1
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Mu X, Evans TD, Zhang F. ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction. Nat Commun 2024; 15:5299. [PMID: 38906854 PMCID: PMC11192931 DOI: 10.1038/s41467-024-49579-1] [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: 03/14/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Adenosine-5'-triphosphate (ATP), the primary energy currency in cellular processes, drives metabolic activities and biosynthesis. Despite its importance, understanding intracellular ATP dynamics' impact on bioproduction and exploiting it for enhanced bioproduction remains largely unexplored. Here, we harness an ATP biosensor to dissect ATP dynamics across different growth phases and carbon sources in multiple microbial strains. We find transient ATP accumulations during the transition from exponential to stationary growth phases in various conditions, coinciding with fatty acid (FA) and polyhydroxyalkanoate (PHA) production in Escherichia coli and Pseudomonas putida, respectively. We identify carbon sources (acetate for E. coli, oleate for P. putida) that elevate steady-state ATP levels and boost FA and PHA production. Moreover, we employ ATP dynamics as a diagnostic tool to assess metabolic burden, revealing bottlenecks that limit limonene bioproduction. Our results not only elucidate the relationship between ATP dynamics and bioproduction but also showcase its value in enhancing bioproduction in various microbial species.
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Affiliation(s)
- Xinyue Mu
- Department of Energy Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Trent D Evans
- Department of Energy Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Fuzhong Zhang
- Department of Energy Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
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2
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Martinez A, Dijkstra P, Megonigal P, Hungate BA. Microbial central carbon metabolism in a tidal freshwater marsh and an upland mixed conifer soil under oxic and anoxic conditions. Appl Environ Microbiol 2024; 90:e0072424. [PMID: 38771053 PMCID: PMC11218644 DOI: 10.1128/aem.00724-24] [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: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
The central carbon (C) metabolic network is responsible for most of the production of energy and biosynthesis in microorganisms and is therefore key to a mechanistic understanding of microbial life in soil communities. Many upland soil communities have shown a relatively high C flux through the pentose phosphate (PP) or the Entner-Doudoroff (ED) pathway, thought to be related to oxidative damage control. We tested the hypothesis that the metabolic organization of the central C metabolic network differed between two ecosystems, an anoxic marsh soil and oxic upland soil, and would be affected by altering oxygen concentrations. We expected there to be high PP/ED pathway activity under high oxygen concentrations and in oxic soils and low PP/ED activity in reduced oxygen concentrations and in marsh soil. Although we found high PP/ED activity in the upland soil and low activity in the marsh soil, lowering the oxygen concentration for the upland soil did not reduce the relative PP/ED pathway activity as hypothesized, nor did increasing the oxygen concentration in the marsh soil increase the PP/ED pathway activity. We speculate that the high PP/ED activity in the upland soil, even when exposed to low oxygen concentrations, was related to a high demand for NADPH for biosynthesis, thus reflecting higher microbial growth rates in C-rich soils than in C-poor sediments. Further studies are needed to explain the observed metabolic diversity among soil ecosystems and determine whether it is related to microbial growth rates.IMPORTANCEWe observed that the organization of the central carbon (C) metabolic processes differed between oxic and anoxic soil. However, we also found that the pentose phosphate pathway/Entner-Doudoroff (PP/ED) pathway activity remained high after reducing the oxygen concentration for the upland soil and did not increase in response to an increase in oxygen concentration in the marsh soil. These observations contradicted the hypothesis that oxidative stress is a main driver for high PP/ED activity in soil communities. We suggest that the high PP/ED activity and NADPH production reflect higher anabolic activities and growth rates in the upland soil compared to the anaerobic marsh soil. A greater understanding of the molecular and biochemical processes in soil communities is needed to develop a mechanistic perspective on microbial activities and their relationship to soil C and nutrient cycling. Such an increased mechanistic perspective is ecologically relevant, given that the central carbon metabolic network is intimately tied to the energy metabolism of microbes, the efficiency of new microbial biomass production, and soil organic matter formation.
