Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session G10: Quantitative Cell Physiology II - Metabolism and Growth |
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Sponsoring Units: DBIO Chair: Terence Hwa, University of California, San Diego Room: Room 202 |
Tuesday, March 7, 2023 11:30AM - 11:42AM |
G10.00001: Quantitative Physiology: Predictive Understanding of Living Systems Terence T Hwa Quantitative physiology is to living systems as physics is to physical systems – both seek for the quantitative description and predictive understanding of the “whole” in terms of the “parts”. Quantitative, physiological measurements allow researchers to discover constraints and formulate phenomenological theories at the macroscopic level. They also identify gaps and puzzles about living systems to be addressed by mechanistic studies. I will review several quantitative physiological studies of bacterial systems which led to the elucidation of the underlying regulatory strategies and mechanisms, as well as other studies for which mechanistic understandings are still outstanding. I will also discuss other areas of microbiology where physiological characterization is conspicuously lacking. |
Tuesday, March 7, 2023 11:42AM - 11:54AM |
G10.00002: The proteome acts as a terminal electron acceptor Abraham Flamholz Microbial metabolism contributes to growth in two key, interrelated ways. Bioenergetic processes like respiration exploit favorable redox transformations (e- transfers) to extract energy from the environment, generating ATP to power homeostasis and biosynthesis. At the same time, metabolic transformations convert nutrients – e.g. ammonia, phosphate, and sugars – into the macromolecules that build cells, e.g. proteins, nucleic acids, and lipids. I will describe a simple mathematical model of resource allocation during microbial growth that explicitly accounts for these dual roles by tracking the nominal oxidation state of carbon (NOSC) in nutrients (e.g. glucose), intermediates (amino acids), products (CO2), and biomass (proteins). Tracking NOSC permits the model to enforce redox homeostasis (balancing of e- flows) and to distinguish between respirations, which require an external terminal e- acceptor like O2, and fermentations, which do not. Incorporating the ATP yields of bioenergetic pathways and ATP costs of biosynthesis into the model predicts that a relatively reduced proteome, carrying more e-/carbon, would be advantageous during fast growth, as it promotes redox homeostasis without occupying ribosomes to produce specific enzymes. I will show how recent proteomic surveys support this prediction in heterotrophs (E. coli) and photoautotrophs (Synechocystis), indicating that the chemical and resource-economic views of microbial physiology should be integrated more fully. |
Tuesday, March 7, 2023 11:54AM - 12:06PM |
G10.00003: Functional Decomposition of Metabolism reveals gross imbalance in the energy budget of aerobically growing bacteria Matteo Mori, Chuankai Cheng, Brian R Taylor, Terence T Hwa Quantifying the contribution of individual molecular reactions to complex physiological functions in living cells is a grand challenge in quantitative biology. We established a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to cellular metabolic functions, e.g., the synthesis of metabolic building blocks such as amino acids and the generation of bioenergy such as ATP. This allowed us to obtain a plethora of results for E. coli growing in a variety of conditions without supervised knowledge on curated metabolic pathways, including the quantification of allocated enzymes to each metabolic function. A quantitative analysis of the cellular energy budget using FDM revealed an outstanding puzzle: We found that the ATP generated as a by-product of metabolic building block synthesis is already sufficient to satisfy most of the known energy need of cells growing aerobically on glucose, without the need of much additional energy synthesis. Yet, the fermentation and respiration pathways are highly active, resulting in more than doubled ATP synthesis flux and costing about 30% of the total carbon intake, without identifiable physiological rationales. This excess in ATP generation disappears for anaerobic growth on glucose. Our results suggest that, unlike popular beliefs, energy is not a limiting resource for aerobically growing E. coli. |
Tuesday, March 7, 2023 12:06PM - 12:18PM |
