Biology subjects

Torres, M. P.

Publications and source records attributed to Torres, M. P..

7 recordsLinked to original sources

bioRxiv2026

Activity of a three-phage combination against Mycobacterium tuberculosis in disease-relevant conditions

Phage therapy offers promise to combat antimicrobial resistance, including drug-resistant tuberculosis (TB). Understanding phage activity against Mycobacterium tuberculosis (Mtb) adapted to physiologic microenvironments, such as hypoxia and acidity in granulomas, is essential since these conditions induce non-replicating states. We evaluated a phage combination against Mtb under hypoxic, acidic (pH 5.5), and stationary-phase conditions in vitro. In planktonic Mtb growth conditions, phage concentrations increased around day seven followed by a significant reduction in Mtb H37Rv load, which was maintained over 31 days. Phage addition prevented regrowth was observed with rifampicin and isoniazid alone. Individual phage stability was differentially affected by acidic media conditions, resulting in variability of antimycobacterial activity. In hypoxic conditions and stationary growth experiments, phage titers remained stable over time with no change in mycobacterial load compared to controls. Model-based predictions were able to adequately capture phage-mycobacterial interactions with and without rifampicin. The lack of antimycobacterial activity in assays with non-replicating mycobacteria suggest that phages need actively replicating mycobacteria to exert lytic activity. Stable phage concentrations in assays with non-replicating mycobacteria suggests low grade phage replication in these conditions. Established models can support future study design through simulations of different experimental scenarios.

microbiology↗

bioRxiv2026

Deep quantitative phosphoproteomics identifies non-canonical pH-sensitive yeast phosphorylation networks

Changes in cellular pH act as potent upstream signals that rewire phosphorylation networks controlling cellular function and disease. In yeast, this response is thought to arise mainly from pH-dependent perturbations to membrane integrity and cell wall stress, which are relayed through TORC2- and PKC-dependent signaling pathways. Yet several proteins exhibit acid-dependent phosphorylation independently of TORC2 and PKC, pointing to additional, uncharacterized acid stress signaling mechanisms. To investigate this possibility, we performed SILAC-based deep phosphoproteomics to distinguish phosphoproteome changes that are dependent on plasma membrane and cell wall stress from those that are independent. Across more than 19,000 unique phosphosites, we identified over 1,000 sites whose acid stress-dependent regulation occurs outside the canonical acid stress pathways. These noncanonical targets were significantly enriched in proteins associated with the plasma membrane, GTPase-mediated signaling, and endocytosis. Motif analysis revealed enrichment of acidophilic substrates implicating the membrane-tethered casein kinase Yck1 as a major mediator of this response. In contrast, canonical acid stress signaling preferentially involved basophilic kinase substrates, while acid-repressed responses were enriched for proline-containing phosphosites involved in cell cycle progression. Collectively, these results uncover a distinct acid-responsive phosphorylation network that operates independently of plasma membrane and cell wall integrity signaling.

systems biology↗

bioRxiv2022

Depletion Assisted Hemin Affinity (DAsHA) Proteomics Reveals an Expanded Landscape of Heme Binding Proteins

Heme b (iron protoporphyrin IX) plays important roles in biology as a metallocofactor and signaling molecule. However, the targets of heme signaling and the network of proteins that mediate the exchange of heme from sites of synthesis or uptake to heme dependent or regulated proteins are poorly understood. Herein, we describe a quantitative mass spectrometry-based chemoproteomics strategy to identify exchange labile hemoproteins in human embryonic kidney HEK293 cells that may be relevant to heme signaling and trafficking. The strategy involves depleting endogenous heme with the heme biosynthetic inhibitor succinylacetone (SA), leaving putative heme binding proteins in their apo-state, followed by the capture of those proteins using hemin-agarose resin and finally elution and identification by mass spectrometry. By identifying only those proteins that interact with high specificity to hemin-agarose relative to control beaded agarose in a SA-dependent manner, we have expanded the number of proteins and ontologies that may be involved in binding and buffering labile heme or are targets of heme signaling. Notably, these include proteins involved in chromatin remodeling, DNA damage response, RNA splicing, cytoskeletal organization and vesicular trafficking, many of which have been associated with heme through complimentary studies published recently. Taken together, these results provide support for the emerging role for heme in an expanded set of cellular processes from genome integrity to protein trafficking and beyond.

biochemistry↗

bioRxiv2021

Sod1 Integrates Oxygen Availability to Redox Regulate NADPH Production and the Thiol Redoxome

Cu/Zn superoxide dismutase (Sod1) is a highly conserved and abundant antioxidant enzyme that detoxifies superoxide (O2-) by catalyzing its conversion to dioxygen (O2) and hydrogen peroxide (H2O2). Using Saccharomyces cerevisiae and mammalian cells, we discovered that a major new aspect of the antioxidant function of Sod1 is to integrate O2 availability to promote NADPH production. The mechanism involves Sod1-derived H2O2 oxidatively inactivating the glycolytic enzyme, glyceraldehyde phosphate dehydrogenase (GAPDH), which in turn re-routes carbohydrate flux to the oxidative phase of the pentose phosphate pathway (oxPPP) to generate NADPH. The aerobic oxidation of GAPDH is exclusively dependent on and rate-limited by Sod1. Thus, Sod1 senses O2 via O2- to balance glycolytic and oxPPP flux, through control of GAPDH activity, for adaptation to life in air. Importantly, this new mechanism for Sod1 antioxidant activity requires the bulk of cellular Sod1, unlike for its role in protection against O2- toxicity, which only requires < 1% of total Sod1. Using mass spectrometry, we identified proteome-wide targets of Sod1-dependent redox signaling, including numerous metabolic enzymes. Altogether, Sod1-derived H2O2 is important for antioxidant defense and a master regulator of metabolism and the thiol redoxome. Significance StatementCu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress, metabolic defects, and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2-) in a manner that produces an oxidant as a byproduct, hydrogen peroxide (H2O2). While much is known about the necessity of scavenging O2-, it is less clear what the physiological roles of Sod1-derived H2O2 are. Herein, we discovered that Sod1-derived H2O2 plays a very important role in antioxidant defense by stimulating the production of NADPH, a vital cellular reductant required for ROS scavenging enzymes, as well as redox regulating a large network of enzymes.

