Adhesion-dependent cells actively sense the mechanical properties of their environment through mechanotransductory processes at focal adhesions, which are integrin-based contacts connecting the extracellular matrix to the cytoskeleton. Here we present first steps towards a quantitative understanding of focal adhesions as mechanosensors. It has been shown experimentally that high levels of force are related to growth of and signaling at focal adhesions. In particular, activation of the small GTPase Rho through focal adhesions leads to the formation of stress fibers. Here we discuss one way in which force might regulate the internal state of focal adhesions, namely by modulating the internal rupture dynamics of focal adhesions. A simple two-spring model shows that the stiffer the environment, the more efficient cellular force is built up at focal adhesions by molecular motors interacting with the actin filaments.
Abstract Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis , leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.
Abstract The quaternary structure with specific stoichiometry is pivotal to the specific function of protein complexes. However, determining the structure of many protein complexes experimentally remains a major bottleneck. Structural bioinformatics approaches, such as the deep learning algorithm Alphafold2‐multimer (AF2‐multimer), leverage the co‐evolution of amino acids and sequence‐structure relationships for accurate de novo structure and contact prediction. Pseudo‐likelihood maximization direct coupling analysis (plmDCA) has been used to detect co‐evolving residue pairs by statistical modeling. Here, we provide evidence that combining both methods can be used for de novo prediction of the quaternary structure and stoichiometry of a protein complex. We achieve this by augmenting the existing AF2‐multimer confidence metrics with an interpretable score to identify the complex with an optimal fraction of native contacts of co‐evolving residue pairs at intermolecular interfaces. We use this strategy to predict the quaternary structure and non‐trivial stoichiometries of Bacillus subtilis spore germination protein complexes with unknown structures. Co‐evolution at intermolecular interfaces may therefore synergize with AI‐based de novo quaternary structure prediction of structurally uncharacterized bacterial protein complexes.
Adhering cells actively probe the mechanical properties of their environment and use the resulting information to position and orient themselves. We show that a large body of experimental observations can be consistently explained from one unifying principle, namely that cells strengthen contacts and cytoskeleton in the direction of large effective stiffness. Using linear elasticity theory to model the extracellular environment, we calculate optimal cell organization for several situations of interest and find excellent agreement with experiments for fibroblasts, both on elastic substrates and in collagen gels: cells orient in the direction of external tensile strain, they orient parallel and normal to free and clamped surfaces, respectively, and they interact elastically to form strings. Our method can be applied for rational design of tissue equivalents. Moreover our results indicate that the concept of contact guidance has to be reevaluated. We also suggest that cell-matrix contacts are upregulated by large effective stiffness in the environment because in this way, build-up of force is more efficient.
Some bacteria, such as Bacillus subtilis, withstand starvation by forming dormant spores that revive when nutrients become available. Although sporulation and spore revival jointly determine survival in fluctuating environments, the relationship between them has been unclear. Here we show that these two processes are linked by a phenotypic "memory" that arises from a carry-over of molecules from the vegetative cell into the spore. By imaging life histories of individual B. subtilis cells using fluorescent reporters, we demonstrate that sporulation timing controls nutrient-induced spore revival. Alanine dehydrogenase contributes to spore memory and controls alanine-induced outgrowth, thereby coupling a spore's revival capacity to the gene expression and growth history of its progenitors. A theoretical analysis, and experiments with signaling mutants exhibiting altered sporulation timing, support the hypothesis that such an intrinsically generated memory leads to a tradeoff between spore quantity and spore quality, which could drive the emergence of complex microbial traits.
<p>Methane (CH<sub>4</sub>) is the most abundant hydrocarbon in the atmosphere, largely originating from biogenic sources that recently have been linked to an increasing number of organisms living in both oxic and anoxic environments. Traditionally, biogenic CH<sub>4</sub> has been regarded as the final product of the anoxic decomposition of organic matter by methanogenic <em>Archaea</em>. However, plants, fungi, algae, lichens and cyanobacteria have recently been shown to produce CH<sub>4</sub> in the presence of oxygen. While methanogens produce CH<sub>4 </sub>enzymatically during anaerobic energy metabolism, the requirements and pathways for CH<sub>4 </sub>production by &#8220;non-methanogenic&#8221; cells are poorly understood. Here, we present a CH<sub>4</sub> formation mechanism that most likely occurs in all living organisms (Ernst et al. 2022). Firstly, we show results from two bacterial species (<em>Bacillus subtilis</em> and <em>Escherichia coli</em>) demonstrating that CH<sub>4</sub> formation is triggered by free iron and reactive oxygen species (ROS), which are generated by metabolic activity and enhanced by oxidative stress. ROS-induced methyl radicals, derived from organic compounds containing sulfur- or nitrogen-bonded methyl groups, are key intermediates that ultimately lead to CH<sub>4</sub>.</p><p>In a second step, we made numerous experiments and collected data from many other model organisms (over 30 species) from the three domains of life<em> </em>(<em>Bacteria, Archaea</em> and <em>Eukarya</em>), including several human cell lines and a non-methanogenic archaeal species. All of the selected species clearly showed CH<sub>4</sub> formation under sterile growth conditions. As the mechanism described for CH<sub>4</sub> formation depends on several factors such as the availability of methylated precursor compounds, free iron, cellular stress factors and antioxidants, production rates can vary by several orders of magnitude. For terrestrial plants and cyanobateria, measured CH<sub>4 </sub>emission rates have been reported to vary by almost four orders of magnitude. In both cases, rates were measured for many species and under varying environmental conditions and stressors, although the formation mechanism(s) were unknown. Our proposed ROS-driven pathway not only provides a mechanistic explanation for the observed CH<sub>4</sub> emissions under oxic conditions but also for the large variability of emission rates observed for terrestrial plants, marine and freshwater algae, fungi, lichens and cyanobacteria, which have caused many controversial discussions since their publication. Furthermore, now it is very clear that any global upscaling will be highly challenging given the complex variables that control emissions from specific organisms.</p><p>In summary, the observed and experimental validated process of CH<sub>4</sub> formation across all living organisms is a major step to better understand biological CH<sub>4</sub> (in addition to the well-described archaeal methanogenesis) formation and cycling on Earth.</p><p>Reference:</p><p>Ernst, L., Steinfeld, B., Barayeu, U., Klintzsch, T., Kurth, M., Grimm, D., Dick, T.P., Rebelein, J.G., Bischofs, I.B., Keppler, F. (2022). ROS-driven methane formation across living organisms. <em>Nature</em>,<em> </em>in press.</p>