G10.00004: Effect of cell-to-cell variability on the signal transduction capability of an isogenic population Swayamshree Patra, Jeremy Moore, Nirag Kadakia, Keita Kamino, Agastya Rana, Thierry Emonet Cells of an isogenic population display significant cell-to-cell variability in sensing capabilities because of variation in protein abundances. With E.Coli chemosensory signaling pathway as our model system, we addressed the general question of how the nonlinear signal transduction capabilities of a diverse population and those of the mean phenotype differ and what are the physiological implications. Using data assimilation techniques we fit the standard nonlinear model of chemotaxis to the response of individual E.Coli cells measured using single cell FRET and characterized the phenotypic diversity in chemosensing capabilities by extracting the parameter values of the model. Visualizing the population in the high-dimensional parameter space gives insight about the different sensing strategies used by the clonal population and correlations among the parameters sheds light on the constraints imposed by regulatory processes. Finally, by analyzing the simulated response of models extracted by measuring hundreds of cells, we explore how variability shapes the signaling transduction capabilities of the diverse population. |
Tuesday, March 7, 2023 12:18PM - 12:30PM |
G10.00005: The physiological response of bacterial cells to temperature shock Kerwyn C Huang Temperature fluctuations are a ubiquitous part of life for all cells, and enteric bacteria often experience large temperature changes as they enter and exit hosts. While the transcriptional programs that respond to extreme temperatures (cold and heat shock) have been studied extensively, how cellular physiology responds to a temperature shift remains largely mysterious. We developed a device that allows us to track the growth of single cells during rapid temperature shifts. We show that instantaneous growth rate decreases upon a temperature downshift in a manner in quantiative agreement with Arrhenius kinetics. By contrast, upon a temperature upshift, growth rate increases slowly, over more than a generation. We show that these growth rate dynamics are a function of the growth rate at the final temperature, and that the normalized dynamics are conserved across temperature shifts and media. We demonstrate that the shift is linked mechanistically to both membrane and ribosomal synthesis, and provide a framework for understanding temperature shifts broadly across bacteria. |
Tuesday, March 7, 2023 12:30PM - 12:42PM |
G10.00006: Biomass transfer on autocatalytic reaction network Wei-Hsiang Lin For a biological system to grow, the biomass must be incorporated, transferred, and accumulated into the underlying reaction network. There are two perspectives for studying growth dynamics of reaction networks: one way is to focus on each node in the networks and study its associated influxes and effluxes. The other way is to focus on a fraction of biomass and study its trajectory along the reaction pathways.The former perspective (analogous to the "Eulerian representation" in fluid mechanics) has been studied extensively, while the latter perspective (analogous to the "Lagrangian representation" in fluid mechanics) has not been systematically explored. |
Tuesday, March 7, 2023 12:42PM - 12:54PM |
G10.00007: On the physiology of Vibrio natriegens and the possible costs of growing "too fast" Leonardo Pacciani-Mori, Terence T Hwa Vibrio natriegens is a marine bacterium with one of the fastest known growth rates: in optimal conditions its population can double in as little as 10 minutes. However, even though it is able to grow so fast, V. natriegens is not a dominant species in the marine environments where it was isolated from. To see whether this may arise from possible tradeoffs between fast growth with other physiological characteristics, we characterized various aspects of V. natriegens' growth physiology, including yield, death, and lag times when switching between nutrients. We compared these results with those of Vibrio splendidus sp. 1A01, a closely related Vibrio species which grows 25% more slowly than V. natriegens even at its optimal growth temperature, which is 10°C lower than that of V. natriegens. No apparent physiological trade-off for V. natriegens could be identified, as V. natriegens performed at least as well as V. 1A01 in all aspects examined. One ability V. natriegens lacks compared to V. 1A01 is the degradation of chitin, a polysaccharide of N-acetylglucosamine (GlcNAc) that is common in the marine environment, even though V. natriegens grows better than V. 1A01 on the monomer GlcNAc itself. Interestingly, When V. natriegens is introduced in a V. 1A01 chitin culture, it strongly inhibits the growth of the whole population, including its own. Our experiments suggest a "tragedy of the commons" scenario wherein the fast growth of V. natriegens on the monomer GlcNAc prevents V. 1A01 from growing, eventually limiting its ability to degrade chitin and generate monomers for both species. Thus, an indirect negative consequence of fast growth may be that it deprives the cells of the possibility to benefit from other species in environments that they cannot excel in. |
