Cell size control - a mechanism for maintaining fitness and function

The maintenance of cell size homeostasis has been studied for years in different cellular systems. With the focus on ‘what regulates cell size’, the question ‘why cell size needs to be maintained’ has been largely overlooked. Recent evidence indicates that animal cells exhibit nonlinear cell size dependent growth rates and mitochondrial metabolism, which are maximal in intermediate sized cells within each cell population. Increases in intracellular distances and changes in the relative cell surface area impose biophysical limitations on cells, which can explain why growth and metabolic rates are maximal in a specific cell size range. Consistently, aberrant increases in cell size, for example through polyploidy, are typically disadvantageous to cellular metabolism, fitness and functionality. Accordingly, cellular hypertrophy can potentially predispose to or worsen metabolic diseases. We propose that cell size control may have emerged as a guardian of cellular fitness and metabolic activity

Mammalian cell growth dynamics in mitosis

The extent and dynamics of animal cell biomass accumulation during mitosis are unknown, primarily because growth has not been quantified with sufficient precision and temporal resolution. Using the suspended microchannel resonator and protein synthesis assays, we quantify mass accumulation and translation rates between mitotic stages on a single-cell level. For various animal cell types, growth rates in prophase are commensurate with or higher than interphase growth rates. Growth is only stopped as cells approach metaphase-to-anaphase transition and growth resumes in late cytokinesis. Mitotic arrests stop growth independently of arresting mechanism. For mouse lymphoblast cells, growth in prophase is promoted by CDK1 through increased phosphorylation of 4E-BP1 and cap-dependent protein synthesis. Inhibition of CDK1-driven mitotic translation reduces daughter cell growth. Overall, our measurements counter the traditional dogma that growth during mitosis is negligible and provide insight into antimitotic cancer chemotherapies

Mass measurements during lymphocytic leukemia cell polyploidization decouple cell cycle- and cell size-dependent growth

Cell size is believed to influence cell growth and metabolism. Consistently, several studies have revealed that large cells have lower mass accumulation rates per unit mass (i.e., growth efficiency) than intermediate-sized cells in the same population. Sizedependent growth is commonly attributed to transport limitations, such as increased diffusion timescales and decreased surface-to-volume ratio. However, separating cell size- and cell cycle-dependent growth is challenging. To address this, we monitored growth efficiency of pseudodiploid mouse lymphocytic leukemia cells during normal proliferation and polyploidization. This was enabled by the development of large-channel suspended microchannel resonators that allow us to monitor buoyant mass of single cells ranging from 40 pg (small pseudodiploid cell) to over 4,000 pg, with a resolution ranging from ∼1% to ∼0.05%. We find that cell growth efficiency increases, plateaus, and then decreases as cell cycle proceeds. This growth behavior repeats with every endomitotic cycle as cells grow into polyploidy. Overall, growth efficiency changes 33% throughout the cell cycle. In contrast, increasing cell mass by over 100-fold during polyploidization did not change growth efficiency, indicating exponential growth. Consistently, growth efficiency remained constant when cell cycle was arrested in G2. Thus, cell cycle is a primary determinant of growth efficiency. As growth remains exponential over large size scales, our work finds no evidence for transport limitations that would decrease growth efficiency

Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence

Cell size varies greatly between cell types, yet within a specific cell type and growth condition, cell size is narrowly distributed. Why maintenance of a cell-type specific cell size is important remains poorly understood. Here we show that growing budding yeast and primary mammalian cells beyond a certain size impairs gene induction, cell-cycle progression, and cell signaling. These defects are due to the inability of large cells to scale nucleic acid and protein biosynthesis in accordance with cell volume increase, which effectively leads to cytoplasm dilution. We further show that loss of scaling beyond a certain critical size is due to DNA becoming limiting. Based on the observation that senescent cells are large and exhibit many of the phenotypes of large cells, we propose that the range of DNA:cytoplasm ratio that supports optimal cell function is limited and that ratios outside these bounds contribute to aging

