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Mejia, G.

Publications and source records attributed to Mejia, G..

7 recordsLinked to original sources

Exploring protein duplication across Archaea genomes

Gene duplication is a major driver of genomic innovation, but whether paralog accumulation scales uniformly with increasing genome size across the domain Archaea remains unclear. This study presents a domain-wide analysis of 1,829 archaeal genomes and their predicted proteomes to evaluate protein family expansions, their distribution, and lineage-specific patterns of gene duplication. Protein family expansions were classified as recent (90% sequence identity), intermediate (70%), or old (40%) duplications based on sequence-identity thresholds within each family. The findings show that gene duplication content is decoupled from overall proteome size at high sequence-identity levels, indicating that recent paralog retention does not correlate with proteome expansion. Archaeal lineages exhibit contrasting gene duplication profiles. All 1,829 genomes contained paralogs at the 40% sequence identity threshold, indicating the widespread presence of ancient or divergent duplication events. In contrast, paralogs detected at the 90% identity threshold, showed substantial variation across lineages. Their proportion reached up to 16.6% in groups such as Halobacteria, whereas only 74 genomes (4.04%) completely lacked paralogs at this threshold. Highly duplicated families are enriched for membrane transport systems (ABC/MFS), central metabolic enzymes (e.g., acetyl-CoA synthetase), a high proportion of uncharacterized functions, and mobile elements, predominantly transposases. Notably, we identified 314 transposase protein families in Archaea, distributed in 161 unique families in Archaea and 153 families shared with Bacteria, suggesting mechanisms of interdomain gene transfer. Overall, paralog accumulation in Archaea is a lineage-specific phenomenon shaped by targeted functional duplications and mobile element activity, rather than a simple consequence of proteome growth.

genomics↗

Colchicine Directly Targets Aldehyde Dehydrogenase 2 (ALDH2) to Suppress Radiation-Induced Senescence and Atherosclerosis

BackgroundIonizing radiation (IR) accelerates atherosclerosis through induction of cellular senescence, DNA damage, defective efferocytosis, and dysregulation of clonal hematopoiesis (CH) drivers. Although low-dose colchicine reduces ischemic cardiovascular events in coronary artery disease, the precise molecular mechanisms underlying its vasculoprotective effects remain incompletely defined, and whether it mitigates radiation-associated vascular injury is unknown. MethodsBone marrow-derived macrophages (BMDMs) were pretreated with low-dose colchicine and exposed to 2 Gy IR. Molecular effects were assessed by RNA-seq, immunoblotting, and molecular docking. In vivo effects were tested in a partial carotid ligation (PLCL) model using spatial proteomics. Human monocyte-derived macrophages (HMDMs) from thoracic malignancy patients were analyzed before and after radiation therapy (RT). ResultsLow-dose colchicine suppressed IR-induced macrophage senescence signaling while preserving NRF2 activity. In a cell-free assay, colchicine directly activated aldehyde dehydrogenase 2 (ALDH2) in a dose-dependent manner (EC50 1-5 nM), identifying ALDH2 as a direct molecular target of colchicine. Following irradiation, colchicine restored ALDH2, reduced mitochondrial (mt)ROS-dependent p90 ribosomal S6 kinase (p90RSK) activation and lipid peroxidation, preserved TET2 and DNMT3A expression, and rescued impaired efferocytosis while preventing nicotinamide adenine dinucleotide (NAD) and adenosine triphosphate (ATP) depletion. These protective effects were ALDH2-dependent, as they were lost with ALDH2 inhibition or depletion and were mimicked by pharmacologic ALDH2 activation. In vivo, colchicine attenuated radiation-induced atherosclerosis and macrophage senescence-associated stemness (SAS). Consistently, macrophages from patients after RT showed reduced ALDH2 with increased mtROS, lipid peroxidation, and senescence. ConclusionThese findings identify ALDH2 as a previously unrecognized molecular target of colchicine that links mitochondrial redox control to suppression of radiation-induced macrophage senescence and atherosclerosis and may contribute to the efficacy of low-dose colchicine in cardiovascular disease.

