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1. PECTATE LYASE LIKE12 patterns the guard cell wall to coordinate turgor pressure and wall mechanics for proper stomatal function in Arabidopsis

   https://doi.org/10.1093/plcell/koab161  

   Chen, Yintong; Li, Wenlong; Turner, Joseph A; Anderson, Charles T (June 2021, The Plant Cell)

   null (Ed.)

   Abstract Plant cell deformations are driven by cell pressurization and mechanical constraints imposed by the nanoscale architecture of the cell wall, but how these factors are controlled at the genetic and molecular levels to achieve different types of cell deformation is unclear. Here, we used stomatal guard cells to investigate the influences of wall mechanics and turgor pressure on cell deformation and demonstrate that the expression of the pectin-modifying gene PECTATE LYASE LIKE12 (PLL12) is required for normal stomatal dynamics in Arabidopsis thaliana. Using nanoindentation and finite element modeling to simultaneously measure wall modulus and turgor pressure, we found that both values undergo dynamic changes during induced stomatal opening and closure. PLL12 is required for guard cells to maintain normal wall modulus and turgor pressure during stomatal responses to light and to tune the levels of calcium cross-linked pectin in guard cell walls. Guard cell-specific knockdown of PLL12 caused defects in stomatal responses and reduced leaf growth, which were associated with lower cell proliferation but normal cell expansion. Together, these results force us to revise our view of how wall-modifying genes modulate wall mechanics and cell pressurization to accomplish the dynamic cellular deformations that underlie stomatal function and tissue growth in plants. 

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2. Cell-Based Model of the Generation and Maintenance of the Shape and Structure of the Multilayered Shoot Apical Meristem of Arabidopsis thaliana

   https://doi.org/10.1007/s11538-018-00547-z  

   Banwarth-Kuhn, Mikahl; Nematbakhsh, Ali; Rodriguez, Kevin W.; Snipes, Stephen; Rasmussen, Carolyn G.; Reddy, G. Venugopala; Alber, Mark (December 2018, Bulletin of Mathematical Biology)

   One of the central problems in animal and plant developmental biology is deciphering how chemical and mechanical signals interact within a tissue to produce organs of defined size, shape, and function. Cell walls in plants impose a unique constraint on cell expansion since cells are under turgor pressure and do not move relative to one another. Cell wall extensibility and constantly changing distribution of stress on the wall are mechanical properties that vary between individual cells and contribute to rates of expansion and orientation of cell division. How exactly cell wall mechanical properties influence cell behavior is still largely unknown. To address this problem, a novel, subcellular element computational model of growth of stem cells within the multilayered shoot apical meristem (SAM) of Arabidopsis thaliana is developed and calibrated using experimental data. Novel features of the model include separate, detailed descriptions of cell wall extensibility and mechanical stiffness, deformation of the middle lamella, and increase in cytoplasmic pressure generating internal turgor pressure. The model is used to test novel hypothesized mechanisms of formation of the shape and structure of the growing, multilayeredSAMbased onWUSconcentration of individual cells controlling cell growth rates and layer-dependent anisotropic mechanical properties of subcellular components of individual cells determining anisotropic cell expansion directions. Model simulations also provide a detailed prediction of distribution of stresses in the growing tissue which can be tested in future experiments. 

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3. Mechanical stimuli activate gene expression via a cell envelope stress sensing pathway

   https://doi.org/10.1038/s41598-023-40897-w  

   Harper, Christine E.; Zhang, Wenyao; Lee, Junsung; Shin, Jung-Ho; Keller, Megan R.; van Wijngaarden, Ellen; Chou, Emily; Wang, Zhaohong; Dörr, Tobias; Chen, Peng; et al (December 2023, Scientific Reports)

