Biology subjects

Lee, C. T.

Publications and source records attributed to Lee, C. T..

At least 19 recordsLinked to original sources

bioRxiv2026

Physics-Guided Neural Reconstruction of Cellular Membranes for 3D Electron Microscopy

AWith advances in three-dimensional electron microscopy modalities, quantitative characterization of membrane ultrastructure has emerged as an approach to interrogate how organization of proteins and other components around the membrane drive structure and function. Hindering these efforts, the confident reconstruction of geometric features such as membrane curvature is challenging since it requires the calculation of higher-order derivatives from discrete membrane representations. Modern advances in using neural networks to learn continuous implicit representations of complex shapes present a promising solution to this problem. This work presents a physics-informed neural network framework for reconstructing membrane geometries to curvature-order accuracy from images using an implicit neural representation. Benchmarking using synthetic data illustrates that physics-based regularization during training improves accuracy of recovered curvatures, improving robustness to image noise. Application to experimental datasets demonstrate that the framework generalizes to complex cellular structure, such as the Golgi apparatus and mitochondria. We further perform three-dimensional curvature analysis of endocytic pits in cells to reveal anisotropic curvatures at the pit neck, previously predicted to be a lower-energy pathway for neck constriction. This work provides a unified framework for reconstructing three-dimensional membrane shape, including curvature, from volumetric imaging data. By capturing membrane geometry more accurately, our approach yields mechanical insights that can be linked to molecular-scale interactions.

cell biology↗

bioRxiv2026

Membrane Phase, Charge, and Curvature Regulate α-Synuclein Binding Dynamics

-Synuclein (Syn) is an intrinsically disordered protein whose interactions with lipid membranes are central to both its physiological function and its role in synucleopathies. While membrane charge, phase, and curvature are each known to influence Syn binding, these properties are typically examined independently, leaving their combined effects on both equilibrium and dynamic membrane association unresolved. Here, we systematically investigate how membrane phase and charge jointly regulate Syn binding, curvature sensitivity, and exchange dynamics using fluorescence microscopy, circular dichroism spectroscopy, and fluorescence recovery after photobleaching (FRAP), complemented by coarse-grained molecular dynamics simulations. Under zwitterionic conditions, Syn preferentially binds highly curved gel-phase membranes, driven by curvature-dependent enrichment of packing defects arising from faceted vesicle morphologies. Incorporation of anionic lipids selectively enhances binding in liquid-phase membranes while attenuating curvature-dependent partitioning in gel-phase membranes. Dynamic measurements reveal that membrane phase and charge also govern the stability of membrane-associated Syn, with gel-phase membranes and anionic lipids promoting kinetically stabilized states. Simulations show that curvature-induced defect formation is strongly amplified in gel-phase membranes but largely insensitive to charge. These findings establish that Syn-membrane interactions are governed by a cooperative interplay between membrane phase, curvature, and charge and highlight the importance of resolving both thermodynamic and kinetic contributions to protein-membrane binding.

biophysics↗

bioRxiv2026

Size-dependent nucleus-vacuole interactions in budding yeast demonstrate a role for steric packing in organelle shape and positioning

Although organelles are often studied one at a time, whole-cell imaging studies show that organelles take up a large part of the cell volume such that they are crowded together. Here we use whole cell soft X-ray tomography imaging to investigate how such crowding affects organelle size scaling, position, and shape, focusing on the nucleus and vacuole of budding yeast. We find that, as the vacuole enlarges beyond normal range, the nucleus loses its normal scaling relation with respect to cell volume, becomes displaced from its normal position near the cell center, and becomes progressively deformed from a sphere into a pancake shape. Using a whole-cell integrated shape modeling framework, we find that these changes are statistically correlated and give rise to distinct modes in cell organization space. Using a simplified mechanical model for two initially spherical compartments contained inside a confined intracellular space, we are able to recapitulate the effects seen in the experimental data, indicating that these observations are consistent with a purely mechanical interaction. Taken together, our work indicates that, in addition to the well-known protein-based organelle-organelle interactions, physical steric packing of organelles inside a limited cellular volume also plays a large role in the inter-organelle relationships and the overall geometry of the cell.

cell biology↗

bioRxiv2026

Saturated cardiolipins are potent disruptors of inner mitochondrial membrane structure and function