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Affiliation(s)
- Ayla Martinez
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Dijkstra
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
- Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, Arizona, USA
| | | | - Bruce A. Hungate
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
- Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, Arizona, USA
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3
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Basier C, Nurse P. TOR regulates variability of protein synthesis rates. EMBO J 2024; 43:1618-1633. [PMID: 38499788 PMCID: PMC11021518 DOI: 10.1038/s44318-024-00075-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Cellular processes are subject to inherent variability, but the extent to which cells can regulate this variability has received little investigation. Here, we explore the characteristics of the rate of cellular protein synthesis in single cells of the eukaryote fission yeast. Strikingly, this rate is highly variable despite protein synthesis being dependent on hundreds of reactions which might be expected to average out at the overall cellular level. The rate is variable over short time scales, and exhibits homoeostatic behaviour at the population level. Cells can regulate the level of variability through processes involving the TOR pathway, suggesting there is an optimal level of variability conferring a selective advantage. While this could be an example of bet-hedging, but we propose an alternative explanation: regulated 'loose' control of complex processes of overall cellular metabolism such as protein synthesis, may lead to this variability. This could ensure cells are fluid in control and agile in response to changing conditions, and may constitute a novel organisational principle of complex metabolic cellular systems.
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Affiliation(s)
- Clovis Basier
- Cell Cycle Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, NY, 10065, USA
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4
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Zhu L, Wang J. Quantifying Landscape-Flux via Single-Cell Transcriptomics Uncovers the Underlying Mechanism of Cell Cycle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308879. [PMID: 38353329 DOI: 10.1002/advs.202308879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/23/2024] [Indexed: 04/25/2024]
Abstract
Recent developments in single-cell sequencing technology enable the acquisition of entire transcriptome data. Understanding the underlying mechanism and identifying the driving force of transcriptional regulation governing cell function directly from these data remains challenging. This study reconstructs a continuous vector field of the cell cycle based on discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium dynamic landscape-flux. It reveals that large fluctuations disrupt the global landscape and genetic perturbations alter landscape-flux, thus identifying key genes in maintaining cell cycle dynamics and predicting associated functional effects. Additionally, it quantifies the fundamental energy cost of the cell cycle initiation and unveils that sustaining the cell cycle requires curl flux and dissipation to maintain the oscillatory phase coherence. This study enables the inference of the cell cycle gene regulatory networks directly from the single-cell transcriptomic data, including the feedback mechanisms and interaction intensity. This provides a golden opportunity to experimentally verify the landscape-flux theory and also obtain its associated quantifications. It also offers a unique framework for combining the landscape-flux theory and single-cell high-through sequencing experiments for understanding the underlying mechanisms of the cell cycle and can be extended to other nonequilibrium biological processes, such as differentiation development and disease pathogenesis.
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Affiliation(s)
- Ligang Zhu
- College of Physics, Jilin University, Changchun, 130021, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Jin Wang
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P. R. China
- Department of Chemistry, Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, USA
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5
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Liu X, Wu L, Si Y, Zhai Y, Niu M, Han M, Su T. Regulating Effect of Exogenous α-Ketoglutarate on Ammonium Assimilation in Poplar. Molecules 2024; 29:1425. [PMID: 38611705 PMCID: PMC11012726 DOI: 10.3390/molecules29071425] [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: 02/28/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Extensive industrial activities and anthropogenic agricultural practices have led to substantial ammonia release to the environment. Although croplands can act as ammonia sinks, reduced crop production under high concentrations of ammonium has been documented. Alpha-ketoglutarate (AKG) is a critical carbon source, displaying pleiotropic physiological functions. The objective of the present study is to disclose the potential of AKG to enhance ammonium assimilation in poplars. It showed that AKG application substantially boosted the height, biomass, and photosynthesis activity of poplars exposed to excessive ammonium. AKG also enhanced the activities of key enzymes involved in nitrogen assimilation: glutamine synthetase (GS) and glutamate synthase (GOGAT), elevating the content of amino acids, sucrose, and the tricarboxylic acid cycle (TCA) metabolites. Furthermore, AKG positively modulated key genes tied to glucose metabolism and ATP synthesis, while suppressing ATP-depleting genes. Correspondingly, both H+-ATPase activity and ATP content increased. These findings demonstrate that exogenously applying AKG improves poplar growth under a high level of ammonium treatment. AKG might function through sufficient carbon investment, which enhances the carbon-nitrogen balance and energy stability in poplars, promoting ammonium assimilation at high doses of ammonium. Our study provides novel insight into AKG's role in improving poplar growth in response to excess ammonia exposure.