cell biology↗

Downregulation of LATS1/2 Drives Endothelial Senescence-Associated Stemness (SAS) and Atherothrombotic Lesion Formation

BackgroundAtherothrombosis, the main event leading to acute coronary syndrome (ACS), is strongly linked to disturbed blood flow (d-flow) regions. Although the involvement of the Hippo pathway and its kinases Large Tumor Suppressor Kinase 1and 2 (LATS 1 and 2) in mechanical stress responses is known, the mechanisms by which d-flow simultaneously induces senescence, proliferation, and atherothrombosis remain unclear. MethodsThe role of endothelial cells (EC)-specific LATS1/2 was examined using EC specific knock-out (EKO) mice in a partial left carotid ligation (PLCL) model. Plaque spatial multi-omics analysis was performed by integrating imaging mass cytometry, sequential immunofluorescence (COMET), and spatial metabolomics at the single-cell level in human and mouse atherosclerotic plaques. ResultsIn tamoxifen-inducible Lats1homo(-/-) /Lats2 homo(-/-) EC-specific knockout (EKO) mice, deletion of LATS1/2 induced by tamoxifen led to fatal outcomes, characterized by severe systemic edema and markedly increased vascular permeability. In contrast, Lats1het(+/-)/Lats2 homo(-/-)-EKO mice survived and developed atherothrombotic plaques exhibiting neovascularization even without further additional dietary or genetic intervention. Spatial proteomics analysis revealed that LATS1/2 depletion in ECs triggered a senescence-associated stemness (SAS) phenotype, primarily driven by CD38 upregulation. Complementary spatial metabolomics profiling demonstrated a significant increase in sulfite and taurine within LATS1/2-deficient plaques, indicating lowered sulfite oxidase (SUOX) activity. Mechanistically, CD38 upregulation was found to suppress SUOX expression, induce the reverse mode of mitochondrial complex V, and increase succinate dehydrogenase (SDH) activity along with ATP consumption. Paradoxically, despite ATP depletion, this metabolic disturbance enhanced glutamate metabolism and the tricarboxylic acid (TCA) cycle, sustaining EC proliferation under energetically stressed conditions. The combined effect of LATS1/2 deletion and CD38 activation established a unique EC phenotype defined by increased SAS, leading to proliferation, senescence, and eventual cell death. These pathological processes culminated in the formation of atherothrombotic plaques, which were attenuated by inhibition of CD38. Notably, a similar phenotype--marked by metabolically active ECs--was observed in human atherothrombotic plaques, suggesting translational relevance. ConclusionLoss of LATS1/2 in ECs induces SAS state that promotes excessive EC proliferation, senescent cell accumulation, and the development of structurally fragile, leaky neo vessels--hallmarks of atherothrombotic lesions. CD38-mediated SUOX deficiency further amplifies this pathological process by inducing mitochondrial dysfunction, depleting ATP, and triggering compensatory upregulation of glutamate and TCA cycle metabolism. These findings identify a novel LATS1/2-CD38-SUOX axis in ECs that orchestrates SAS-driven atherothrombosis. Targeting CD38 may represent a promising therapeutic strategy to mitigate vascular dysfunction and plaque instability in high-risk ACS patients. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/660635v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@149d313org.highwire.dtl.DTLVardef@1c0988borg.highwire.dtl.DTLVardef@15efec9org.highwire.dtl.DTLVardef@1a96e03_HPS_FORMAT_FIGEXP M_FIG C_FIG Under normal physiological conditions, LATS1/2 and Lamin A work together to suppress CD38 expression. Lamin A binds directly to the CD38 promoter to repress transcription, and LATS1/2 interact with Lamin A to reinforce this suppression. This collaboration helps maintain low CD38 activity and preserves cellular NAD levels. However, under disturbed flow (d-flow), both LATS1/2 and Lamin A are downregulated. The loss of this dual repression leads to increased CD38 NADase expression. Elevated CD38 accelerates NAD consumption, causing NAD depletion--a hallmark of cellular senescence. Reduced NAD disrupts key metabolic and stress-response pathways, contributing to the onset of the senescent state. At the same time, CD38 suppresses sulfite oxidase (SUOX), leading to sulfite accumulation and mitochondrial redox imbalance. This shift activates the reverse mode of mitochondrial Complex V, which decreases ATP production and increases mitochondrial ROS, intensifying metabolic and oxidative stress in endothelial cells (ECs). In response, ECs compensate by upregulating succinate dehydrogenase (SDH), enhancing TCA cycle activity and glutamate metabolism. This metabolic adaptation provides the biosynthetic building blocks needed for cell growth and proliferation. As a result, ECs adopt a paradoxical phenotype: they show classical features of stress-induced senescence (such as NAD depletion, oxidative stress, and cell cycle arrest signals), while simultaneously undergoing metabolic activation and proliferation, also mediated by YAP. This defines a non-canonical endothelial program known as senescence-associated stemness (SAS), characterized by the formation of abnormal, proliferative, yet fragile neovessels. These dysfunctional vessels contribute to atherothrombosis, setting this process apart from the more stable lesions typical of conventional atherosclerosis.