Cardiolipin (CL) is a four-acyl chained, mitochondrial-specific phospholipid crucial for maintenance of inner mitochondrial membrane (IMM) structure and function. In healthy tissues, CL acyl chains are highly unsaturated and maintained by a conserved remodeling pathway. However, dysregulation of CL acyl chain composition can arise from mutations in the CL transacylase, Tafazzin (TAZ), resulting in Barth syndrome (BTHS), where patients exhibit heightened mitochondrial dysfunction. Cells lacking TAZ accumulate three-acyl chained monolysocardiolipin (MLCL) as well as CL species with saturated acyl chains (CLsat). While the presence of MLCL destabilizes electron transport chain (ETC) complexes and IMM-shaping proteins, the contributions of CLsat to mitochondrial dysfunction have not been elucidated. Here, we find that treatment of TAZ knockout cells with exogenous saturated fatty acids causes accumulation of CLsat and loss of IMM structure despite only minimal changes in MLCL composition. Imaging of cells with elevated CLsat showed reduced fluidity of the inner membrane. Biophysical measurements and molecular dynamics analyses showed that di-saturated (C16:0 18:1)2 CL species order and rigidify membranes, while also losing the intrinsic lipid curvature characteristic of tetra-unsaturated CL. These results implicate CLsat as a potential driver of mitochondrial dysfunction and an additional therapeutic target in mitigating BTHS pathology.

cell biology↗

bioRxiv2025

Emergence of population-level feedback control by transposon-plasmid coevolution

The origins of adaptive functions remain poorly understood, despite considerable interest1-5. Here, we report the de novo evolution of population-level feedback control in clonal Escherichia coli strains containing high-copy plasmids, enabling these strains to express green fluorescent protein (GFP) in response to tetracycline. Selection maintains tetA+ and tetA- plasmids within single cells, due to negative feedback from the toxic effects of a tetA-gfp tetracycline resistance transposon. At high plasmid copy numbers, the intracellular equilibrium of tetA+ and tetA- plasmids robustly responds to tetracycline through rapid evolutionary dynamics6-8. Theory predicts that the GFP response to tetracycline is determined by the covariance between GFP expression and bacterial fitness. Our findings show that small mutational changes can result in large qualitative changes to population-level behavior. Here, the evolution of polymorphic intracellular populations of mobile genetic elements allows host populations to dynamically respond to antibiotic in the environment.

systems biology↗

bioRxiv2025

Mechanochemical feedback between confinement and actin crosslinking drives the shape dynamics of liquid-like droplets

Several actin-binding proteins can form liquid-liquid phase-separated condensates that promote actin filament assembly and bundling, which is crucial for local actin network organization. Previous studies have established that phase-separated condensates composed of actin-binding proteins, such as vasodilator-stimulated phosphoprotein (VASP) and Lamellipodin (Lpd), restrict the organization of actin filaments to structures such as rings, shells, discs, and rods through kinetic trapping. However, the mechanism by which crosslinker multivalency, actin growth, and condensate properties tune actin organization and droplet shape is not well understood. Using a combination of agent-based simulations and experiments, we find that the deformability of the droplet interface allows for the emergence of not just tightly-bundled actin rings but also weakly-bundled actin discs. We find two major quantitative relationships between actin bundling and droplet deformation. The first relationship shows that the crosslinked bundle thickness and droplet diameter followed a power law, consistent with experiments. The second one is that the kinetics of droplet deformation follows a dynamic snapping behavior that depends on the droplet surface tension and the multivalent VASP-actin binding kinetics. We predicted that these two relationships were generalizable to dynamic multimers and to weak actin crosslinkers. Our predictions were experimentally tested using two additional condensate-forming proteins, lamellipodin and RGG. Taken together, we show that mechanochemical feedback between the droplet interface properties and crosslinker multivalency tune actin organization and control the dynamics of droplet deformation by actin networks.

biophysics↗

bioRxiv2025

Cell-specific RNA isoform remodeling in the aging mouse brain

Aging is associated with increases in risk of multiple chronic diseases and at the cellular level, with disruptions in RNA homeostasis. Single-cell transcriptomic studies have revealed RNA abundance heterogeneity across brain cell types but the more complex changes in RNA processing such as alternative splicing, isoform usage, transcription start and polyadenylation site selection remain uncharacterized. Here, we combine single-cell analysis with long-read nanopore sequencing to capture full-length RNA isoforms and uncover temporal changes in RNA transcription, processing, and alternative splicing in the aging mouse cortex and hippocampus. By profiling transcriptomes from young adult to very old mice, we identify non-linear, cell-type-specific isoform expression changes and isoform usage shifts, primarily driven by transcription start site selection. These aging-associated isoform changes alter the coding potential and poly(A) site position of genes. Our data also reveal a high proportion of senescence in immune cells, far exceeding that of other cell types. We also identify isoform markers that, when applied to a machine learning model, distinguish senescent from normal immune cells. This study provides a full-length RNA isoform-based atlas of the aging mouse brain, offering insights into RNA metabolism remodeling across brain cell types throughout the lifespan.