Tuesday, March 7, 2023 12:54PM - 1:06PM |
G10.00008: Principles of resource allocation under the active control of ribosome synthesis in bacteria Ryan Thiermann, Jin Yang, Farshad Abdollah-Nia, John T Sauls, Taylor Rytlewski, Sarah Cox, James Williamson, Zulfar Ghulam-Jelani, Jue Wang, Victoria Castillo, Suckjoon Jun Bacteria are often assumed to allocate cellular resources to maximize their exponential growth rate. This postulate, derived from studies of Escherichia coli, is commonly interpreted as an economic principle, in which the cell balances supply of and demand for “metabolic currencies” such as amino acids during steady-state growth. However, testing these predictions has been a major experimental challenge. Here, we show that Bacillus subtilis, another model bacterial organism, deviates from this growth maximization paradigm. To this end, we modulated the rate of rRNA and ribosome synthesis by controlling the cellular GTP concentration. In nutrient limited conditions, perturbations to ribosome production always reduced the growth rate. In stark contrast, under inhibition of translation with antibiotics, increased ribosome production led to faster growth. Using proteomics and LC/MS, we trace this submaximal growth to a reduction in GTP level upon translation inhibition, which leads to overproduction of metabolic enzymes at the expense of ribosomal proteins. We conclude that different organisms follow organism-specific resource allocation principles, perhaps as a consequence of evolution. |
Tuesday, March 7, 2023 1:06PM - 1:18PM |
G10.00009: Dynamic allocation of proteomic resources by E. coli in rich and minimal media Terence T Hwa, Chenhao Wu, Matteo Mori, Christina Ludwig Rapid adaptation to changing environment is central to bacterial fitness. In rich medium, Escherichia coli primarily direct gene expression towards ribosome biogenesis and cell growth. Upon transition to minimal medium, a large number of biosynthesis genes must be turned on before growth can resume. Quantitative proteomics reveals a hierarchy of growth bottlenecks in amino acid biosynthesis, establishing a simple positive relation between the onset time of many enzymes across biosynthesis pathways and the fractional “reserve” of these enzymes maintained while growing in rich medium when they are not needed. A coarse-grained kinetic model quantitatively captures the enzyme recovery kinetics across many pathways, based solely on snapshots of the proteome right before and long after the transition, without invoking any ad hoc fitting parameters. These results establish the adoption of an “as-needed” gene expression program across biosynthetic pathways and the simple regulatory strategies underlying this program. |
Tuesday, March 7, 2023 1:18PM - 1:30PM |
G10.00010: Adaptability and sensitivity in gene regulatory responses out of equilibrium Gabriel Salmon, Sara Mahdavi, Patill Daghlian, Hernan G Garcia, Rob Phillips Cells adapt to environments and tune gene expression by controlling the concentrations of proteins (and their associated kinetics) in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these networks can and do consume biochemical energy. How does this dissipation enable cellular behaviors? This open question demands quantitative models that transcend thermodynamic equilibrium. Here we study the control of a simple, ubiquitous gene regulatory motif to explore the consequences of departing equilibrium in kinetic cycles. Employing graph theory, we find that dissipation unlocks nonmonotonicity and enhanced sensitivity of gene expression with respect to a variable that tunes transition rates (like a transcription factor). For example, these features allow a single transcription factor to act as both a repressor and activator at different levels or achieve multimodal outputs. We systematically dissect how energetically-driving individual transitions, or pairs of transitions, generates exceptional phenotypic responses. Our work quantifies necessary conditions and detectable consequences of energy expenditure. These richer mathematical behaviors may empower cells (existing in nature or designed in tomorrow's synthetic biology) to accomplish sophisticated regulation with simpler architectures than those required at equilibrium. |
Tuesday, March 7, 2023 1:30PM - 1:42PM |
