Biology subjects

Hernandez, A. C.

Publications and source records attributed to Hernandez, A. C..

4 recordsLinked to original sources

bioRxiv2026

ModCRElib: A standalone package to model cis-regulatory elements.

SummaryThe ModCRElib package provides various tools for the analysis and modelling of transcription factor(TF)-DNA and regulatory complex inter-protein interactions. It takes structural information on these interactions to predict TF binding motifs, generate binding profiles along DNA sequences that score the binding affinity, predict TF binding sites and model the structure of higher order regulatory complexes. It is capable of working with a variety of input data formats and sources. The user may follow the analysis pipeline as outlined in the documentation or the user can make use of any of the multiple functionalities in an isolated manner. The package takes the service offered by the ModCRE server and enables users to apply its tools in an unrestricted and customizable manner. In this paper we provide 5 example uses of ModCRElib. This includes (i) TF binding affinity prediction, (ii) TF binding aggregation, (iii) characterization of specificity in TF binding sites along target DNA sequences,(iv) modelling TF bound to predicted binding sites, and (v) the generation of statistical potential derived scoring profiles of TF interacting with DNA. Availabilityhttps://github.com/structuralbioinformatics/ModCRElib Contactbaldo.oliva@upf.edu Supplementary informationAvailable at https://github.com/structuralbioinformatics/ModCRElib. doi:10.5281/zenodo.17484081

bioinformatics↗

bioRxiv2025

Continuum architecture dynamics of vesicle tethering in exocytosis

Essential for eukaryotic organisms, multiple copies of the exocyst complex tether each secretory vesicle to the plasma membrane (PM) in constitutive exocytosis. The exocyst higher-order structure (ExHOS) that coordinates the action of these multiple exocysts remains unexplored. We integrated particle-tracking, super-resolution microscopy and cryo-electron tomography in a model that time-resolves the continuum conformational landscape of the ExHOS and functionally annotates its different conformations. We found that 7 exocysts form flexible ring-shaped ExHOS that tether vesicles at <45 nm from the PM. The ExHOS, initially 19 nm in radius, rapidly expands while it pulls the vesicle towards the PM. Subsequently, the ExHOS stabilizes, securing the vesicle at [~]4 nm from the PM. After fusion, Sec18 mediates the ExHOS disassembly when its radius is 38 nm. By resolving the fundamental biophysical principles of tethering we bridged the gap between static isolated structures and the dynamic and multimeric nature of exocytosis.

cell biology↗

bioRxiv2020

Characterization of an ECF56-family sigma factor from Streptomyces venezuelae reveals a highly conserved regulome

Bacteria often possess alternative sigma factors that initiate the transcription of specific genes under environmental stresses, the largest and most diverse group being the extracytoplasmic function (ECF) sigma factors. The regulation of ECF activity is crucial for ensuring the distinct transcription of stress responsive genes only occurs under the appropriate conditions. While most ECFs are comprised of only the core {sigma}2 and {sigma}4 regions, a unique form of ECF sigma factor regulation also contains a C-terminal extension bearing homology to the NTF2 superfamily of protein domains. While previous work has shown that this NTF2 domain can affect transcriptional activity in vivo in ECF41 and ECF42, its role in the newly classified ECF56 subgroup is unknown. In this work, we show that truncation of the C-terminus of the ECF56 sigma factor SVEN_4562 of Streptomyces venezuelae upregulates its activity in a hybrid assay. Through transcriptomics in S. venezuelae, we found that this truncated ECF56 sigma factor has a highly conserved promoter sequence in vivo. Bioinformatic assays illustrated that deep branches of the Actinobacteria phylum contained putative ECF56 promoter motifs identical to those found in the S. venezuelae ECF56 regulon. We validated these findings through ex situ hybrid assays illustrating that truncated ECF56 sigma factors from phylogenetically diverse Actinobacteria activate transcription from these promoters. Importantly, our work shows that the genetic infrastructure of the ECF56 family of sigma factors is highly conserved and performs important functions yet to be understood in Actinobacteria. ImportanceMost ECF sigma-factors rely on anti-sigma factor regulation; in contrast, the unique classes of ECF sigma-factors that contain a C-terminal extension are thought to respond directly to an environmental signal. Here we show that the cis-acting regulatory element of the ECF56 regulon is likely highly conserved in many Actinobacteria, with exact nucleotide level conservation over ~2 billion years of evolution. The high conservation of this genetic architecture, as well as a conserved gene content within the regulon, strongly point to a specialized and important role in Actinobacteria biology.

microbiology↗

bioRxiv2019

Chemoinformatic-guided engineering of polyketide synthases

Polyketide synthase (PKS) engineering is an attractive method to generate new molecules such as commodity, fine and specialty chemicals. A significant challenge in PKS design is engineering a partially reductive module to produce a saturated {beta}-carbon through a reductive loop exchange. In this work, we sought to establish that chemoinformatics, a field traditionally used in drug discovery, could provide a viable strategy to reductive loop exchanges. We first introduced a set of donor reductive loops of diverse genetic origin and chemical substrate structures into the first extension module of the lipomycin PKS (LipPKS1). Product titers of these engineered unimodular PKSs correlated with atom pair chemical similarity between the substrate of the donor reductive loops and recipient LipPKS1, reaching a titer of 165 mg/L of short chain fatty acids produced by Streptomyces albus J1074 harboring these engineered PKSs. Expanding this method to larger intermediates requiring bimodular communication, we introduced reductive loops of divergent chemosimilarity into LipPKS2 and determined triketide lactone production. Collectively, we observed a statistically significant correlation between atom pair chemosimilarity and production, establishing a new chemoinformatic method that may aid in the engineering of PKSs to produce desired, unnatural products.

biochemistry↗