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Affiliation(s)
- Xiaoning Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China (Y.Z.)
| | - Liangdan Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China (Y.Z.)
| | - Yujia Si
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China (Y.Z.)
| | - Yujie Zhai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China (Y.Z.)
| | - Mingyi Niu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China (Y.Z.)
| | - Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China (Y.Z.)
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China (Y.Z.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
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6
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Micaletto M, Fleurier S, Dion S, Denamur E, Matic I. The protein carboxymethyltransferase-dependent aspartate salvage pathway plays a crucial role in the intricate metabolic network of Escherichia coli. SCIENCE ADVANCES 2024; 10:eadj0767. [PMID: 38335294 PMCID: PMC10857468 DOI: 10.1126/sciadv.adj0767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Protein carboxymethyltransferase (Pcm) is a highly evolutionarily conserved enzyme that initiates the conversion of abnormal isoaspartate to aspartate residues. While it is commonly believed that Pcm facilitates the repair of damaged proteins, a number of observations suggest that it may have another role in cell functioning. We investigated whether Pcm provides a means for Escherichia coli to recycle aspartate, which is essential for protein synthesis and other cellular processes. We showed that Pcm is required for the energy production, the maintenance of cellular redox potential and of S-adenosylmethionine synthesis, which are critical for the proper functioning of many metabolic pathways. Pcm contributes to the full growth capacity both under aerobic and anaerobic conditions. Last, we showed that Pcm enhances the robustness of bacteria when exposed to sublethal antibiotic treatments and improves their fitness in the mammalian urinary tract. We propose that Pcm plays a crucial role in E. coli metabolism by ensuring a steady supply of aspartate.
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Affiliation(s)
- Maureen Micaletto
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Sebastien Fleurier
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Sara Dion
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
| | - Erick Denamur
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, 75018 Paris, France
| | - Ivan Matic
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
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7
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Flamholz AI, Goyal A, Fischer WW, Newman DK, Phillips R. The proteome is a terminal electron acceptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578293. [PMID: 38352589 PMCID: PMC10862836 DOI: 10.1101/2024.01.31.578293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. E. coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of metabolic flexibility, we developed a mathematical model coupling redox chemistry with principles of cellular resource allocation. Our integrated model clarifies key phenomena, including demonstrating that autotrophs grow slower than heterotrophs because of constraints imposed by intracellular production of reduced carbon. Our model further indicates that growth is improved by adapting the redox state of biomass to nutrients, revealing an unexpected mode of evolution where proteins accumulate mutations benefiting organismal redox balance.
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Affiliation(s)
- Avi I. Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research; Bengaluru 560089
| | - Woodward W. Fischer
- Division of Geological & Planetary Sciences, California Institute of Technology; Pasadena, CA 91125
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
- Division of Geological & Planetary Sciences, California Institute of Technology; Pasadena, CA 91125
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
- Department of Physics, California Institute of Technology; Pasadena, CA 91125, USA
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8
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Rothman DH. Slow closure of Earth's carbon cycle. Proc Natl Acad Sci U S A 2024; 121:e2310998121. [PMID: 38241442 PMCID: PMC10823250 DOI: 10.1073/pnas.2310998121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/07/2023] [Indexed: 01/21/2024] Open
Abstract
Carbon near the Earth's surface cycles between the production and consumption of organic carbon; the former sequesters carbon dioxide while the latter releases it. Microbes attempt to close the loop, but the longer organic matter survives, the slower microbial degradation becomes. This aging effect leaves observable quantitative signatures: Organic matter decays at rates that are inversely proportional to its age, while microbial populations and concentrations of organic carbon in ocean sediments decrease at distinct powers of age. Yet mechanisms that predict this collective organization remain unknown. Here, I show that these and other observations follow from the assumption that the decay of organic matter is limited by progressively rare extreme fluctuations in the energy available to microbes for decomposition. The theory successfully predicts not only observed scaling exponents but also a previously unobserved scaling regime that emerges when microbes subsist on the minimum energy flux required for survival. The resulting picture suggests that the carbon cycle's age-dependent dynamics are analogous to the slow approach to equilibrium in disordered systems. The impact of these slow dynamics is profound: They preclude complete oxidation of organic carbon in sediments, thereby freeing molecular oxygen to accumulate in the atmosphere.
