing alternative evolutionary paths to cancer.
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Affiliation(s)
- Solip Park
- Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain.
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Ben Lehner
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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34
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Gerhardt KP, Rao SD, Olson EJ, Igoshin OA, Tabor JJ. Independent control of mean and noise by convolution of gene expression distributions. Nat Commun 2021; 12:6957. [PMID: 34845228 PMCID: PMC8630168 DOI: 10.1038/s41467-021-27070-5] [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: 03/10/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022] Open
Abstract
Gene expression noise can reduce cellular fitness or facilitate processes such as alternative metabolism, antibiotic resistance, and differentiation. Unfortunately, efforts to study the impacts of noise have been hampered by a scaling relationship between noise and expression level from individual promoters. Here, we use theory to demonstrate that mean and noise can be controlled independently by expressing two copies of a gene from separate inducible promoters in the same cell. We engineer low and high noise inducible promoters to validate this result in Escherichia coli, and develop a model that predicts the experimental distributions. Finally, we use our method to reveal that the response of a promoter to a repressor is less sensitive with higher repressor noise and explain this result using a law from probability theory. Our approach can be applied to investigate the effects of noise on diverse biological pathways or program cellular heterogeneity for synthetic biology applications.
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Affiliation(s)
- Karl P Gerhardt
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Satyajit D Rao
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Evan J Olson
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
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35
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Gao R, Helfant LJ, Wu T, Li Z, Brokaw SE, Stock AM. A balancing act in transcription regulation by response regulators: titration of transcription factor activity by decoy DNA binding sites. Nucleic Acids Res 2021; 49:11537-11549. [PMID: 34669947 PMCID: PMC8599769 DOI: 10.1093/nar/gkab935] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022] Open
Abstract
Studies of transcription regulation are often focused on binding of transcription factors (TFs) to a small number of promoters of interest. It is often assumed that TFs are in great excess to their binding sites (TFBSs) and competition for TFs between DNA sites is seldom considered. With increasing evidence that TFBSs are exceedingly abundant for many TFs and significant variations in TF and TFBS numbers occur during growth, the interplay between a TF and all TFBSs should not be ignored. Here, we use additional decoy DNA sites to quantitatively analyze how the relative abundance of a TF to its TFBSs impacts the steady-state level and onset time of gene expression for the auto-activated Escherichia coli PhoB response regulator. We show that increasing numbers of decoy sites progressively delayed transcription activation and lowered promoter activities. Perturbation of transcription regulation by additional TFBSs did not require extreme numbers of decoys, suggesting that PhoB is approximately at capacity for its DNA sites. Addition of decoys also converted a graded response to a bi-modal response. We developed a binding competition model that captures the major features of experimental observations, providing a quantitative framework to assess how variations in TFs and TFBSs influence transcriptional responses.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Libby J Helfant
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Ti Wu
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Zeyue Li
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Samantha E Brokaw
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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36
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Expression level is a major modifier of the fitness landscape of a protein coding gene. Nat Ecol Evol 2021; 6:103-115. [PMID: 34795386 DOI: 10.1038/s41559-021-01578-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/01/2021] [Indexed: 11/09/2022]
Abstract
The phenotypic consequence of a genetic mutation depends on many factors including the expression level of a gene. However, a comprehensive quantification of this expression effect is still lacking, as is a further general mechanistic understanding of the effect. Here, we measured the fitness effect of almost all (>97.5%) single-nucleotide mutations in GFP, an exogenous gene with no physiological function, and URA3, a conditionally essential gene. Both genes were driven by two promoters whose expression levels differed by around tenfold. The resulting fitness landscapes revealed that the fitness effects of at least 42% of all single-nucleotide mutations within the genes were expression dependent. Although only a small fraction of variation in fitness effects among different mutations can be explained by biophysical properties of the protein and messenger RNA of the gene, our analyses revealed that the avoidance of stochastic molecular errors generally underlies the expression dependency of mutational effects and suggested protein misfolding as the most important type of molecular error among those examined. Our results therefore directly explained the slower evolution of highly expressed genes and highlighted cytotoxicity due to stochastic molecular errors as a non-negligible component for understanding the phenotypic consequence of mutations.
