Biology subjects

Saiz, L.

Publications and source records attributed to Saiz, L..

5 recordsLinked to original sources

bioRxiv2023

Chaperone-driven entropic separation of amyloid nanofilament bundles

The disassembly of misfolded protein aggregates is a requirement for the proper functioning of cells. It has implications in multiple neuropathologies, such as Alzheimers and Parkinsons diseases. The active unbundling of fibrillar aggregates has recently been identified as a key, rate-limiting step in the disassembly process. Yet, the nature of the underlying molecular mechanism remains an outstanding question. Here, we develop a coarse-grained computational approach from the atomistic structural information and show that the interactions of molecules tethered to fibrils lead to entropic forces consistent with the unbundling process observed in amyloid -synuclein disaggregation by Hsp70. We uncover two main types of entropic effects, categorized as intra- and inter-protofilament, which are differentially affected by the system parameters and conditions. Our results show that only highly efficient chaperone systems can overcome the free energy cost of the lateral association between two protofilaments. Through the analysis of cryo-electron tomography and high-speed atomic force microscopy data, we find that co-chaperone networks and ATP hydrolysis are needed to achieve the conditions for highly efficient entropic force generation. We highlight the implications of these results for the design of targeted therapies for the underlying neuropathologies.

biophysics↗

bioRxiv2023

The unreasonable effectiveness of equilibrium gene regulation through the cell cycle

Systems like the prototypical lac operon can reliably hold the repression of transcription upon DNA replication across cell cycles with just ten repressor molecules per cell and, in addition, behave as if they were at equilibrium. The origin of this type of phenomena is still an unresolved question of major implications. Here, we develop a general theory to analyze strong perturbations in quasi-equilibrium systems and use it to quantify the effects of DNA replication in gene regulation. We find a scaling law that connects actual transcription with its predicted equilibrium values in terms of a single kinetic parameter. We show that even the simplest, exceptionally reliable natural system functions beyond the physical limits of naive regulation through compensatory mechanisms that suppress nonequilibrium effects. We validate the approach with both in vivo cell-population and single-cell characterization of the lac operon. Analyses of synthetic systems without adjuvant activators, such as the cAMP receptor protein (CRP), do not show this reliability. Our results provide a rationale for the function of CRP, beyond just being a tunable activator, as a mitigator of cell cycle perturbations.

biophysics↗

bioRxiv2022

TE invasion fuels molecular adaptation in laboratory populations of Drosophila melanogaster

Transposable elements are mobile genetic parasites that frequently invade new host genomes through horizontal transfer. Invading TEs often exhibit a burst of transposition, followed by reduced transposition rates as repression evolves in the host. We recreated the horizontal transfer of P-element DNA transposons into a D. melanogaster host, and followed the expansion of TE copies and evolution of host repression in replicate laboratory populations reared at different temperatures. We observed that while populations maintained at high temperatures rapidly go extinct after TE invasion, those maintained at lower temperatures persist, allowing for TE spread and the evolution of host repression. We also surprisingly discovered that invaded populations experienced recurrent insertion of P-elements into a specific long non-coding RNA, lncRNA:CR43651, and that these insertion alleles are segregating at unusually high frequency in experimental populations, indicative of positive selection. We propose that, in addition to driving the evolution of repression, transpositional bursts of invading TEs can drive molecular adaptation.

evolutionary biology↗

bioRxiv2021

Robustness of DNA Looping Across Multiple Divisions in Individual Bacteria

DNA looping has emerged as a central paradigm of transcriptional regulation as it is shared across many living systems. One core property of DNA looping-based regulation is its ability to greatly enhance repression or activation of genes with only a few copies of transcriptional regulators. However, this property based on small number of proteins raises the question of the robustness of such a mechanism with respect to the large intracellular perturbations taking place during growth and division of the cell. Here we address the issue of sensitivity to variations of intracellular parameters of gene regulation by DNA looping. We use the lac system as a prototype to experimentally identify the key features of the robustness of DNA looping in growing E. coli cells. Surprisingly, we observe time intervals of tight repression spanning across division events, which can sometimes exceed ten generations. Remarkably, the distribution of such long time intervals exhibits memoryless statistics that is mostly insensitive to repressor concentration, cell division events, and the number of distinct loops accessible to the system. By contrast, gene regulation becomes highly sensitive to these perturbations when DNA looping is absent. Using stochastic simulations, we propose that the robustness to division events of memoryless distributions emerges from the competition between fast, multiple re-binding events of repressors and slow initiation rate of the RNA-polymerase. We argue that fast re-binding events are a direct consequence of DNA looping that ensures robust gene repression across a range of intracellular perturbations. Significance statementIt is well-established that certain intracellular regulators can stabilize DNA loops to greatly enhance activation or repression of gene transcription. In vitro but also in vivo ensemble measurements have determined that only a few copies of regulators are in fact needed to stably form DNA loops. In view of such a small number, we address the issue of sensitivity of gene regulation by DNA looping to variations of intracellular parameters in individual growing E. coli bacteria. Surprisingly, we find that DNA looping from the lac system is robust to a range of perturbations including divisions during which cells can maintain tight repression over many generations. We propose a mechanism that governs the observed robustness across a range of intracellular perturbations.

biophysics↗

bioRxiv2021

Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites

The prevalent one-dimensional alignment of genomic signals to a reference landmark is a cornerstone of current methods to study transcription and its DNA-dependent processes but it is prone to mask potential relations among multiple DNA elements. We developed a systematic approach to align genomic signals to multiple locations simultaneously by expanding the dimensionality of the genomic-coordinate space. We analyzed transcription in human and uncovered a complex dependence on the relative position of neighboring transcription start sites (TSSs) that is consistently conserved among cell types. The dependence ranges from enhancement to suppression of transcription depending on the relative distances to the TSSs, their intragenic position, and the transcriptional activity of the gene. Our results reveal a conserved hierarchy of alternative TSS usage within a previously unrecognized level of genomic organization and provide a general methodology to analyze complex functional relationships among multiple types of DNA elements.

bioinformatics↗