molecular biology↗

Rhizosphere Microbiome Influence on Tomato Growth under Low-Nutrient Settings

Studies have shown that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates the role of Plant Growth-Promoting Rhizobacteria (PGPR) in enhancing the growth of Solanum lycopersicum under hydroponic conditions. We hypothesised that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. Our hydroponic system, with treatments consisting of 50% reduced fertiliser application supplemented with a soil-derived inoculum, exhibited greater bacterial diversity and biomass than controls, suggesting a successful enrichment of PGPR that compensates for nutrient deficiencies. Using 16S rRNA gene sequencing, we found a significant enrichment (p [≤] 0.001) and correlation with beneficial plant traits (p [≤] 0.05) of bacterial genera such as Luteolibacter, Sphingopyxis, and Kaistia. Shotgun metagenomics identified the critical role of Methyloversatilis in nitrogen fixation and other key taxa bacterial proteins in plant-bacteria interactions. Additionally, our findings identify core taxa across different cultivation systems. These results support the potential for microbiome engineering to enhance microbial diversity and plant productivity, offering a path to reduce fertiliser use in agriculture and improve sustainability.

genomics↗

Unraveling the Genomic and Environmental Diversity of the Ubiquitous Solirubrobacter

2.Solirubrobacter, a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and bacterial interactions of Solirubrobacter. Analyzing the limited genomic sequences available for this genus, we uncovered a pangenome consisting of 19,645 protein families, with 2,644 constituting a strict core genome. While reported isolates do not exhibit motility, we intriguingly discovered the presence of flagellin genes, albeit with an incomplete flagellum assembly pathway. Our examination of 16S ribosomal genes unveiled a considerable diversity (3,166 operational taxonomic units OTUs) of Solirubrobacter in Mexican soils, and co-occurrence network analysis indicated its extensive connectivity with other bacterial taxa. Through phylogenomic analysis, we delved into the relatedness of sequenced strains and notably dismissed ASM999324v1 as a member of this genus. Our investigation extended to the metagenomic diversity of Solirubrobacter across various environments, affirming its pervasive presence in rhizospheres and certain soils. This broader pangenomic view revealed genes linked to transcription, signal transduction, defense mechanisms, and carbohydrate metabolism, highlighting Solirubrobacters adaptability. We observed that Solirubrobacters prevalence in rhizospheres is geographically indiscriminate, prompting intriguing questions about its potential interactions with plants and the biotic and abiotic determinants of its soil occurrence. Given its richness and diversity, Solirubrobacter might be a versatile yet overlooked keystone species in its environments, meriting further recognition and study. 3. Impact statementThis study explored the enigmatic world of Solirubrobacter, a widespread microbe commonly found in soils and plants across various regions. Despite its prevalence, little is known about its genetic diversity and functionality and how it thrives in diverse environments. Our research unveils the genetic secrets of Solirubrobacter, shedding light on its adaptability and ecological interactors and roles. We showed that Solirubrobacter environmental prevalence makes it a good candidate for studying the genetic basis of being a successful microbe associated with soil and plants. 4. Data summaryData, scripts and statistical analysis available in GitHub: https://github.com/genomica-fciencias-unam/Solirubrobacter Sequences, phylogenetic analysis, raw data structures: https://doi.org/10.6084/m9.figshare.24446521 16S rRNA gene raw data: https://www.ncbi.nlm.nih.gov/sra/PRJNA603586 https://www.ncbi.nlm.nih.gov/sra/PRJNA603590 Shotgun metagenomes: https://www.ncbi.nlm.nih.gov/bioproject/603603 All supporting data, code, and protocols are within the article, supplementary files, and described repositories.