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37
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Guharajan S, Chhabra S, Parisutham V, Brewster RC. Quantifying the regulatory role of individual transcription factors in Escherichia coli. Cell Rep 2021; 37:109952. [PMID: 34758318 PMCID: PMC8667592 DOI: 10.1016/j.celrep.2021.109952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/02/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022] Open
Abstract
Gene regulation often results from the action of multiple transcription factors (TFs) acting at a promoter, obscuring the individual regulatory effect of each TF on RNA polymerase (RNAP). Here we measure the fundamental regulatory interactions of TFs in E. coli by designing synthetic target genes that isolate individual TFs' regulatory effects. Using a thermodynamic model, each TF's regulatory interactions are decoupled from TF occupancy and interpreted as acting through (de)stabilization of RNAP and (de)acceleration of transcription initiation. We find that the contribution of each mechanism depends on TF identity and binding location; regulation immediately downstream of the promoter is insensitive to TF identity, but the same TFs regulate by distinct mechanisms upstream of the promoter. These two mechanisms are uncoupled and can act coherently, to reinforce the observed regulatory role (activation/repression), or incoherently, wherein the TF regulates two distinct steps with opposing effects.
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Affiliation(s)
- Sunil Guharajan
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Shivani Chhabra
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Robert C Brewster
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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38
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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39
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Silvis MR, Rajendram M, Shi H, Osadnik H, Gray AN, Cesar S, Peters JM, Hearne CC, Kumar P, Todor H, Huang KC, Gross CA. Morphological and Transcriptional Responses to CRISPRi Knockdown of Essential Genes in Escherichia coli. mBio 2021; 12:e0256121. [PMID: 34634934 PMCID: PMC8510551 DOI: 10.1128/mbio.02561-21] [Citation(s) in RCA: 30] [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: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 01/03/2023] Open
Abstract
CRISPR interference (CRISPRi) has facilitated the study of essential genes in diverse organisms using both high-throughput and targeted approaches. Despite the promise of this technique, no comprehensive arrayed CRISPRi library targeting essential genes exists for the model bacterium Escherichia coli, or for any Gram-negative species. Here, we built and characterized such a library. Each of the ∼500 strains in our E. coli library contains an inducible, chromosomally integrated single guide RNA (sgRNA) targeting an essential (or selected nonessential) gene and can be mated with a pseudo-Hfr donor strain carrying a dcas9 cassette to create a CRISPRi knockdown strain. Using this system, we built an arrayed library of CRISPRi strains and performed population and single-cell growth and morphology measurements as well as targeted follow-up experiments. These studies found that inhibiting translation causes an extended lag phase, identified new modulators of cell morphology, and revealed that the morphogene mreB is subject to transcriptional feedback regulation, which is critical for the maintenance of morphology. Our findings highlight canonical and noncanonical roles for essential genes in numerous aspects of cellular homeostasis. IMPORTANCE Essential genes make up only ∼5 to 10% of the genetic complement in most organisms but occupy much of their protein synthesis and account for almost all antibiotic targets. Despite the importance of essential genes, their intractability has, until recently, hampered efforts to study them. CRISPRi has facilitated the study of essential genes by allowing inducible and titratable depletion. However, all large-scale CRISPRi studies in Gram-negative bacteria thus far have used plasmids to express CRISPRi components and have been constructed in pools, limiting their utility for targeted assays and complicating the determination of antibiotic effects. Here, we use a modular method to construct an arrayed library of chromosomally integrated CRISPRi strains targeting the essential genes of the model bacterium Escherichia coli. This library enables targeted studies of essential gene depletions and high-throughput determination of antibiotic targets and facilitates studies targeting the outer membrane, an essential component that serves as the major barrier to antibiotics.
