Involvement of DNA curvature in intergenic regions of prokaryotes

It is known that DNA curvature plays a certain role in gene regulation. The distribution of curved DNA in promoter regions is evolutionarily preserved, and it is mainly determined by temperature of habitat. However, very little is known on the distribution of DNA curvature in termination sites. Our main objective was to comprehensively analyze distribution of curved sequences upstream and downstream to the coding genes in prokaryotic genomes. We applied CURVATURE software to 170 complete prokaryotic genomes in a search for possible typical distribution of DNA curvature around starts and ends of genes. Performing cluster analyses and other statistical tests, we obtained novel results regarding various factors influencing curvature distribution in intergenic regions, such as growth temperature, A+T composition and genome size. We also analyzed intergenic regions between converging genes in 15 selected genomes. The results show that six genomes presented peaks of curvature excess larger than 3 SDs. Insufficient statistics did not allow us to draw further conclusion. Our hypothesis is that DNA curvature could affect transcription termination in many prokaryotes either directly, through contacts with RNA polymerase, or indirectly, via contacts with some regulatory proteins

Supramolecular structure in the membrane of Staphylococcus aureus

The fundamental processes of life are organized and based on common basic principles. Molecular organizers, often interacting with the membrane, capitalize on cellular polarity to precisely orientate essential processes. The study of organisms lacking apparent polarity or known cellular organizers (e.g., the bacterium Staphylococcus aureus) may enable the elucidation of the primal organizational drive in biology. How does a cell choose from infinite locations in its membrane? We have discovered a structure in the S. aureus membrane that organizes processes indispensable for life and can arise spontaneously from the geometric constraints of protein complexes on membranes. Building on this finding, the most basic cellular positioning system to optimize biological processes, known molecular coordinators could introduce further levels of complexity. All life demands the temporal and spatial control of essential biological functions. In bacteria, the recent discovery of coordinating elements provides a framework to begin to explain cell growth and division. Here we present the discovery of a supramolecular structure in the membrane of the coccal bacterium Staphylococcus aureus, which leads to the formation of a large-scale pattern across the entire cell body; this has been unveiled by studying the distribution of essential proteins involved in lipid metabolism (PlsY and CdsA). The organization is found to require MreD, which determines morphology in rod-shaped cells. The distribution of protein complexes can be explained as a spontaneous pattern formation arising from the competition between the energy cost of bending that they impose on the membrane, their entropy of mixing, and the geometric constraints in the system. Our results provide evidence for the existence of a self-organized and nonpercolating molecular scaffold involving MreD as an organizer for optimal cell function and growth based on the intrinsic self-assembling properties of biological molecules

Structure and function of bacterial dynamin-like proteins

Membrane dynamics are essential for numerous cellular processes in eukaryotic and prokaryotic cells. In eukaryotic cells, membrane fusion and fission are often catalyzed by large GTPases of the dynamin protein family. These proteins couple GTP hydrolysis to membrane deformation, which eventually leads to fusion or fission of the lipid bilayer. Mutations in eukaryotic dynamin-like proteins (DLPs) are associated with various diseases underscoring the importance to fully understand the biochemistry of these proteins. In recent years, a wealth of structural and biochemical data have been published that allow a detailed analysis of how dynamins or DLPs modulate biological membranes. However, less is known about the function of bacterial DLPs, although structural data exist. This review summarizes current knowledge about bacterial dynamins and discusses structural and functional properties in comparison to their eukaryotic counterparts

Methods and measures for investigating microscale motility

Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how these diverse lifeforms navigate their surroundings. Herein, we give an overview of different experimental, analytical, and mathematical methods used to study a suite of microscale motility mechanisms across different scales encompassing molecular-, individual- to population-level. We identify transferable techniques, pressing challenges, and future directions in the field. This review can serve as a starting point for researchers who are interested in exploring and quantifying the movements of organisms in the microscale world.Comment: 24 pages, 2 figure

The N-Terminal Amphipathic Helix of the Topological Specificity Factor MinE Is Associated with Shaping Membrane Curvature

Pole-to-pole oscillations of the Min proteins in Escherichia coli are required for the proper placement of the division septum. Direct interaction of MinE with the cell membrane is critical for the dynamic behavior of the Min system. In vitro, this MinE-membrane interaction led to membrane deformation; however, the underlying mechanism remained unclear. Here we report that MinE-induced membrane deformation involves the formation of an amphipathic helix of MinE2–9, which, together with the adjacent basic residues, function as membrane anchors. Biochemical evidence suggested that the membrane association induces formation of the helix, with the helical face, consisting of A2, L3, and F6, inserted into the membrane. Insertion of this helix into the cell membrane can influence local membrane curvature and lead to drastic changes in membrane topology. Accordingly, MinE showed characteristic features of protein-induced membrane tubulation and lipid clustering in in vitro reconstituted systems. In conclusion, MinE shares common protein signatures with a group of membrane trafficking proteins in eukaryotic cells. These MinE signatures appear to affect membrane curvature