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms

The type III receptor tyrosine kinase (RTK) KIT plays a crucial role in the transmission of cellular signals through phosphorylation events that are associated with a switching of the protein conformation between inactive and active states. D816V KIT mutation is associated with various pathologies including mastocytosis and cancers. D816V-mutated KIT is constitutively active, and resistant to treatment with the anti-cancer drug Imatinib. To elucidate the activating molecular mechanism of this mutation, we applied a multi-approach procedure combining molecular dynamics (MD) simulations, normal modes analysis (NMA) and binding site prediction. Multiple 50-ns MD simulations of wild-type KIT and its mutant D816V were recorded using the inactive auto-inhibited structure of the protein, characteristic of type III RTKs. Computed free energy differences enabled us to quantify the impact of D816V on protein stability in the inactive state. We evidenced a local structural alteration of the activation loop (A-loop) upon mutation, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. A thorough normal mode analysis of several MD conformations led to a plausible molecular rationale to propose that JMR is able to depart its auto-inhibitory position more easily in the mutant than in wild-type KIT and is thus able to promote kinase mutant dimerization without the need for extra-cellular ligand binding. Pocket detection at the surface of NMA-displaced conformations finally revealed that detachment of JMR from the kinase domain in the mutant was sufficient to open an access to the catalytic and substrate binding sites

Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case

Background: Model based design plays a fundamental role in synthetic biology. Exploiting modularity, i.e. using biological parts and interconnecting them to build new and more complex biological circuits is one of the key issues. In this context, mathematical models have been used to generate predictions of the behavior of the designed device. Designers not only want the ability to predict the circuit behavior once all its components have been determined, but also to help on the design and selection of its biological parts, i.e. to provide guidelines for the experimental implementation. This is tantamount to obtaining proper values of the model parameters, for the circuit behavior results from the interplay between model structure and parameters tuning. However, determining crisp values for parameters of the involved parts is not a realistic approach. Uncertainty is ubiquitous to biology, and the characterization of biological parts is not exempt from it. Moreover, the desired dynamical behavior for the designed circuit usually results from a trade-off among several goals to be optimized. Results: We propose the use of a multi-objective optimization tuning framework to get a model-based set of guidelines for the selection of the kinetic parameters required to build a biological device with desired behavior. The design criteria are encoded in the formulation of the objectives and optimization problem itself. As a result, on the one hand the designer obtains qualitative regions/intervals of values of the circuit parameters giving rise to the predefined circuit behavior; on the other hand, he obtains useful information for its guidance in the implementation process. These parameters are chosen so that they can effectively be tuned at the wet-lab, i.e. they are effective biological tuning knobs. To show the proposed approach, the methodology is applied to the design of a well known biological circuit: a genetic incoherent feed-forward circuit showing adaptive behavior. Conclusion: The proposed multi-objective optimization design framework is able to provide effective guidelines to tune biological parameters so as to achieve a desired circuit behavior. Moreover, it is easy to analyze the impact of the context on the synthetic device to be designed. That is, one can analyze how the presence of a downstream load influences the performance of the designed circuit, and take it into account.Research in this area is partially supported by Spanish government and European Union (FEDER-CICYT DPI2011-28112-C04-01, and DPI2014-55276-C5-1-R). Yadira Boada thanks grant FPI/2013-3242 of Universitat Politecnica de Valencia; Gilberto Reynoso-Meza gratefully acknowledges the partial support provided by the postdoctoral fellowship BJT-304804/2014-2 from the National Council of Scientific and Technologic Development of Brazil (CNPq) for the development of this work. We are grateful to Alejandra Gonzalez-Bosca for her collaboration on this topic while doing her Bachelor thesis, and to Dr. Jose Luis Pitarch from Universidad de Valladolid for his advise in algorithmic implementations and for proof reading the manuscript.Boada Acosta, YF.; Reynoso Meza, G.; Picó Marco, JA.; Vignoni, A. (2016). Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case. BMC Systems Biology. 10:1-19. https://doi.org/10.1186/s12918-016-0269-0S11910ERASynBio. Next steps for european synthetic biology: a strategic vision from erasynbio. Report, ERASynBio. 2014. https://www.erasynbio.eu/lw_resource/datapool/_items/item_58/erasynbiostrategicvision.pdf .Way J, Collins J, Keasling J, Silver P. Integrating biological redesign: Where synthetic biology came from and where it needs to go. Cell. 2014; 157(1):151–61.Canton B, Labno A, Endy D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. 2008; 26(7):787–93.De Lorenzo V, Danchin A. Synthetic biology: discovering new worlds and new words. EMBO Rep. 2008; 9(9):822–7.Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R. Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol. 2014; 15(4):289–94.Takahashi CN, Miller AW, Ekness F, Dunham MJ, Klavins E. A low cost, customizable turbidostat for use in synthetic circuit characterization. ACS Synth Biol. 2015; 4(1):32–8. [doi: 10.1021/sb500165g ].Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics. 2010; 26(7):925–31.Medema MH, van Raaphorst R, Takano E, Breitling R. Computational tools for the synthetic design of biochemical pathways. Nat Rev Microbiol. 2012; 10(3):191–202.Marchisio MA, Stelling J. Automatic design of digital synthetic gene circuits. PLoS Comput Biol. 2011; 7(2):e1001083. [doi: 10.1371/journal.pcbi.1001083 ].Rodrigo G, Carrera J, Landrain TE, Jaramillo A. Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Lett. 2012; 586(15):2037–42.Crook N, Alper HS. Model-based design of synthetic, biological systems. Chem Eng Sci. 2013; 103:2–11.Jayanthi S, Nilgiriwala K, Del Vecchio D. Retroactivity controls the temporal dynamics of gene transcription. ACS Synth Biol. 2013; 2(8):431–41.Mélykúti B, Hespanha JP, Khammash M. Equilibrium distributions of simple biochemical reaction systems for time-scale separation in stochastic reaction networks. J R Soc Interface. 2014; 11(97):20140054.Oyarzún DA, Lugagne JB, Stan GB. Noise propagation in synthetic gene circuits for metabolic control. ACS Synth Biol. 2015; 4(2):116–25. [doi: 10.1021/sb400126a ].Picó J, Vignoni A, Picó-Marco E, Boada Y. Modelado de sistemas bioquímicos: De la ley de acción de masas a la aproximación lineal del ruido. Revista Iberoamericana de Automática e Informática Industrial RIAI. 2015; 12(3):241–52.Feng X-j-J, Hooshangi S, Chen D, Li G, Weiss R, Rabitz H. Optimizing genetic circuits by global sensitivity analysis. Biophys J. 2004; 87(4):2195–202.Dasika MS, Maranas CD. Optcircuit: An optimization based method for computational design of genetic circuits. BMC Syst Biol. 2008; 2:24.Rodrigo G, Carrera J, Jaramillo A. Genetdes. Bioinformatics. 2007; 23(14):1857–8.Otero-Muras I, Banga JR. Multicriteria global optimization for biocircuit design. 2014. arXiv preprint arXiv:1402.7323.Banga JR. Optimization in computational systems biology. BMC Syst Biol. 2008; 2:47.Sendin J, Exler O, Banga JR. Multi-objective mixed integer strategy for the optimisation of biological networks. IET Syst Biol. 2010; 4(3):236–48.Miller M, Hafner M, Sontag E, Davidsohn N, Subramanian S, Purnick PE, Lauffenburger D, Weiss R. Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity. PLoS Comput Biol. 2012; 8(7):1002579.Ellis T, Wang X, Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol. 2009; 27(5):465–71.Koeppl H, Hafner M, Lu J. Mapping behavioral specifications to model parameters in synthetic biology. BMC Bioinforma. 2013; 14(Suppl 10):9.Chiang AWT, Hwang M-JJ. A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits. BMC Bioinforma. 2013; 14 Suppl 16:5.Ma W, Trusina A, El-Samad H, Lim WA, Tang C. Defining network topologies that can achieve biochemical adaptation. Cell. 2009; 138(4):760–73.Chiang AWT, Liu W-CC, Charusanti P, Hwang M-JJ. Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters. BMC Syst Biol. 2014; 8:4.Reynoso-Meza G, Blasco X, Sanchis J, Martínez M. Controller tuning using evolutionary multi-objective optimisation: current trends and applications. Control Eng Pract. 2014; 28:58–73.Alon U. An Introduction To Systems Biology. Design Principles of Biological Circuits. London: Chapman & Hall/ CRC Mathematical and computational Biology Series; 2006.Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000; 403(6767):335–8.Hsiao V, de los Santos ELC, Whitaker WR, Dueber JE, Murray RM. Design and implementation of a biomolecular concentration tracker. ACS Synth Biol. 2015; 4(2):150–61. [doi: 10.1021/sb500024b ].Franco E, Giordano G, Forsberg P-O, Murray RM. Negative autoregulation matches production and demand in synthetic transcriptional networks. ACS Synth Biol. 2014; 3(8):589–99. [doi: 10.1021/sb400157z ].Strelkowa N, Barahona M. Switchable genetic oscillator operating in quasi-stable mode. J R Soc Interface. 2010; 7(48):1071–82.Basu S, Mehreja R, Thiberge S, Chen MT, Weiss R. Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci U S A. 2004; 101(17):6355–60.Bleris L, Xie Z, Glass D, Adadey A, Sontag E, Benenson Y. Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template. Mol Syst Biol. 2011; 7(519):1–12. [doi: 10.1038/msb.2011.49 ].Hart Y, Antebi YE, Mayo AE, Friedman N, Alon U. Design principles of cell circuits with paradoxical components. Proc Natl Acad Sci. 2012; 109(21):8346–51.Zhang Q, Bhattacharya S, Andersen ME. Ultrasensitive response motifs: basic amplifiers in molecular signalling networks. Open Biol. 2013; 3(4):130031.Weber M, Buceta J, Others. Dynamics of the quorum sensing switch: stochastic and non-stationary effects. BMC Syst Biol. 2013; 7(1):6.Womelsdorf T, Valiante TA, Sahin NT, Miller KJ, Tiesinga P. Dynamic circuit motifs underlying rhythmic gain control, gating and integration. Nat Neurosci. 2014; 17(8):1031–9.Arpino JAJ, Hancock EJ, Anderson J, Barahona M, Stan G-BVB, Papachristodoulou A, Polizzi K. Tuning the dials of synthetic biology. Microbiology. 