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Affiliation(s)
- Melanie R. Silvis
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Hendrik Osadnik
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Andrew N. Gray
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cameron C. Hearne
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Parth Kumar
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Horia Todor
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Carol A. Gross
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
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40
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Liu Y, Huang Y, Lu R, Xin F, Liu G. Synthetic biology applications of the yeast mating signal pathway. Trends Biotechnol 2021; 40:620-631. [PMID: 34666896 DOI: 10.1016/j.tibtech.2021.09.007] [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: 08/09/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022]
Abstract
Cell fusion is a fundamental biological process that is involved in the development of most eukaryotic organisms. During the fusion process in Saccharomyces cerevisiae, cells respond to pheromones to trigger the MAPK (mitogen-activated protein kinase) cascade to initiate mating, followed by polarization, cell-wall remodeling, membrane fusion, and karyogamy. We highlight the applications of the yeast mating signal pathway in promoter engineering for tuning the expression of output genes, as well as in metabolic engineering for decoupling growth and metabolism, biosensors for sensitive detection and signal amplification, genetic circuits for programmable biological functionalities, and artificial consortia for cell-cell communication. Strategies such as exploiting rational engineering of modular circuits and optimizing the reproductive pathway to precisely maneuver physiological events have implications for scientific research and industrial development.
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Affiliation(s)
- Ying Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Yuxin Huang
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Ran Lu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Fengxue Xin
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Guannan Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China; Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Jiangsu Province, China.
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41
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Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell 2021; 184:4579-4592.e24. [PMID: 34297925 PMCID: PMC8382161 DOI: 10.1016/j.cell.2021.06.033] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/13/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Antibacterial agents target the products of essential genes but rarely achieve complete target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic approaches fails to discern the most attractive bacterial targets: those whose incomplete inhibition results in major fitness costs. In contrast, gene "vulnerability" is a continuous, quantifiable trait that relates the magnitude of gene inhibition to the effect on bacterial fitness. We developed a CRISPR interference-based functional genomics method to systematically titrate gene expression in Mycobacterium tuberculosis (Mtb) and monitor fitness outcomes. We identified highly vulnerable genes in various processes, including novel targets unexplored for drug discovery. Equally important, we identified invulnerable essential genes, potentially explaining failed drug discovery efforts. Comparison of vulnerability between the reference and a hypervirulent Mtb isolate revealed incomplete conservation of vulnerability and that differential vulnerability can predict differential antibacterial susceptibility. Our results quantitatively redefine essential bacterial processes and identify high-value targets for drug development.
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Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sophie Lavalette
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joshua B Wallach
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.
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42
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Abstract
Bacterial protein synthesis rates have evolved to maintain preferred stoichiometries at striking precision, from the components of protein complexes to constituents of entire pathways. Setting relative protein production rates to be well within a factor of two requires concerted tuning of transcription, RNA turnover, and translation, allowing many potential regulatory strategies to achieve the preferred output. The last decade has seen a greatly expanded capacity for precise interrogation of each step of the central dogma genome-wide. Here, we summarize how these technologies have shaped the current understanding of diverse bacterial regulatory architectures underpinning stoichiometric protein synthesis. We focus on the emerging expanded view of bacterial operons, which encode diverse primary and secondary mRNA structures for tuning protein stoichiometry. Emphasis is placed on how quantitative tuning is achieved. We discuss the challenges and open questions in the application of quantitative, genome-wide methodologies to the problem of precise protein production. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- James C Taggart
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Current affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
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43
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Biesiadecka MK, Sliwa P, Tomala K, Korona R. An Overexpression Experiment Does Not Support the Hypothesis That Avoidance of Toxicity Determines the Rate of Protein Evolution. Genome Biol Evol 2021; 12:589-596. [PMID: 32259256 PMCID: PMC7250497 DOI: 10.1093/gbe/evaa067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2020] [Indexed: 12/22/2022] Open
