Biology subjects

Martinez-Pastor, M.

Publications and source records attributed to Martinez-Pastor, M..

5 recordsLinked to original sources

bioRxiv2026

A Bayesian Multi-Species Approach Infers Gene Regulatory Networks Across Non-Model Organisms

Control of gene expression by transcription factors (TFs) is a critical mechanism for cells to maintain homeostasis in response to environmental signals. Gene network models that predict regulatory interactions between transcription factors and the genes they control aid in understanding these complex processes. These models are useful as they provide testable hypotheses of regulatory interactions, transcription factor function, and accelerate the study of uncharacterized transcription factors. However, inference of these models is computationally challenging due to the vast quantity of data required given the many possible states of the regulatory network. Microbial genomes encode hundreds of transcription factors, with numerous interactions that require substantial functional genomics datasets to infer. This problem is accentuated in understudied organisms, species that would greatly benefit from an inferred network for biological discovery, where the lack of available data is particularly constraining for effective inference. To address this problem, we have developed GRN-BMuSeR (Gene Regulatory Networks from Bayesian MUlti-SpEcies Regression), a novel multitask approach to gene regulatory network inference that leverages gene orthology between closely related species to improve inference performance. We evaluate its performance on a dataset from the well-studied bacterial species Bacillus subtilis, demonstrating improved performance in multitask settings. Applying the model to simulated data reveals utility in multi-species contexts. Finally, we apply our models to infer GRNs and explore predictions for two hypersaline-adapted archaeal species. We leverage a rich dataset from Halobacterium salinarum to inform the inference of the gene regulatory network of Haloferax volcanii, for which a more limited genomics dataset was available. We generate a large compendium of gene expression data for Hfx.volcanii for GRN inference input. Through exploration of resultant network predictions, we show concordance with known TF functions and discover hundreds of novel TF functional predictions. Moving forward, our results provide a framework to generate testable hypotheses that will serve to guide experimental work and accelerate discovery in these understudied species.

systems biology↗

bioRxiv2024

Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

For microbial cells, an appropriate response to changing environmental conditions is critical for viability. Transcription regulatory proteins, or transcription factors (TFs) sense environmental signals to change gene expression. However, it remains unclear how TFs and their corresponding gene regulatory networks are selected over evolutionary time scales. The function of TFs and how they evolve are particularly understudied in archaeal organisms. Here we identified, characterized, and compared the function of the RosR transcription factor across three related hypersaline adapted archaeal model species. RosR was previously characterized as a global regulator of gene expression during oxidative stress in the species Halobacterium salinarum (hsRosR). Here we use functional genomics and quantitative phenotyping to demonstrate that, despite strong sequence conservation of RosR across species, its function diverges substantially. Surprisingly, RosR in Haloferax volcanii (hvRosR) and Haloferax mediterranei (hmRosR) regulates genes whose products function in motility and outer membrane structure, leading to significant defects in motility when rosR is deleted. Given weak conservation and degeneration in cis-regulatory sequences recognized by the RosR TF across species, we hypothesize that the RosR regulatory network is readily rewired during evolution across related species of archaea. SIGNIFICANCE STATEMENTO_LIGene regulation enables cells to sense and respond to environmental signals. The mechanisms by which gene regulatory circuits change and adapt over evolutionary time scales remain unclear, especially in understudied domains of life like the archaea. C_LIO_LIHere we demonstrate that the archaeal-specific RosR transcription protein plays fundamentally different roles in environmental response of related archaeal species (oxidative stress protection vs motility). This divergence likely occurred through reduced selectivity of RosR for certain DNA sequence motifs. C_LIO_LIThese findings are surprising given strong sequence and structural conservation of RosR and suggest that transcription regulator function can diverge rapidly through flexible protein-DNA interactions. This mechanism of divergence is shared between eukaryotes and archaea, suggesting ancient origins. C_LI Subject categories: Bioinformatics, microbiology, genetics, gene regulatory networks

