A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Elucidating the Energetics of Bacterial Signal Transduction: Insights From Phoq

Bacteria transduce signals across the membrane using two-component systems, consisting of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. The histidine kinase, PhoQ, serves as a master regulator of virulence response in S. typhimurium and E. coli. It also is inhibited by divalent cations, particularly Mg2+. While the periplasmic sensor domain of this protein has a unique function, the cytoplasmic portion of this modular protein is made of structurally conserved domains found in many other bacterial sensor kinases. Signal transduction through these conserved domains is thought to be universal; however, the structural and energetic rearrangements that occur during signaling have generated numerous models. Through Bayesian inference we constructed a two-state model based on cysteine crosslinking data and homologous crystal structures. These two signaling states differ in membrane depth of the periplasmic acidic patch as well as the reciprocal displacement of diagonal helices along the dimer interface. Comparative studies of multiple histidine kinases suggest that diagonal displacement of helices is a common mode of signal transduction. A similar scissor-like model was previously ruled out in CheA-linked chemoreceptors; therefore, this new evidence suggests that sensor His-kinase and CheA-linked receptors possess different signaling mechanisms. To unify the various signaling mechanisms that exist for the different protein domains, we built a thermodynamic model based on Linked Equilibrating Domains (LED). We used this model to quantitatively interpret functional data of single-point Ala, Phe and Cys mutants throughout the signal transducing regions of PhoQ. Data from 35 mutants, including both activating and deactivating phenotypes, were globally fit using LED, and gross features such as Vmax and Kd were related to more nuanced population distributions and thermodynamic coupling. LED analysis highlights the principles by which individual signaling domains can be connected to create a functional signal transducer. These principles allow us to quantitatively explain signaling in histidine kinases and are likely to be broadly applicable to many other signal transduction proteins

Accessing and interpreting hydration dynamics on biological surfaces

Hydration water is necessary for protein function. It was long thought that the hydration water was simply an innocent solvent. However, current findings show that water is not an innocent solvent but an active player. It is now thought that hydration water plays a crucial role in biomolecular recognition by mediating the thermodynamic interaction between a protein and its ligand. The current challenge is to measure the hydration water and protein side chain thermodynamical properties.In this thesis we present site-specific measurements of hydration water motion on an array of biomolecular surfaces. We rationalize the hydration water motion in terms of the biomolecular surface properties. We find that the hydration water surrounding globular proteins contains information about the chemical and geometrical topology of the protein surface. We then present instrumentation developments to the Overhauser dynamic nuclear polarization (ODNP) methodology that made such measurements possible.We then introduce a new technique to measure the protein dynamic transition site- specifically and thus a new way to probe the coupling between a protein and the sur- rounding hydration water. We present measurements made on a small folded peptide system, the Trp Cage, and find that the hydration water motion and the protein dy- namic transition temperature are homogeneous across the surface of the peptide.Finally we discuss the development of a high field pulse EPR spectrometer that features arbitrary waveform generation capabilities. We showcase the applicability of this instrument and discuss the applicability of this instrument to the study of protein structure and dynamics

Evolution of multicellularity by collective integration of spatial information

At the origin of multicellularity, cells may have evolved aggregation in response to predation, for functional specialisation or to allow large-scale integration of environmental cues. These group-level properties emerged from the interactions between cells in a group, and determined the selection pressures experienced by these cells. We investigate the evolution of multicellularity with an evolutionary model where cells search for resources by chemotaxis in a shallow, noisy gradient. Cells can evolve their adhesion to others in a periodically changing environment, where a cell's fitness solely depends on its distance from the gradient source. We show that multicellular aggregates evolve because they perform chemotaxis more efficiently than single cells. Only when the environment changes too frequently, a unicellular state evolves which relies on cell dispersal. Both strategies prevent the invasion of the other through interference competition, creating evolutionary bi-stability. Therefore, collective behaviour can be an emergent selective driver for undifferentiated multicellularity.Animal sciencesAnalysis and Stochastic

Metodologías innovadoras basadas en 19F-RMN de ligando y técnicas computacionales para el estudio de procesos de reconocimiento molecular azúcar-lectina

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Farmacia, leída el 08-06-2021Carbohydrates play a central role in a large myriad of biological processes. They are found in all living organisms in nature, participating in different functions ranging from their use as energy source or as structural fragments, to infection-related processes in complex organisms. In vertebrates, they are located both in the cell surface and in the extracellular space, forming very diverse and intricate structures, but they are also present in the nucleus and cytoplasm of eukaryotic cells bound to proteins (glycoproteins). Their location almost ubiquitous in the organism confers them the capacity of mediate in a large number of ‘communication’ processes with other entities, for instance, in cell-cell, cell-molecule and cell-matrix interactions. In addition, carbohydrates intervene in molecular recognition processes between different organisms, such as the pathogen and parasite recognition by host cells...Los carbohidratos juegan un papel fundamental en una enorme variedad de procesos biológicos. Se encuentran en todos los organismos vivos en la naturaleza, donde intervienen en funciones que abarcan desde su uso como fuente de energía o como fragmentos estructurales, hasta procesos de infección en organismos superiores. En vertebrados, se localizan tanto en la superficie celular como en el espacio extracelular, formando estructuras muy diversas y complejas, pero también están presentes en el núcleo y citoplasma de células eucariotas unidos a proteínas (glicoproteínas). Su localización casi universal en el organismo les confiere la capacidad de intervenir en un gran número de procesos de ‘comunicación’ con otras entidades, por ejemplo, interacciones intercelulares, célula-molécula y célula-matriz extracelular. Además, los carbohidratos median procesos de reconocimiento molecular entre distintos organismos, como el reconocimiento de patógenos y parásitos por la célula de un huésped...Fac. de FarmaciaTRUEunpu