Optimal signal processing in small stochastic biochemical networks

We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function performed by the network. Specifically, we study the maximum mutual information between the input (chemical) signal and the output (genetic) response attainable by the network in the context of an analytic model of particle number fluctuations. We perform this analysis for all biochemical circuits, including various feedback loops, that can be built out of 3 chemical species, each under the control of one regulator. We find that a generic network, constrained to low molecule numbers and reasonable response times, can transduce more information than a simple binary switch and, in fact, manages to achieve close to the optimal information transmission fidelity. These high-information solutions are robust to tenfold changes in most of the networks' biochemical parameters; moreover they are easier to achieve in networks containing cycles with an odd number of negative regulators (overall negative feedback) due to their decreased molecular noise (a result which we derive analytically). Finally, we demonstrate that a single circuit can support multiple high-information solutions. These findings suggest a potential resolution of the "cross-talk" dilemma as well as the previously unexplained observation that transcription factors which undergo proteolysis are more likely to be auto-repressive.Comment: 41 pages 7 figures, 5 table

Investigating the Role of Carotenoids in Membrane Organization of \u3ci\u3ePantoea\u3c/i\u3e sp. YR343

Bacterial cell membranes are complex mixtures of lipids and proteins, the combination of which confers biophysical properties to the membrane and allows it to respond to environmental conditions. Pantoea sp. YR343 is a plant-associated gram-negative gamma-proteobacteria characterized by the presence of carotenoids in the membrane. Pantoea sp. YR343 mutants lacking phytoene synthase (encoded by crtB), which catalyzes the first step in carotenoid biosynthesis, failed to produce carotenoids and displayed enhanced sensitivity to reactive oxygen species. The crtB mutant also displayed unexpected defects in biofilm formation, secretion of indole-3-acetic acid, and root colonization compared to wildtype cells. We hypothesized that the phenotypic defects observed in the crtB mutant were due to the changes in both lipid and protein composition which modulate the biophysical properties of the membrane and influence signaling and transport.Mass spectrometry analysis of the lipid head and tails revealed a significant abundance of phosphotidylethanolamine and unsaturated fatty acids in the crtB mutant cells. Using both fluorescence anisotropy (FA) and atomic force microscopy on whole cells, we showed that the crtB mutant membranes were less fluid when compared to wildtype membranes. We further characterized the membranes using spheroplasts and natural extract vesicles, which showed that presence of the outer wall does not impact membrane fluidity, but the presence of membrane proteins and carotenoids do have a strong impact. Proteomic profiling of wildtype and crtB mutant membranes revealed a significant loss of several membrane protein classes in the crtB mutant. Among the different classes of proteins, signaling and transport, outer membrane biogenesis and cell motility protein classes were the most affected in the mutant. The loss of specific protein classes may explain, at least in part, the phenotypic defects associated with the crtB mutant.Our study highlights the importance of carotenoids beyond its anti-oxidant potential. Loss of bacterial carotenoids changes membrane organization and dynamics by affecting the composition and distribution of both lipids and membrane proteins. Importantly, carotenoids regulate membrane fluidity, which is an important parameter for bacterial adaptation and survival

Proteome sequence features carry signatures of the environmental niche of prokaryotes

<p>Abstract</p> <p>Background</p> <p>Prokaryotic environmental adaptations occur at different levels within cells to ensure the preservation of genome integrity, proper protein folding and function as well as membrane fluidity. Although specific composition and structure of cellular components suitable for the variety of extreme conditions has already been postulated, a systematic study describing such adaptations has not yet been performed. We therefore explored whether the environmental niche of a prokaryote could be deduced from the sequence of its proteome. Finally, we aimed at finding the precise differences between proteome sequences of prokaryotes from different environments.</p> <p>Results</p> <p>We analyzed the proteomes of 192 prokaryotes from different habitats. We collected detailed information about the optimal growth conditions of each microorganism. Furthermore, we selected 42 physico-chemical properties of amino acids and computed their values for each proteome. Further, on the same set of features we applied two fundamentally different machine learning methods, Support Vector Machines and Random Forests, to successfully classify between bacteria and archaea, halophiles and non-halophiles, as well as mesophiles, thermophiles and mesothermophiles. Finally, we performed feature selection by using Random Forests.</p> <p>Conclusions</p> <p>To our knowledge, this is the first time that three different classification cases (domain of life, halophilicity and thermophilicity) of proteome adaptation are successfully performed with the same set of 42 features. The characteristic features of a specific adaptation constitute a signature that may help understanding the mechanisms of adaptation to extreme environments.</p