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Affiliation(s)
- Daniel H Rothman
- Lorenz Center, Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
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9
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Luzia L, Battjes J, Zwering E, Jansen D, Melkonian C, Teusink B. A fast method to distinguish between fermentative and respiratory metabolisms in single yeast cells. iScience 2024; 27:108767. [PMID: 38235328 PMCID: PMC10793178 DOI: 10.1016/j.isci.2023.108767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/27/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Saccharomyces cerevisiae adjusts its metabolism based on nutrient availability, typically transitioning from glucose fermentation to ethanol respiration as glucose becomes limiting. However, our understanding of the regulation of metabolism is largely based on population averages, whereas nutrient transitions may cause heterogeneous responses. Here we introduce iCRAFT, a method that couples the ATP Förster resonance energy transfer (FRET)-based biosensor yAT1.03 with Antimycin A to differentiate fermentative and respiratory metabolisms in individual yeast cells. Upon Antimycin A addition, respiratory cells experienced a sharp decrease of the normalized FRET ratio, while respiro-fermentative cells showed no response. Next, we tracked changes in metabolism during the diauxic shift of a glucose pre-grown culture. Following glucose exhaustion, the entire cell population experienced a progressive rise in cytosolic ATP produced via respiration, suggesting a gradual increase in respiratory capacity. Overall, iCRAFT is a robust tool to distinguish fermentation from respiration, offering a new single-cell opportunity to study yeast metabolism.
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Affiliation(s)
- Laura Luzia
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Julius Battjes
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Emile Zwering
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Derek Jansen
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Chrats Melkonian
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
- Bioinformatics Group, Wageningen University and Research, 6700AP Wageningen, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
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10
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Gwin CM, Gupta KR, Lu Y, Shao L, Rego EH. Spatial segregation and aging of metabolic processes underlie phenotypic heterogeneity in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569614. [PMID: 38076906 PMCID: PMC10705497 DOI: 10.1101/2023.12.01.569614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Individual cells within clonal populations of mycobacteria vary in size, growth rate, and antibiotic susceptibility. Heterogeneity is, in part, determined by LamA, a protein found exclusively in mycobacteria. LamA localizes to sites of new cell wall synthesis where it recruits proteins important for polar growth and establishing asymmetry. Here, we report that in addition to this function, LamA interacts with complexes involved in oxidative phosphorylation (OXPHOS) at a subcellular location distinct from cell wall synthesis. Importantly, heterogeneity depends on a unique extension of the mycobacterial ATP synthase, and LamA mediates the coupling between ATP production and cell growth in single cells. Strikingly, as single cells age, concentrations of proteins important for oxidative phosphorylation become less abundant, and older cells rely less on oxidative phosphorylation for growth. Together, our data reveal that central metabolism is spatially organized within a single mycobacterium and varies within a genetically identical population of mycobacteria. Designing therapeutic regimens to account for this heterogeneity may help to treat mycobacterial infections faster and more completely.
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Affiliation(s)
- Celena M. Gwin
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Kuldeepkumar R. Gupta
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Yao Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Lin Shao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - E. Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
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11
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Wehrens M, Krah LHJ, Towbin BD, Hermsen R, Tans SJ. The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells. Cell Rep 2023; 42:113284. [PMID: 37864793 DOI: 10.1016/j.celrep.2023.113284] [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: 11/21/2022] [Revised: 07/17/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023] Open
Abstract
The inherent stochasticity of metabolism raises a critical question for understanding homeostasis: are cellular processes regulated in response to internal fluctuations? Here, we show that, in E. coli cells under constant external conditions, catabolic enzyme expression continuously responds to metabolic fluctuations. The underlying regulatory feedback is enabled by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system, which controls catabolic enzyme expression based on metabolite concentrations. Using single-cell microscopy, genetic constructs in which this feedback is disabled, and mathematical modeling, we show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. Modeling identifies four noise propagation modes, including one specific to CRP regulation. Together, these modes correctly predict noise circulation at perturbed cAMP levels. The cAMP-CRP system may thus have evolved to control internal metabolic fluctuations in addition to external growth conditions. We conjecture that second messengers may more broadly function to achieve cellular homeostasis.