genomics↗

Anticancer drug doxorubicin spontaneously reacts with GTP and dGTP

Here we reported a spontaneous reaction between anticancer drug doxorubicin and GTP or dGTP. Incubation of doxorubicin with GTP or dGTP at 37 {degrees}C or above yields a covalent product: the doxorubicin-GTP or -dGTP conjugate where a covalent bond is formed between the C14 position of doxorubicin and the 2-amino group of guanine. Density functional theory calculations show the feasibility of this spontaneous reaction. Fluorescence imaging studies demonstrate that the doxorubicin-GTP and -dGTP conjugates cannot enter nuclei although they rapidly accumulate in human SK-OV-3 and NCI/ADR-RES cells. Consequently, the doxorubicin-GTP and -dGTP conjugates are less cytotoxic than doxorubicin. We also demonstrate that doxorubicin binds to ATP, GTP, and other nucleotides with a dissociation constant (Kd) in the sub-millimolar range. Since human cells contain millimolar levels of ATP and GTP, these results suggest that doxorubicin may target ATP and GTP, energy molecules that support essential processes in living organisms.

cancer biology↗

Metabolic effects of aripiprazole and olanzapine multiple-dose treatment in healthy volunteers. Association with pharmacogenetics.

BackgroundAripiprazole and olanzapine are atypical antipsychotics. Both drugs can induce metabolic changes, however, the metabolic side effects produced by aripiprazole are more benign. ObjectivesTo evaluate if aripiprazole and olanzapine alter prolactin levels, lipid and glucose metabolism and hepatic, hematological, thyroid and renal function. MethodsTwenty-four healthy volunteers received 5 daily oral doses of 10 mg aripiprazole and 5 mg olanzapine in a crossover randomized clinical trial and were genotyped for 51 polymorphisms in 17 genes by qPCR. Drug plasma concentrations were measured by LC-MS. The biochemical and hematological analyses were performed by enzymatic methods. ResultsOlanzapine induced hyperprolactinemia but not aripiprazole. DRD3 Ser/Gly and ABCB1 rs10280101, rs12720067 and rs11983225 polymorphisms and CYP3A phenotype had an impact on plasma prolactin levels. C-peptide concentrations were higher after aripiprazole administration and were influenced by COMT rs4680 and rs13306278 polymorphisms. Olanzapine and the UGT1A1 rs887829 polymorphism were associated with elevated glucose levels. CYP3A poor metabolizers had increased insulin levels. Triglyceride concentrations were decreased due to olanzapine and aripiprazole treatment and were variable based on CYP3A phenotypes and the APOC3 rs4520 genotype. Cholesterol levels were also decreased and depended on HTR2A rs6314 polymorphism. All hepatic enzymes, platelet and albumin levels and prothrombin time were altered during both treatments. Additionally, olanzapine reduced the leucocyte count, aripiprazole increased free T4 and both decreased uric acid concentrations. ConclusionsShort term treatment with aripiprazole and olanzapine had a significant influence on the metabolic parameters. However, it seems that aripiprazole provokes less severe metabolic changes.

pharmacology and toxicology↗