Abstract
The misfolding avoidance hypothesis postulates that sequence mutations render proteins cytotoxic and therefore the higher the gene expression, the stronger the operation of selection against substitutions. This translates into prediction that relative toxicity of extant proteins is higher for those evolving faster. In the present experiment, we selected pairs of yeast genes which were paralogous but evolving at different rates. We expressed them artificially to high levels. We expected that toxicity would be higher for ones bearing more mutations, especially that overcrowding should rather exacerbate than reverse the already existing differences in misfolding rates. We did find that the applied mode of overexpression caused a considerable decrease in fitness and that the decrease was proportional to the amount of excessive protein. However, it was not higher for proteins which are normally expressed at lower levels (and have less conserved sequence). This result was obtained consistently, regardless whether the rate of growth or ability to compete in common cultures was used as a proxy for fitness. In additional experiments, we applied factors that reduce accuracy of translation or enhance structural instability of proteins. It did not change a consistent pattern of independence between the fitness cost caused by overexpression of a protein and the rate of its sequence evolution.
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Affiliation(s)
| | - Piotr Sliwa
- Department of Genetics, Faculty of Biotechnology, University of Rzeszów, Poland
| | - Katarzyna Tomala
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Cracow, Poland
| | - Ryszard Korona
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Cracow, Poland
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44
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Abstract
Many studies have focused on the mechanisms of long-term retention of gene duplicates, such as the gain of functions or reciprocal losses. However, such changes are more likely to occur if the duplicates are maintained for a long period. This time span will be short if duplication is immediately deleterious. We measured the distribution of fitness effects of gene duplication for 899 genes in budding yeast. We find that gene duplication is more likely to be deleterious than beneficial. However, contrary to previous models, in general, gene duplication does not affect fitness by altering the organization of protein complexes. We show that expression attenuation may protect complexes from the effects of gene duplication. Gene duplication is ubiquitous and a major driver of phenotypic diversity across the tree of life, but its immediate consequences are not fully understood. Deleterious effects would decrease the probability of retention of duplicates and prevent their contribution to long-term evolution. One possible detrimental effect of duplication is the perturbation of the stoichiometry of protein complexes. Here, we measured the fitness effects of the duplication of 899 essential genes in the budding yeast using high-resolution competition assays. At least 10% of genes caused a fitness disadvantage when duplicated. Intriguingly, the duplication of most protein complex subunits had small to nondetectable effects on fitness, with few exceptions. We selected four complexes with subunits that had an impact on fitness when duplicated and measured the impact of individual gene duplications on their protein–protein interactions. We found that very few duplications affect both fitness and interactions. Furthermore, large complexes such as the 26S proteasome are protected from gene duplication by attenuation of protein abundance. Regulatory mechanisms that maintain the stoichiometric balance of protein complexes may protect from the immediate effects of gene duplication. Our results show that a better understanding of protein regulation and assembly in complexes is required for the refinement of current models of gene duplication.
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45
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Chiang AH, Chang J, Wang J, Vitkup D. Exons as units of phenotypic impact for truncating mutations in autism. Mol Psychiatry 2021; 26:1685-1695. [PMID: 33110259 DOI: 10.1038/s41380-020-00876-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorders (ASD) are a group of related neurodevelopmental diseases displaying significant genetic and phenotypic heterogeneity. Despite recent progress in understanding ASD genetics, the nature of phenotypic heterogeneity across probands remains unclear. Notably, likely gene-disrupting (LGD) de novo mutations affecting the same gene often result in substantially different ASD phenotypes. Nevertheless, we find that truncating mutations affecting the same exon frequently lead to strikingly similar intellectual phenotypes in unrelated ASD probands. Analogous patterns are observed for two independent proband cohorts and several other important ASD-associated phenotypes. We find that exons biased toward prenatal and postnatal expression preferentially contribute to ASD cases with lower and higher IQ phenotypes, respectively. These results suggest that exons, rather than genes, often represent a unit of effective phenotypic impact for truncating mutations in autism. The observed phenotypic patterns are likely mediated by nonsense-mediated decay (NMD) of splicing isoforms, with autism phenotypes usually triggered by relatively mild (15-30%) decreases in overall gene dosage. We find that each ASD gene with recurrent mutations can be characterized by a parameter, phenotype dosage sensitivity (PDS), which quantifies the relationship between changes in a gene's dosage and changes in a given disease phenotype. We further demonstrate analogous relationships between exon LGDs and gene expression changes in multiple human tissues. Therefore, similar phenotypic patterns may be also observed in other human genetic disorders.