genomics↗

bioRxiv2025

Coupling between membrane undulations and lipid curvature leads to transient local enrichment of cardiolipin in mitochondrial membranes

Organelles such as mitochondria have characteristic shapes that are critical to their function. Recent efforts have revealed that the curvature contributions of individual lipid species can be a factor in the generation of membrane shape in these organelles. Inspired by lipidomics data from yeast mitochondrial membranes, we used Martini coarse-grained molecular dynamics simulations to investigate how lipid composition facilitates membrane shaping. We found that increasing lipid saturation increases bending rigidity while reducing the monolayer spontaneous curvature. We also found that systems containing cardiolipin exhibited decreased bending rigidity and increased spontaneous curvature when compared to bilayers containing its precursor, phosphatidylglycerol. This finding contradicts some prior experimental results that suggest that bilayers containing tetraoleoyl cardiolipin have greater rigidity than dioleoyl phosphatidylcholine bilayers. To investigate this discrepancy, we analyzed our simulations for correlations between lipid localization and local curvature. We found that there are transient correlations between curved lipids such as cardiolipin (CDL) and phosphatidylethanolamine (PE) and curvature; these interactions enrich specific bilayer undulatory modes and cause bilayer softening. Furthermore, we show that curvature-localization of some lipids such as cardiolipin can influence lipids in the opposing leaflet. These observations add to the emerging evidence that lipid geometric features give rise to local interactions, which can cause membrane compositional heterogeneities. The cross-talk between composition-driven tuning of membrane properties and membrane shape has implications for membrane organization and its related functions. SIGNIFICANCEThe material properties of phospholipid membranes are a function of the lipid composition. Theabundance of cardiolipin in the mitochondrial inner membrane implies a functional role for this special lipid. We explore the interactions of cardiolipin with other lipids with varying lipid saturation using coarse-grained molecular dynamics simulations. We find that membranes containing cardiolipin have higher spontaneous curvature and lower bending rigidity when compared to membranes without cardiolipin - in line with prior models and experiments. We also show that the low bending rigidity of cardiolipin-containing symmetric, and flat bilayered systems is due to the transient partitioning of cardiolipin to undulations due to curvature sensing. This is a mechanism for forming lateral membrane heterogeneities in otherwise symmetric systems.

biophysics↗

bioRxiv2025

Keystone engineering enables collective range expansion in microbial communities

Keystone engineers profoundly influence microbial communities by altering their shared environment, often by modifying key resources. Here, we show that in an antibiotic-treated microbial community, bacterial spread is controlled by keystone engineering affecting dispersal--an effect hidden in well-mixed environments. Focusing on two pathogens, non-motile Klebsiella pneumoniae and motile Pseudomonas aeruginosa, we found that both tolerate a {beta}-lactam antibiotic, with Pseudomonas being more resilient and dominating in well-mixed cultures. During range expansion, however, the antibiotic inhibits Pseudomonas ability to spread unless it is near Klebsiella--Klebsiella degrades the antibiotic to create a "clear zone" that allows Pseudomonas to expand, at the expense of Klebsiellas own growth, thus acting as a keystone engineer. As Pseudomonas spreads, it competitively suppresses Klebsiella. Our modeling and experimental analyses reveal that this keystone effect operates at a millimeter scale. We also observed similar keystone engineering by a Bacillus species isolated from a hospital sink, in both pairwise and eight-member bacterial communities with its co-isolates. These findings suggest that spatially explicit experiments are essential to understand certain keystone engineering mechanisms and have implications for surface-associated microbial communities like biofilms, as well as for diagnosing and treating polymicrobial infections involving drug-degrading, non-motile (e.g., Klebsiella), and drug-tolerant, motile (e.g., Pseudomonas) bacteria.