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Affiliation(s)
- Martijn Wehrens
- AMOLF, 1098 XG Amsterdam, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, 3584 CT Utrecht, the Netherlands
| | - Laurens H J Krah
- Theoretical Biology Group, Biology Department, Utrecht University, 3584 CH Utrecht, the Netherlands; Centre for Complex Systems Studies, Utrecht University, 3584 CE Utrecht, the Netherlands
| | - Benjamin D Towbin
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Rutger Hermsen
- Theoretical Biology Group, Biology Department, Utrecht University, 3584 CH Utrecht, the Netherlands; Centre for Complex Systems Studies, Utrecht University, 3584 CE Utrecht, the Netherlands
| | - Sander J Tans
- AMOLF, 1098 XG Amsterdam, the Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands.
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12
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Kohiyama M, Herrick J, Norris V. Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle. Life (Basel) 2023; 13:1890. [PMID: 37763294 PMCID: PMC10532879 DOI: 10.3390/life13091890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division.
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Affiliation(s)
- Masamichi Kohiyama
- Institut Jacques Monod, Université Paris Cité, CNRS, 75013 Paris, France;
| | - John Herrick
- Independent Researcher, 3 rue des Jeûneurs, 75002 Paris, France;
| | - Vic Norris
- CBSA UR 4312, University of Rouen Normandy, University of Caen Normandy, Normandy University, 76000 Rouen, France
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13
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Martier AT, Maurice YV, Conrad KM, Mauvais-Jarvis F, Mondrinos MJ. Sex-specific actions of estradiol and testosterone on human fibroblast and endothelial cell proliferation, bioenergetics, and vasculogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550236. [PMID: 37546849 PMCID: PMC10402012 DOI: 10.1101/2023.07.23.550236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Progress toward the development of sex-specific tissue engineered systems has been hampered by the lack of research efforts to define the effects of sex-specific hormone concentrations on relevant human cell types. Here, we investigated the effects of defined concentrations of estradiol (E2) and dihydrotestosterone (DHT) on primary human dermal and lung fibroblasts (HDF and HLF), and human umbilical vein endothelial cells (HUVEC) from female (XX) and male (XY) donors in both 2D expansion cultures and 3D stromal vascular tissues. Sex-matched E2 and DHT stimulation in 2D expansion cultures significantly increased the proliferation index, mitochondrial membrane potential, and the expression of genes associated with bioenergetics (Na+/K+ ATPase, somatic cytochrome C) and beneficial stress responses (chaperonin) in all cell types tested. Notably, cross sex hormone stimulation, i.e., DHT treatment of XX cells in the absence of E2 and E2 stimulation of XY cells in the absence of DHT, decreased bioenergetic capacity and inhibited cell proliferation. We used a microengineered 3D vasculogenesis assay to assess hormone effects on tissue scale morphogenesis. E2 increased metrics of vascular network complexity compared to vehicle in XX tissues. Conversely, and in line with results from 2D expansion cultures, E2 potently inhibited vasculogenesis compared to vehicle in XY tissues. DHT did not significantly alter vasculogenesis in XX or XY tissues but increased the number of non-participating endothelial cells in both sexes. This study establishes a scientific rationale and adaptable methods for using sex hormone stimulation to develop sex-specific culture systems.