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Affiliation(s)
- Andrew H Chiang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Jonathan Chang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Jiayao Wang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Dennis Vitkup
- Department of Biomedical Informatics, Columbia University, New York, NY, USA. .,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA.
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46
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Fagny M, Austerlitz F. Polygenic Adaptation: Integrating Population Genetics and Gene Regulatory Networks. Trends Genet 2021; 37:631-638. [PMID: 33892958 DOI: 10.1016/j.tig.2021.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
The adaptation of populations to local environments often relies on the selection of optimal values for polygenic traits. Here, we first summarize the results obtained from different quantitative genetics and population genetics models, about the genetic architecture of polygenic traits and their response to directional selection. We then highlight the contribution of systems biology to the understanding of the molecular bases of polygenic traits and the evolution of gene regulatory networks involved in these traits. Finally, we discuss the need for a unifying framework merging the fields of population genetics, quantitative genetics and systems biology to better understand the molecular bases of polygenic traits adaptation.
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Affiliation(s)
- Maud Fagny
- UMR7206 Eco-Anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France.
| | - Frédéric Austerlitz
- UMR7206 Eco-Anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
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47
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Lalanne J, Parker DJ, Li G. Spurious regulatory connections dictate the expression-fitness landscape of translation factors. Mol Syst Biol 2021; 17:e10302. [PMID: 33900014 PMCID: PMC8073009 DOI: 10.15252/msb.202110302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts.
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Affiliation(s)
- Jean‐Benoît Lalanne
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Darren J Parker
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Gene‐Wei Li
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
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48
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Ong JY, Pence JT, Molik DC, Shepherd HAM, Goodson HV. Yeast grown in continuous culture systems can detect mutagens with improved sensitivity relative to the Ames test. PLoS One 2021; 16:e0235303. [PMID: 33730086 PMCID: PMC7968628 DOI: 10.1371/journal.pone.0235303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/18/2021] [Indexed: 11/20/2022] Open
Abstract
Continuous culture systems allow for the controlled growth of microorganisms over a long period of time. Here, we develop a novel test for mutagenicity that involves growing yeast in continuous culture systems exposed to low levels of mutagen for a period of approximately 20 days. In contrast, most microorganism-based tests for mutagenicity expose the potential mutagen to the biological reporter at a high concentration of mutagen for a short period of time. Our test improves upon the sensitivity of the well-established Ames test by at least 20-fold for each of two mutagens that act by different mechanisms (the intercalator ethidium bromide and alkylating agent methyl methanesulfonate). To conduct the tests, cultures were grown in small, inexpensive continuous culture systems in media containing (potential) mutagen, and the resulting mutagenicity of the added compound was assessed via two methods: a canavanine-based plate assay and whole genome sequencing. In the canavanine-based plate assay, we were able to detect a clear relationship between the amount of mutagen and the number of canavanine-resistant mutant colonies over a period of one to three weeks of exposure. Whole genome sequencing of yeast grown in continuous culture systems exposed to methyl methanesulfonate demonstrated that quantification of mutations is possible by identifying the number of unique variants across each strain. However, this method had lower sensitivity than the plate-based assay and failed to distinguish the different concentrations of mutagen. In conclusion, we propose that yeast grown in continuous culture systems can provide an improved and more sensitive test for mutagenicity.