ecology↗

bioRxiv2024

The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution

The functions of cells and proteins depend on their biochemical microenvironment. To understand how biochemical constraints shaped protein structural evolution, we coupled the extensive genetic and metabolic data from the Saccharomycotina subphylum with the capability of AlphaFold2 to systematically predict protein structures from sequence. Determining how 11,269 enzyme structures catalysing 361 different metabolic reactions evolved over 400 million years alongside their molecular functions, we report that metabolism has shaped the structural evolution of enzymes at different levels: the organisms overall metabolism; the topological organisation of the metabolic network; and each enzymes molecular properties. For example, structural evolution depends on each enzymes reaction mechanism, on the variability rather than the amount of metabolic flux, and on biosynthetic cost. Evolutionary cost-optimization is stronger on highly abundant enzymes and acts differently on different structural domains, with the exception of small-molecule binding sites, which are prioritised over other structural domains and lack cost-optimisation. Finally, while enzyme surfaces are less constrained, surface residues can also be exposed to positive selection for the co-evolution of protein-protein interaction sites. Accessing AlphaFolds power to predict protein structures systematically and across species barriers, facilitating the integration of protein structures with functional genomics, we were thus able to map biological constraints which shape protein structural evolution at scale and over long timelines.

systems biology↗

bioRxiv2024

Spatial Modeling Algorithms for Reactions and Transport (SMART) in Biological Cells

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Herein, we present our software, Spatial Modeling Algorithms for Reaction and Transport (SMART), a package that takes in high-level user specifications about cell signaling networks and molecular transport, and then assembles and solves the associated mathematical and computational systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including YAP/TAZ mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally-derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.

systems biology↗

bioRxiv2023

Improved Activity and Kinetics of Endoglucanase Biofuel Enzyme with Addition of an AzoTAB Surfactant

Endoglucanases degrade {beta}-1,4-glycosidic bonds of crystalline cellulose into insoluble or soluble cellooligosaccharides at the solid-liquid interface. The enhanced activity and kinetics of endoglucanase from Aspergillus niger with addition of a light responsive azobenzene trimethyl ammonium bromide (azoTAB) surfactant is studied. AzoTAB is a photoresponsive surfactant that exists as a relatively-hydrophobic trans isomer under visible light (434 nm) and a relatively-hydrophilic cis isomer under UV light (350 nm). Endoglucanase catalytic activity can be controlled with light illumination slightly for microcrystalline cellulose natural substate ([~]15%) and significantly for p-nitrophenol-based model substrate ([~]2-fold) by switching between the trans (higher enzyme binding affinity, resulting higher enzyme unfolding) and cis form of azoTAB. Endoglucanase activity increases 45% towards avicel crystalline substate and 4-fold towards 4-nitrophenyl {beta}-D-cellobioside substrate in the presence of 0.4 mM azoTAB under UV light (90% cis and 10% trans isomers). In comparison, endoglucanase catalytic activity increases 5-10% towards crystalline cellulose substrate with the addition of sodium dodecyl benzene sulfonate (SDBS), sodium dodecyl sulfate (SDS) and dodecyl trimethyl ammonium (DTAB). 0.4 mM AzoTAB-UV addition leads to an increase of maximum endoglucanase adsorption (Emax) from 7.89 mg enzyme/g avicel to 12.92 mg enzyme/g avicel and catalytic enzyme efficiency (kcat/KM) from 0.031 L/(mg.s) to 0.061 L/(mg.s). It is found that adsorbed enzyme concentration on substrate correlates to enzyme specific activity for azoTAB containing reaction. Additionally, 40-50% activity enhancement and increased bound enzyme to substrate are detected with azoTAB addition at different enzyme, substrate, and inhibitor concentrations. Improvement of substrate properties of azoTAB addition is associated with lower reciprocal terms of Michaelis constant (KM), the adsorption coefficient (Kad) and fractal parameter (h) values similar to the presence of other surfactants in this study and the literature. Furthermore, 45-50% activity enhancement via azoTAB surfactant preserved for all three cellulase enzyme mixture of endoglucanase, cellohydrolase and {beta}-glucosidase. Consequently, azoTAB can be applied as profitable additive for the heterogenous enzymatic cellulose hydrolysis, resulting in a 30% decrease in the enzyme load based on the specific activity, adsorption, and fractal kinetics results.