2013; 159(Pt 7):1236–53.Zagaris A, Kaper HGG, Kaper TJJ. Analysis of the computational singular perturbation reduction method for chemical kinetics. J Nonlinear Sci. 2004; 14(1):59–91.Anderson J, Chang Y-C-C, Papachristodoulou A. Model decomposition and reduction tools for large-scale networks in systems biology. Automatica. 2011; 47(6):1165–74.Prescott TP, Papachristodoulou A. Layered decomposition for the model order reduction of timescale separated biochemical reaction networks. J Theor Biol. 2014; 356:113–22.Hancock EJ, Stan GB, Arpino JAJ, Papachristodoulou A. Simplified mechanistic models of gene regulation for analysis and design. J R Soc Interface. 2015; 12(108).Miettinen K, Vol. 12. Nonlinear Multiobjective Optimization. Boston: Kluwer Academic Publishers; 1999.Miettinen K, Ruiz F, Wierzbicki AP. Introduction to multiobjective optimization: interactive approaches. In: Multiobjective Optimization. Berlin: Springer: 2008. p. 27–57.Deb K, Bandaru S, Greiner D, Gaspar-Cunha A, Tutum CC. An integrated approach to automated innovization for discovering useful design principles: Case studies from engineering. Appl Soft Comput. 2014; 15(0):42–56.Ang J, Ingalls B, McMillen D. Probing the input-output behavior of biochemical and genetic systems: System identification methods from control theory In: Johnson ML, Brand L, editors. Methods in Enzymology. Academic Press: 2011. p. 279–317, doi: 10.1016/B978-0-12-381270-4.00010-X .Mattson CA, Messac A. Pareto frontier based concept selection under uncertainty, with visualization. Optim Eng. 2005; 6(1):85–115.Reynoso-Meza G, Sanchis J, Blasco X, Martínez M. Design of continuous controllers using a multiobjective differential evolution algorithm with spherical pruning. Appl Evol Comput. 2010;532–541.Reynoso-Meza G, García-Nieto S, Sanchis J, Blasco X. Controller tuning using multiobjective optimization algorithms: a global tuning framework. IEEE Trans Control Syst Technol. 2013; 21(2):445–58.Reynoso-Meza G, Sanchis J, Blasco X, Herrero JM. Multiobjective evolutionary algortihms for multivariable PI controller tuning. Expert Syst Appl. 2012; 39:7895–907.Anderson C. Anderson promoter collection [online]. 2006. http://parts.igem.org/Promoters/Catalog/Anderson . Accesed 20 Feb 2015.Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol. 2009; 27(10):946–50.Egbert RG, Klavins E. Fine-tuning gene networks using simple sequence repeats. PNAS. 2012; 109(42):16817–22. [doi: 10.1073/pnas.1205693109 ].Hair JF, Suárez MG. Análisis Multivariante vol. 491. Madrid: Prentice Hall; 1999.Blasco X, Herrero JM, Sanchis J, Martínez M. A new graphical visualization of n-dimensional pareto front for decision-making in multiobjective optimization. Inf Sci. 2008; 178(20):3908–24. [doi: 10.1016/j.ins.2008.06.010 ].Reynoso-Meza G, Blasco X, Sanchis J, Herrero JM. Comparison of design concepts in multi-criteria decision-making using level diagrams. Inform Sci. 2013; 221:124–41.Goentoro L, Shoval O, Kirschner MW, Alon U. The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell. 2009; 36(5):894–9.Rodrigo G, Elena SF. Structural discrimination of robustness in transcriptional feedforward loops for pattern formation. PloS ONE. 2011; 6(2):16904.Kim J, Khetarpal I, Sen S, Murray RM. Synthetic circuit for exact adaptation and fold-change detection. Nucleic Acids Res. 2014; 42(2):6078–89. [doi: 10.1093/nar/gku233 ].Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, et al. Biomodels: ten-year anniversary. Nucleic Acids Res. 2015; 43(D1):542–8.Ang J, Bagh S, Ingalls BP, McMillen DR. Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network. J Theor Biol. 2010; 266(4):723–38.Biobrick Foundation. 2006. Part Registry [online]. http://partsregistry.org/ . Accessed 20 Feb 2015.BIOSS. 2006. BIOSS Toolbox [online]. http://www.bioss.uni-freiburg.de/cms/toolbox-home.html . Accessed 20 Feb 2015.BioFab. 2006. International Open Facility Advancing Biotechnology [online]. http://www.biofab.org/ . Accessed 20 Feb 2015.Vallerio M, Hufkens J, Van Impe J, Logist F. An interactive decision-support system for multi-objective optimization of nonlinear dynamic processes with uncertainty. Expert Syst Appl. 2015; 42(21):7710–31.Frangopol DM, Maute K. Life-cycle reliability-based optimization of civil and aerospace structures. Comput Struct. 2003; 81(7):397–410.Lozano M, Molina D, Herrera F. Editorial scalability of evolutionary algorithms and other metaheuristics for large-scale continuous optimization problems. Soft Comput. 2011; 15(11):2085–7.Santana-Quintero LV, Montano AA, Coello CAC. A review of techniques for handling expensive functions in evolutionary multi-objective optimization. In: Computational Intelligence in Expensive Optimization Problems. Berlin: Springer: 2010. p. 29–59