   Abstract Mechanosensitive mechanisms are often used to sense damage to tissue structure, stimulating matrix synthesis and repair. While this kind of mechanoregulatory process is well recognized in eukaryotic systems, it is not known whether such a process occurs in bacteria. In Vibrio cholerae , antibiotic-induced damage to the load-bearing cell wall promotes increased signaling by the two-component system VxrAB, which stimulates cell wall synthesis. Here we show that changes in mechanical stress within the cell envelope are sufficient to stimulate VxrAB signaling in the absence of antibiotics. We applied mechanical forces to individual bacteria using three distinct loading modalities: extrusion loading within a microfluidic device, direct compression and hydrostatic pressure. In all cases, VxrAB signaling, as indicated by a fluorescent protein reporter, was increased in cells submitted to greater magnitudes of mechanical loading, hence diverse forms of mechanical stimuli activate VxrAB signaling. Reduction in cell envelope stiffness following removal of the endopeptidase ShyA led to large increases in cell envelope deformation and substantially increased VxrAB response, further supporting the responsiveness of VxrAB. Our findings demonstrate a mechanosensitive gene regulatory system in bacteria and suggest that mechanical signals may contribute to the regulation of cell wall homeostasis. 

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4. UNRAVELING MOLECULAR MECHANISMS OF ANTIBIOTIC RESISTANCE THROUGH MULTISCALE SIMULATIONS AND EXPLAINABLE MACHINE LEARNING

   Song, Zilin (May 2022, SMU Scholar)

   Pathogen resistance to β-lactam antibiotics compromises effective treatments of superbug infections. One major source of β-lactam resistance is the bacterial production of β-lactamases, which could effectively hydrolyze β-lactam drugs. In this thesis, the hydrolysis of various β-lactam antibiotics by class A serine-based β-lactamases (ASβLs) were investigated using hybrid Quantum Mechanical / Molecular Mechanical (QM/MM) minimum energy pathway (MEP) calculations and explainable machine learning (ML) approaches. The TEM-1/benzylpenicillin acylation reaction with QM/MM chain-of-states reaction pathways was firstly revisited. I proposed two decomposition methods for energy contribution analysis based on perturbing ML regression models. Both methods were shown to be model implementation invariant and successfully bridged the discrepancies between two pioneering mechanistic studies. The Toho-1 ASβL acylations of ampicillin and cefalexin were then investigated. I reported that the acylation pathway selection can be ligand dependent: ampicillin could undergo acylation via Lys73 or Glu166 acting as the general base while cefalexin acylation is limited to Lys73 as the general base. An explainable artificial intelligence (XAI) method, the Boltzmann-weighted Cumulative Integrated Gradients (BCIG), was developed to explain the different acylation pathway viability found for ampicillin and cefalexin. Lastly, conformational factors determining the GES-5/imipenem deacylation activity was investigated using edge-conditioned convolutional graph-learning (GL) methods. Critical mechanistic insights were derived from perturbative response of the GL latent representations, which explained the different deacylation reactivity between the two imipenem pyrroline tautomer states and identified the orientation of the carbapenem 6α-hydroxyethyl as the key factor that impacts the deacylation barrier heights. In summary, my thesis focuses on bridging QM/MM chain-of-states reaction pathway calculations and explainable ML to derive essential mechanistic insights into β-lactam resistance driven by ASβLs. 

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5. Gap junctions amplify spatial variations in cell volume in proliferating tumor spheroids

   https://doi.org/10.1038/s41467-020-19904-5  

   McEvoy, Eoin; Han, Yu Long; Guo, Ming; Shenoy, Vivek B. (December 2020, Nature Communications)

   null (Ed.)

   Abstract Sustained proliferation is a significant driver of cancer progression. Cell-cycle advancement is coupled with cell size, but it remains unclear how multiple cells interact to control their volume in 3D clusters. In this study, we propose a mechano-osmotic model to investigate the evolution of volume dynamics within multicellular systems. Volume control depends on an interplay between multiple cellular constituents, including gap junctions, mechanosensitive ion channels, energy-consuming ion pumps, and the actomyosin cortex, that coordinate to manipulate cellular osmolarity. In connected cells, we show that mechanical loading leads to the emergence of osmotic pressure gradients between cells with consequent increases in cellular ion concentrations driving swelling. We identify how gap junctions can amplify spatial variations in cell volume within multicellular spheroids and, further, describe how the process depends on proliferation-induced solid stress. Our model may provide new insight into the role of gap junctions in breast cancer progression. 

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