bioengineering↗

bioRxiv2023

Membrane mechanics dictate axonal morphology and function

Axons are thought to be ultrathin membrane cables of a relatively uniform diameter, designed to conduct electrical signals, or action potentials. Here, we demonstrate that unmyelinated axons are not simple cylindrical tubes. Rather, axons have nanoscopic boutons repeatedly along their length interspersed with a thin cable with a diameter of [~]60 nm like pearls-on-a-string. These boutons are only [~]200 nm in diameter and do not have synaptic contacts or a cluster of synaptic vesicles, hence non-synaptic. Our in silico modeling suggests that axon pearling can be explained by the mechanical properties of the membrane including the bending modulus and tension. Consistent with modeling predictions, treatments that disrupt these parameters like hyper- or hypo-tonic solutions, cholesterol removal, and non-muscle myosin II inhibition all alter the degree of axon pearling, suggesting that axon morphology is indeed determined by the membrane mechanics. Intriguingly, neuronal activity modulates the cholesterol level of plasma membrane, leading to shrinkage of axon pearls. Consequently, the conduction velocity of action potentials becomes slower. These data reveal that biophysical forces dictate axon morphology and function and that modulation of membrane mechanics likely underlies plasticity of unmyelinated axons.

neuroscience↗

bioRxiv2023

PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease

Interstitial lung diseases (ILDs) are a heterogeneous group of disorders that can develop in patients with connective tissue diseases (CTD). Establishing autoimmunity in ILD impacts prognosis and treatment. ILD patients are screened for autoimmunity by assaying for anti-nuclear autoantibodies, rheumatoid factors and other non-specific tests. However, this approach has not been rigorously validated and may miss autoimmunity that manifests as autoantibodies to tissue antigens not previously defined in ILD. Here, we use Phage Immunoprecipitation-Sequencing (PhIP-Seq) to conduct a large, multi-center unbiased autoantibody discovery screen of ILD patients and controls. PhIP-Seq identified 17 novel autoreactive targets, and machine learning classifiers derived from these targets discriminated ILD serum from controls. Among these 17 candidates, we validated Cadherin Related Family Member 5 (CDHR5) as an autoantigen and found CDHR5 autoantibodies in patients with rheumatologic disorders and importantly, subjects not previously diagnosed with autoimmunity. Lung tissue of CDHR5 autoreactive patients showed transcriptional profiles consistent with activation of NF{kappa}B signaling and upregulation of chitotriosidase (CHIT1), a molecular pathway linked to fibrosis. Our study shows PhIP-Seq uncovers novel autoantibodies in ILD patients not revealed by standard clinical tests. Furthermore, CDHR5 autoantibodies may define a novel molecular endotype of ILD characterized by inflammation and fibrosis.

molecular biology↗

bioRxiv2023

Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome

Cristae are high curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous mechanisms for lipids have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the IMM against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. The model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that CL is essential in low oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of CL is dependent on the surrounding lipid and protein components of the IMM. SynopsisO_LIcritical lipidic breakpoint for yeast mitochondria phenocopies the loss of cristae-shaping proteins in the IMM. C_LIO_LIsaturation controls membrane mechanical properties and modulates ATP synthase oligomerization. C_LIO_LImitochondrial-specific lipid cardiolipin can functionally compensate for increased phospholipid saturation and is required for cristae formation in low oxygen environments. C_LIO_LImathematical model for cristae membrane tubules predicts a snapthrough instability mediated by both protein and lipid-encoded curvatures. C_LI Synopsis Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/532310v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@196aefforg.highwire.dtl.DTLVardef@1bafcadorg.highwire.dtl.DTLVardef@122f502org.highwire.dtl.DTLVardef@35afd_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Spatiotemporal modeling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology

The modification of neural circuits depends on the strengthening and weakening of synaptic connections. Synaptic strength is often correlated to the density of the ionotropic, glutamateric receptors, AMPAR, (-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor) at the postsynaptic density (PSD). While AMPAR density is known to change based on complex biological signaling cascades, the effect of geometric factors such as dendritic spine shape, size, and curvature remain poorly understood. In this work, we developed a deterministic, spatiotemporal model to study the dynamics of AMPAR during long term potentiation (LTP). This model includes a minimal set of biochemical events that represent the upstream signaling events, trafficking of AMPAR to and from the PSD, lateral diffusion in the plane of the spine membrane, and the presence of an extrasynaptic AMPAR pool. Using idealized and realistic spine geometries, we show that the dynamics and increase of bound AMPAR at the PSD depends on a combination of endo- and exocytosis, membrane diffusion, availability of free AMPAR, and intracellular signaling interactions. We also found non-monotonic relationships between spine volume and change in AMPAR at the PSD, suggesting that spines restrict changes in AMPAR to optimize resources and prevent runaway potentiation. Significance StatementSynaptic plasticity involves dynamic biochemical and physical remodeling of small protrusions called dendritic spines along the dendrites of neurons. Proper synaptic functionality within these spines requires changes in receptor number at the synapse, which has implications for down-stream neural functions, such as learning and memory formation. In addition to being signaling subcompartments, spines also have unique morphological features that can play a role in regulating receptor dynamics on the synaptic surface. We have developed a spatiotemporal model that couples biochemical signaling and receptor trafficking modalities in idealized and realistic spine geometries to investigate the role of biochemical and biophysical factors in synaptic plasticity. Using this model, we highlight the importance of spine size and shape in regulating bound AMPAR dynamics that govern synaptic plasticity, and predict how spine shape might act to reset synaptic plasticity as a built-in resource optimization and regulation tool.