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Affiliation(s)
- Joseph Y. Ong
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Julia T. Pence
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - David C. Molik
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Heather A. M. Shepherd
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Holly V. Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
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49
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Kovács K, Farkas Z, Bajić D, Kalapis D, Daraba A, Almási K, Kintses B, Bódi Z, Notebaart RA, Poyatos JF, Kemmeren P, Holstege FCP, Pál C, Papp B. Suboptimal Global Transcriptional Response Increases the Harmful Effects of Loss-of-Function Mutations. Mol Biol Evol 2021; 38:1137-1150. [PMID: 33306797 PMCID: PMC7947755 DOI: 10.1093/molbev/msaa280] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The fitness impact of loss-of-function mutations is generally assumed to reflect the loss of specific molecular functions associated with the perturbed gene. Here, we propose that rewiring of the transcriptome upon deleterious gene inactivation is frequently nonspecific and mimics stereotypic responses to external environmental change. Consequently, transcriptional response to gene deletion could be suboptimal and incur an extra fitness cost. Analysis of the transcriptomes of ∼1,500 single-gene deletion Saccharomyces cerevisiae strains supported this scenario. First, most transcriptomic changes are not specific to the deleted gene but are rather triggered by perturbations in functionally diverse genes. Second, gene deletions that alter the expression of dosage-sensitive genes are especially harmful. Third, by elevating the expression level of downregulated genes, we could experimentally mitigate the fitness defect of gene deletions. Our work shows that rewiring of genomic expression upon gene inactivation shapes the harmful effects of mutations.
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Affiliation(s)
- Károly Kovács
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Zoltán Farkas
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Djordje Bajić
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
- Logic of Genomic Systems Laboratory, Department of Systems Biology, CNB-CSIC, Madrid, Spain
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Microbial Sciences Institute, Yale University West Campus, West Haven, CT
| | - Dorottya Kalapis
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Andreea Daraba
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Karola Almási
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Bálint Kintses
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
- HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Zoltán Bódi
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Richard A Notebaart
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, Department of Systems Biology, CNB-CSIC, Madrid, Spain
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Csaba Pál
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Balázs Papp
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
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50
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Bruggeman FJ, Planqué R, Molenaar D, Teusink B. Searching for principles of microbial physiology. FEMS Microbiol Rev 2021; 44:821-844. [PMID: 33099619 PMCID: PMC7685786 DOI: 10.1093/femsre/fuaa034] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/02/2020] [Indexed: 12/27/2022] Open
Abstract
Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selective pressures and physicochemical constraints? If so, a broadly-applicable theory might be developed that predicts common microbiological behaviours. Microbial systems biologists have been working out the contours of this theory for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, metabolism, cell composition and steady-state growth. The theory makes predictions about fitness costs and benefits of protein expression, physicochemical constraints on cell growth and characteristics of optimal metabolisms that maximise growth rate. Comparisons of the theory with experimental data indicates that microorganisms often aim for maximisation of growth rate, also in the presence of stresses; they often express optimal metabolisms and metabolic proteins at optimal concentrations. This review explains the current status of the theory for microbiologists; its roots, predictions, experimental evidence and future directions.
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Affiliation(s)
- Frank J Bruggeman
- Systems Biology Lab, AIMMS, De Boelelaan 1108, 1081 HZ, VU University, Amsterdam, The Netherlands
| | - Robert Planqué
- Department of Mathematics, De Boelelaan 1111, 1081 HV, VU University, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Systems Biology Lab, AIMMS, De Boelelaan 1108, 1081 HZ, VU University, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Biology Lab, AIMMS, De Boelelaan 1108, 1081 HZ, VU University, Amsterdam, The Netherlands
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