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Affiliation(s)
- Ashley T. Martier
- Department of Biomedical Engineering, Tulane University School of Science & Engineering, New Orleans, LA, USA
| | - Yasmin V. Maurice
- Department of Biomedical Engineering, Tulane University School of Science & Engineering, New Orleans, LA, USA
| | - K. Michael Conrad
- Department of Biomedical Engineering, Tulane University School of Science & Engineering, New Orleans, LA, USA
| | - Franck Mauvais-Jarvis
- Tulane Center for Excellence in Sex-based Biology and Medicine, New Orleans, LA, USA
- Section of Endocrinology, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana VA Medical Center, New Orleans, LA, USA
| | - Mark J. Mondrinos
- Department of Biomedical Engineering, Tulane University School of Science & Engineering, New Orleans, LA, USA
- Tulane Center for Excellence in Sex-based Biology and Medicine, New Orleans, LA, USA
- Department of Physiology, Tulane University School of Medicine, New Orleans, LA, USA
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14
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Bi S, Kargeti M, Colin R, Farke N, Link H, Sourjik V. Dynamic fluctuations in a bacterial metabolic network. Nat Commun 2023; 14:2173. [PMID: 37061520 PMCID: PMC10105761 DOI: 10.1038/s41467-023-37957-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/06/2023] [Indexed: 04/17/2023] Open
Abstract
The operation of the central metabolism is typically assumed to be deterministic, but dynamics and high connectivity of the metabolic network make it potentially prone to generating fluctuations. However, time-resolved measurements of metabolite levels in individual cells that are required to characterize such fluctuations remained a challenge, particularly in small bacterial cells. Here we use single-cell metabolite measurements based on Förster resonance energy transfer, combined with computer simulations, to explore the real-time dynamics of the metabolic network of Escherichia coli. We observe that steplike exposure of starved E. coli to glycolytic carbon sources elicits large periodic fluctuations in the intracellular concentration of pyruvate in individual cells. These fluctuations are consistent with predicted oscillatory dynamics of E. coli metabolic network, and they are primarily controlled by biochemical reactions around the pyruvate node. Our results further indicate that fluctuations in glycolysis propagate to other cellular processes, possibly leading to temporal heterogeneity of cellular states within a population.
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Affiliation(s)
- Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Manika Kargeti
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Niklas Farke
- University of Tübingen, D-72076, Tübingen, Germany
| | - Hannes Link
- University of Tübingen, D-72076, Tübingen, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany.
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15
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Huang D, Johnson AE, Sim BS, Lo TW, Merrikh H, Wiggins PA. The in vivo measurement of replication fork velocity and pausing by lag-time analysis. Nat Commun 2023; 14:1762. [PMID: 36997519 PMCID: PMC10063678 DOI: 10.1038/s41467-023-37456-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractAn important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell. To capture these dynamics, we develop lag-time analysis, a method for measuring in vivo dynamics. Using this approach, we provide quantitative locus-specific measurements of fork velocity, in units of kilobases per second, as well as replisome pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In this work, we quantitatively characterize known phenomena, detect brief, locus-specific pauses at ribosomal DNA loci in wild-type cells, and observe temporal fork velocity oscillations in three highly-divergent bacterial species.
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16
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Zhou GJ, Zhang F. Applications and Tuning Strategies for Transcription Factor-Based Metabolite Biosensors. BIOSENSORS 2023; 13:428. [PMID: 37185503 PMCID: PMC10136082 DOI: 10.3390/bios13040428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/17/2023]
Abstract
Transcription factor (TF)-based biosensors are widely used for the detection of metabolites and the regulation of cellular pathways in response to metabolites. Several challenges hinder the direct application of TF-based sensors to new hosts or metabolic pathways, which often requires extensive tuning to achieve the optimal performance. These tuning strategies can involve transcriptional or translational control depending on the parameter of interest. In this review, we highlight recent strategies for engineering TF-based biosensors to obtain the desired performance and discuss additional design considerations that may influence a biosensor's performance. We also examine applications of these sensors and suggest important areas for further work to continue the advancement of small-molecule biosensors.
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Affiliation(s)
- Gloria J. Zhou
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA;
- Division of Biology & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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17
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Mu X, Zhang F. Diverse mechanisms of bioproduction heterogeneity in fermentation and their control strategies. J Ind Microbiol Biotechnol 2023; 50:kuad033. [PMID: 37791393 PMCID: PMC10583207 DOI: 10.1093/jimb/kuad033] [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: 06/17/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
Microbial bioproduction often faces challenges related to populational heterogeneity, where cells exhibit varying biosynthesis capabilities. Bioproduction heterogeneity can stem from genetic and non-genetic factors, resulting in decreased titer, yield, stability, and reproducibility. Consequently, understanding and controlling bioproduction heterogeneity are crucial for enhancing the economic competitiveness of large-scale biomanufacturing. In this review, we provide a comprehensive overview of current understandings of the various mechanisms underlying bioproduction heterogeneity. Additionally, we examine common strategies for controlling bioproduction heterogeneity based on these mechanisms. By implementing more robust measures to mitigate heterogeneity, we anticipate substantial enhancements in the scalability and stability of bioproduction processes. ONE-SENTENCE SUMMARY This review summarizes current understandings of different mechanisms of bioproduction heterogeneity and common control strategies based on these mechanisms.