biochemistry↗

bioRxiv2020

Combinatorial phosphorylation modulates the structure and function of the G protein gamma subunit in yeast

Protein intrinsically disordered regions (IDRs) are often targets of combinatorial post-translational modifications (PTMs) that serve to regulate protein structure and/or function. Emerging evidence suggests that the N-terminal tails of G protein {gamma} subunits - essential components of heterotrimeric G protein complexes - are intrinsically disordered, highly phosphorylated governors of G protein signaling. Here, we demonstrate that the yeast G{gamma} Ste18 undergoes combinatorial, multi-site phosphorylation within its N-terminal IDR. Phosphorylation at S7 is responsive to GPCR activation and osmotic stress while phosphorylation at S3 is responsive to glucose stress and is a quantitative indicator of intracellular pH. Each site is phosphorylated by a distinct set of kinases and both are also interactive, such that phosphomimicry at one site affects phosphorylation on the other. Lastly, we show that phosphorylation produces subtle yet clear changes in IDR structure and that different combinations of phosphorylation modulate the activation rate and amplitude of the scaffolded MAPK Fus3. These data place G{gamma} subunits among the growing list of intrinsically disordered proteins that exploit combinatorial post-translational modification to govern signaling pathway output.

molecular biology↗

bioRxiv2019

SAPH-ire TFx: A Machine Learning Recommendation Method and Webtool for the Prediction of Functional Post-Translational Modifications

Protein post-translational modifications (PTMs) are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof, the number of functional PTMs in the eukaryotic proteome is currently underestimated. Furthermore, not all PTMs are functionally equivalent. Therefore, computational approaches that can confidently recommend the functional potential of experimental PTMs are essential. To address this challenge, we developed SAPH-ire TFx (https://saphire.biosci.gatech.edu/): a multi-feature neural network model and web resource optimized for recommending experimental PTMs with high potential for biological impact. The model is rigorously benchmarked against independent datasets and alternative models, exhibiting unmatched performance in the recall of known functional PTM sites and the recommendation of PTMs that were later confirmed experimentally. An analysis of feature contributions to model outcome provides further insight on the need for multiple rather than single features to capture the breadth of functional data in the public domain. Contactmtorres35@gatech.edu Supplementary InformationSee Tables S1-S6 & Figures S1-S4. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/731026v2_figS1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@4dbe8dorg.highwire.dtl.DTLVardef@1936d5org.highwire.dtl.DTLVardef@15eef8aorg.highwire.dtl.DTLVardef@1c07cea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S1.C_FLOATNO ROC curves at different KFSC thresholds. (unfurled in Figure 1E). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/731026v2_figS4.gif" ALT="Figure 4"> View larger version (20K): org.highwire.dtl.DTLVardef@48e892org.highwire.dtl.DTLVardef@9cf372org.highwire.dtl.DTLVardef@32da4dorg.highwire.dtl.DTLVardef@99fd89_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S4.C_FLOATNO Model recall and recommendation comparison for PTMs associated with validated functional SLiMs from the ELM resource. C_FIG

bioinformatics↗

bioRxiv2018

Host identity and functional traits determine the community composition of the arbuscular mycorrhizal fungi in facultative epiphytic plant species

The epiphytic vascular flora is scarce and facultative in semiarid Mediterranean ecosystems, thus covering diverse taxonomic groups. However, differently to terrestrial conditions, little is known about the factors driving mycorrhizal communities in epiphytic environments. Here, we investigated the arbuscular mycorrhizal fungi (AMF) harboured by 31 plant species occurring in the trunks of Phoenix dactylifera. We wanted to ascertain if host identity and plant functional traits shape mycorrhizal communities. Specifically, we tested the plant life-cycle (perennial versus annual), the plant life-form (herbaceous versus woody), the plant origin (exotic versus native) and the plant species.\n\nThe roots were examined by molecular and phylogenetic analysis of AMF community. The plant affiliation to species strongly influenced the AMF assemblages. Plant life-form and plant life-cycle also shaped AMF interactions. The AMF community differed between annual and perennial species and higher AMF richness was detected in perennial plants. The indicator species analysis revealed three Operational Taxonomic Units belonging to the Glomeraceae, associated with annual species. However, the epiphytic plants associated with AMF irrespective of whether they were native or not, probably because here no functional differences derive from plant origin.\n\nIMPORTANCEArbuscular mycorrhizal (AM) symbiosis has a decisive role in plant nutrient and water uptake by plants, with particular importance in stressful environments. Under semiarid conditions, the facultative epiphytic flora should cope with harsh conditions. While numerous studies have been conducted on factors driving terrestrial AM assemblages, the epiphytic environment remains unexplored. We offer new insights into composition of AM communities as shaped by epiphytic plant host identity and functional traits.

microbiology↗