microbiology↗

bioRxiv2023

TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii

Maintaining intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repressor (DtxR) family transcription factors (TFs) that together regulate the iron response through an interconnected transcriptional regulatory network (TRN). However, the metal specificity of DtxR TFs and the conservation of the TRN remained poorly understood. Here we identified and characterized the TRN of Haloferax volcanii for comparison. Genetic analysis demonstrated that Hfx. volcanii relies on three DtxR transcriptional regulators (Idr, SirR, and TroR), with TroR as the primary regulator of iron homeostasis. Bioinformatics and molecular approaches revealed that TroR binds a conserved cis-regulatory motif located [~]100 nt upstream of the start codon of iron-related target genes. Transcriptomics analysis demonstrated that, under conditions of iron sufficiency, TroR repressed iron uptake and induced iron storage mechanisms. TroR repressed the expression of one other DtxR TF, Idr. This reduced DtxR TRN complexity relative to that of Hbt. salinarum appeared correlated with natural variations in iron availability. Based on these data, we hypothesize that increasing TRN complexity appears selected for under variable environmental conditions such as iron availability.

microbiology↗

bioRxiv2022

Comparative Analysis of rRNA removal methods for RNA-seq Differential Expression in Halophilic Archaea

Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high ratio rRNA:mRNA (80-90%: [~]10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA and therefore requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here we show that after the discontinuation of the previous version of RiboZero (Illumina) that was useful to partially deplete rRNA from halophilic archaea, archaeal transcriptomics studies have experienced a standstill. To overcome this limitation, here we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper we provide insights to the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.

genomics↗

bioRxiv2022

Comparative analysis of genome-wide protein-DNA interactions across domains of life reveals unique binding patterns for hypersaline archaeal histones

DNA-binding proteins with roles in chromatin architecture and transcriptional regulation are present in all three domains of life. Histones package DNA and regulate gene expression in eukaryotes, and find their evolutionary origin in the domain of life Archaea. Previously characterised archaeal histones have a somewhat conserved functional role in nucleosome formation and DNA packaging. However, previous research has indicated that the histone-like proteins of high salt-adapted archaea, or halophiles, appear to function differently. The sole histone protein encoded by the model halophilic species Halobacterium salinarum is non-essential, is involved in direct and indirect transcriptional regulation, and does not appear to package DNA. Here we use protein-DNA binding assays, computational analysis, and quantitative phenotyping to compare DNA binding patterns across halophilic histone proteins, bacterial and archaeal TFs, NAPs, and eukaryotic histones. Like TFs, halophilic histones bind the genome too sparsely to compact the genome. However, unlike TFs, binding occurs in both coding and intergenic regions. Unlike histones, halophilic histone occupancy is not depleted at the start sites of genes, and halophilic genomes lack the dinucleotide periodicity known to facilitate histone binding. We detect unique sequence preferences for histone binding in halophiles. Together these data suggest that the non-essentiality and genome-wide binding features of halophilic histone-like proteins are conserved across halophiles; they bind DNA in ways resembling both TFs and chromatin proteins, but do not appear to play a role in forming chromatin. IMPORTANCEMost cells in eukaryotic species - from yeast to humans- possess histone proteins that pack and unpack DNA in response to environmental cues. These essential proteins regulate the genes necessary for important cellular processes, including development and stress protection. The domain of life Archaea represent the evolutionary progenitors of eukaryotes. The universal conservation of the primary sequences of histone proteins across archaeal lineages suggests that eukaryotic histones originated in the Archaea. However, archaeal histones lack N-terminal tails and, in some species, package DNA in a continuous helix with no linker DNA between nucleosomes. We recently discovered that histones in hypersaline adapted archaeal species do not package DNA, and can act like transcription factors (TFs) to regulate stress response gene expression. Here we compare hypersaline histone function to a variety of DNA binding proteins across the tree of life, revealing a mosaic of functions for hypersaline-adapted histones.

microbiology↗