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Affiliation(s)
- Xinyue Mu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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18
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Chandrasekharan A, Varadarajan SN, Lekshmi A, Santhoshkumar TR. Real-time simultaneous imaging of temporal alterations in cytoplasmic and mitochondrial redox in single cells during cell division and cell death. Free Radic Biol Med 2023; 194:33-41. [PMID: 36427748 DOI: 10.1016/j.freeradbiomed.2022.11.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/17/2022] [Indexed: 11/24/2022]
Abstract
Cytosolic and organelle redox are highly interrelated, and their alterations play critical roles in both physiological and pathological cell states. This highly regulated process is crucial in life-death decisions of cells. Among organelles, the mitochondrion is the major source of intracellular-ROS and contributes to oxidation damage-induced cell death. Increase in cytosolic-redox and mitochondrial-redox is evident in cells undergoing diverse forms of cell death, such as apoptosis, necrosis, and necroptosis. The hierarchical profiling of redox signaling at the cytosol and mitochondria in a single cell is important to understand the relative contribution of each species in the initiation and shaping of cell death. Here, we demonstrate the potential application of ratiometric redox GFP (roGFP) and intensity-based redox-sensitive RFP (rxRFP) targeted to mitochondria in revealing both rapid and slow progressing changes in redox during cell division and in cells undergoing multiple modes of cell death. To generate imaging quality signal, single-cell clones stably expressing both roGFP at the cytosol and rxRFP probes targeted to mitochondria were generated. The cells provided sufficient temporal resolution with imaging-ready signal for the real-time visualization of rapidly progressing redox alterations at the cytosol and mitochondria. The long-time imaging of the cells revealed that a moderate increase in cytosolic ROS marks the division stage. Similarly, distinct forms of cell death trigger a unique and temporally regulated redox change at the cytosol and mitochondria, suggesting the potential utility of the sensor cells to dissect the nature of cell death pathways induced by specific forms of stress.
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Affiliation(s)
- Aneesh Chandrasekharan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Shankara Narayanan Varadarajan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Asha Lekshmi
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - T R Santhoshkumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India.
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19
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Chatzitheodoridou D, D'Ario M, Jones I, Piñeros L, Serbanescu D, O'Donnell F, Cadart C, Swaffer MP. Meeting report - Cell size and growth: from single cells to the tree of life. J Cell Sci 2022; 135:jcs260634. [PMID: 36259425 DOI: 10.1242/jcs.260634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
In April 2022, The Company of Biologists hosted their first post-pandemic in-person Workshop at Buxted Park Country House in the Sussex countryside. The Workshop, entitled 'Cell size and growth: from single cells to the tree of life', gathered a small group of early-career and senior researchers with expertise in cell size spanning a broad range of organisms, including bacteria, yeast, animal cells, embryos and plants, and working in fields from cell biology to ecology and evolutionary biology. The programme made ample room for fruitful discussions and provided a much-needed opportunity to discuss the most recent findings relating to the regulation of cell size and growth, identify the emerging challenges for the field, and build a community after the pandemic.
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Affiliation(s)
| | - Marco D'Ario
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ian Jones
- Department of Cancer Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, SW3 6JB, UK
| | - Liliana Piñeros
- Department of Cellular and Molecular Medicine, KU Leuven, Campus Gasthuisberg O&N1bis gebouw 402-20, Herestraat 49, B-3000 Leuven, Belgium
| | - Diana Serbanescu
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Frank O'Donnell
- The Company of Biologists, 94 Station Road, Histon, Cambridge, CB24 9LF, UK
| | - Clotilde Cadart
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200, USA
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