G10.00011: Cellular adaptations of yeast to freeze-thaw Charuhansini Kulkarni, Nithila M Kumar, Ankita Ray, Zeenat Rashida, Shashi Thutupalli We study the survival of Saccaromyces cerevisiae when exposed to cycles of freeze (77K) and thaw (298 K), followed by growth. A "wild-type" population of cells has a ~2% survival rate upon exposure to a single cycle. However, under experimental evolution, we found that the population survival fraction increased to ~70% within ~25 cycles. Compared to the initial wild-type cells, we found that these "evolved" cell types displayed increased mass density, lower cellular volumes and lower cytoplasmic fluidity, together with increased basal levels of a glass-forming sugar, trehalose. Our measurements of the cellular growth rates and associated thermal fluxes using calorimetry indicate different nutrient utilization characteristics for the evolved cells. Further, when subjected to a stronger selection i.e. exposure to multiple (3) consecutive cycles of freeze-thaw before growth, we found that the cells evolved to exhibit significantly lower cytoplasmic fluidity compared to the weaker selection regime while achieving similar survival rates. Altogether, these point to an underlying mechanical adaptation of yeast to these extreme environmental perturbations. |
Tuesday, March 7, 2023 1:42PM - 1:54PM |
G10.00012: A novel electrical device demonstrates localized stimulation triggers cell-type-specific proliferation in biofilms Colin J Comerci, Alan Gillman, Leticia Galera-Laporta, Edgar Gutierrez, Alex Groisman, Joseph Larkin, Jordi Garcia-Ojalvo, Gürol M Süel Biological systems ranging from bacteria to mammals utilize electrochemical signaling. While artificial electrochemical signals have been utilized to characterize neural tissue responses, the effects of such stimuli on non-neural systems remain unclear. To pursue this question, we developed a novel experimental platform that combines a microfluidic chip with a multi-electrode array (MiCMA) to enable localized electrochemical stimulation of bacterial biofilms. The device also allows simultaneous measurement of the physiological response within the biofilm with single-cell resolution. We find that stimulation of an electrode locally changes the ratio of the two major cell types comprising Bacillus subtilis biofilms, namely motile and extracellular matrix-producing cells. Specifically, stimulation promotes the proliferation of motile cells, but not matrix cells, even though these two cell types are genetically identical and reside in the same microenvironment. Our work thus reveals that an electronic interface can selectively target bacterial cell types, enabling control of biofilm composition and development. |
Tuesday, March 7, 2023 1:54PM - 2:06PM |
G10.00013: Dynamical States of Self-Organised Waves in a Giant Single-Celled Organism Feeding on Light Eldad Afik, Tony J Liu, Elliot M Meyerowitz Living Systems often seem to follow an intrinsic predictive model of the world — a defining trait of Anticipatory Systems. Here we study Caulerpa, a marine green alga, which appears to predict the day/night light cycle. Our experimental results indicate that self-organized waves propagating throughout the organism are coupled to an effective self-sustained oscillator, and respond to time-dependent illumination. |
Tuesday, March 7, 2023 2:06PM - 2:18PM |
G10.00014: Utilizing massively parallel CRISPRi assays to investigate antibiotic tolerance Keiran Stevenson, Guillaume Lambert, Louis B Cortes CRISPR based inteference assays are highly useful screens that have been developed for use in mammalian cells but they have not found as much utility in bacteria due to the toxcitity of the cas9 the primary workhorse for CRISPR systems. We have devevloped a system that uses an inactivated form of cas12a to rapidly screen the entire Escherichia coli genome using gene knockdown in a wide range of conditions. |
Tuesday, March 7, 2023 2:18PM - 2:30PM |
G10.00015: Growth Rate of Pathogenic Bacterial Species in the Presence of Zinc Oxide Ahmed Majgaonkar With its implementations proven in ceramics, chemicals, and glass industries, zinc oxide (ZnO) has a wide range of applications. It also exhibits antibacterial properties at the nanoscale. We intend to use a range of ZnO nanoparticle concentrations to study the effects on the growth rate of different species of pathogenic bacteria with our experiment focused primarily on the use of ZnO nanopowder. Previously conducted studies have indicated promising results with staphylococci. We plan to extend this research to bacterial species with differing morphological and Gram-staining characteristics. A theoretical study will also be conducted highlighting the correlation between the shape and size of a ZnO nanoparticle and its bactericidal properties. |
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