neuroscience↗

bioRxiv2022

Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which an organosulfur-auxotrophy caused by deletion of homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. We discovered that an uncharacterized gene YLL058Wp, herein named Hydrogen sulfide utilizing-1 (HSU1), acts as a homocysteine synthase and allows the cells to substitute for Met17p by re-assimilating hydrosulfide ions leaked from met17{Delta} cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity. SummarySulfur limitation activates a dormant hydrogen sulfide fixation route via a novel homocysteine synthase Hsu1p (YLL058Wp).

molecular biology↗

bioRxiv2021

Mem3DG: Modeling Membrane Mechanochemical Dynamics in 3D using Discrete Differential Geometry

Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to approximation-based methods (e.g., finite element method), the class of discrete mesh models offers greater flexibility to simulate complex physics and shapes in three dimensions; its formulation produces an efficient algorithm while maintaining coordinate-free geometric descriptions. However, ambiguities in geometric definitions in the discrete context have led to a lack of consensus on which discrete mesh model is theoretically and numerically optimal; a bijective relationship between the terms contributing to both the energy and forces from the discrete and smooth geometric theories remains to be established. We address this and present an extensible framework, Mem3DG, for modeling 3D mechanochemical dynamics of membranes based on Discrete Differential Geometry (DDG) on triangulated meshes. The formalism of DDG resolves the inconsistency and provides a unifying perspective on how to relate the smooth and discrete energy and forces. To demonstrate, Mem3DG is used to model a sequence of examples with increasing mechanochemical complexity: recovering classical shape transformations such as 1) biconcave disk, dumb-bell, and unduloid and 2) spherical bud on spherical, flat-patch membrane; investigating how the coupling of membrane mechanics with protein mobility jointly affects phase and shape transformation. As high-resolution 3D imaging of membrane ultrastructure becomes more readily available, we envision Mem3DG to be applied as an end-to-end tool to simulate realistic cell geometry under user-specified mechanochemical conditions. Why it mattersCellular membranes have shapes and shape changes which characterize cells/organelles, and support nutrient trafficking among other critical processes. Modeling membrane shape changes using mechanical principles can provide insight into how cells robustly bend membranes to support life. Mathematical and computational strategies to solve the equations describing membrane shape evolution can be complex and challenging without simplifying assumptions. Here, we present a new, general, numerical approach to model arbitrary 3D membrane shapes in response to interaction with curvature sensing and generating membrane proteins. The accompanying implementation, Mem3DG, is a software tool to make computational membrane mechanics accessible to the general researcher. HighlightsO_LIIntroduces a discrete theory for membrane mechanics which connects with smooth theory C_LIO_LIDiscrete energy/force are functions of basic geometric quantities C_LIO_LIRecipes for extending the discrete framework with additional physics are provided C_LIO_LIDescribes a user-friendly software implementation called Mem3DG C_LIO_LIMem3DG is designed to facilitate modeling in tandem with experimental studies C_LI Significance and noveltyHelfrich Hamiltonian is widely used to model biomembranes. Many numerical methods have been developed to solve the geometric PDE. Compared to approximation-based methods, discrete-mesh-based models have many advantages when incorporating multiphysics in 3D due to their flexibility, efficiency, and straightforward implementation. However, there is no consensus on which mesh-based model is optimal, and a connection between the discrete and smooth geometric theory remains obscure. In this work, we provide a unifying perspective by identifying fundamental geometric invariants of the discrete force derived from a discrete energy. As a demonstration of generality of the framework to various physics, we follow a formulaic procedure to derive additional physics such as interfacial line tension, surface-bulk adsorption, protein lateral diffusion, and curvature-dependent protein aggregation.

biophysics↗