A5016577421- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Aging, and Longevity in Model Organisms
- Evolution and Genetic Dynamics
- Plant Gene Expression Analysis
- Bioinformatics and Genomic Networks
- Fermentation and Sensory Analysis
- RNA and protein synthesis mechanisms
- Botanical Research and Applications
- Biofuel production and bioconversion
- Plant nutrient uptake and metabolism
- Enzyme Structure and Function
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- Protein Structure and Dynamics
- Ubiquitin and proteasome pathways
- Gene Regulatory Network Analysis
- GABA and Rice Research
- Yeasts and Rust Fungi Studies
- Mitochondrial Function and Pathology
- Microbial Metabolites in Food Biotechnology
- Plant Reproductive Biology
- Metabolomics and Mass Spectrometry Studies
- Plant Molecular Biology Research
- Genomics and Phylogenetic Studies
Center for Research and Advanced Studies of the National Polytechnic Institute
2015-2025
Instituto Politécnico Nacional
2013-2023
Centro de Investigación en Materiales Avanzados
2020-2023
Instituto Tecnológico Superior de Irapuato
2022-2023
Instituto de Estudios Avanzados
2019-2020
Harvard University
2004-2010
Center for Systems Biology
2008-2010
Universidad Nacional Autónoma de México
1997-2008
Boston University
2008
ABSTRACT The production of traditional agave spirits in Mexico, such as mezcal, involves a process that uses environmental microorganisms to ferment the cooked must from plants. By analysing these microorganisms, researchers can understand dynamics microbial communities at interface natural and human‐associated environments. This study involved 16S ITS amplicon sequencing 99 fermentation tanks 42 distilleries across Mexico. Agave species used, methods, climatic conditions biogeographic...
Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution isogenic yeast populations different initial ploidy study adaptation increasing ethanol. Whole-genome sequencing more than 30 evolved over 100 adapted clones isolated throughout two-year experiment revealed how a interplay de novo single nucleotide mutations, copy...
In the yeast Saccharomyces cerevisiae, two NADP+-dependent glutamate dehydrogenases (NADP-GDHs) encoded by GDH1 and GDH3 catalyze synthesis of from ammonium α-ketoglutarate. The GDH2-encoded NAD+-dependent dehydrogenase degrades producing Until very recently, it was considered that only one biosynthetic NADP-GDH present in S. cerevisiae. This fact hindered understanding physiological role each isoenzyme mechanisms involved α-ketoglutarate channeling for biosynthesis. this study, we purified...
Many duplicate genes maintain functional overlap despite divergence over long evolutionary time scales. Deleting one member of a paralogous pair often has no phenotypic effect, unless its paralog is also deleted. It been suggested that this compensation might be mediated by active up-regulation expression gene in response to deletion paralog. However, it not clear how prevalent such responsiveness is, nor whether hardwired or dependent on feedback from environmental conditions. Here, we...
Lifespan is influenced by a large number of conserved proteins and gene-regulatory pathways. Here, we introduce strategy for systematically finding such longevity factors in Saccharomyces cerevisiae scoring the genetic interactions (epistasis) among these factors. Specifically, developed an automated competition-based assay chronological lifespan, defined as stationary-phase survival yeast populations, used it to phenotype over 5,600 single- or double-gene knockouts at unprecedented...
Significance Many studies have focused on the mechanisms of long-term retention gene duplicates, such as gain functions or reciprocal losses. However, changes are more likely to occur if duplicates maintained for a long period. This time span will be short duplication is immediately deleterious. We measured distribution fitness effects 899 genes in budding yeast. find that deleterious than beneficial. contrary previous models, general, does not affect by altering organization protein...
It has been considered that the yeast Saccharomyces cerevisiae, like many other microorganisms, synthesizes glutamate through action of NADP+-glutamate dehydrogenase (NADP+-GDH), encoded by GDH1, or combined glutamine synthetase and synthase (GOGAT), GLN1 GLT1, respectively. A double mutant S. cerevisiae lacking NADP+-GDH GOGAT activities was constructed. This strain able to grow on ammonium as sole nitrogen source thus synthesize an alternative pathway. computer search for similarities...
Summary Dietary restriction is arguably the most promising nonpharmacological intervention to extend human life and health span. Yet, only few genetic regulators mediating cellular response dietary are known, question remains which other regulatory factors involved. Here, we measured at genomewide level chronological lifespan of Saccharomyces cerevisiae gene deletion strains under two nitrogen source regimens, glutamine (nonrestricted) γ‐aminobutyric acid (restricted). We identified 473...
The chronological lifespan of Saccharomyces cerevisiae has been pivotal in advancing our understanding aging eukaryotic cells. However, gaining a genome-wide perspective this trait remains challenging due to substantial discrepancies observed across large-scale gene-deletion screens. In study, we performed meta-analysis compile ranked catalog key processes and regulators driving longevity yeast, ensuring their robustness diverse experimental setups. These consistent factors were enriched...
In Saccharomyces cerevisiae, the TORC1 pathway regulates transition from rapid fermentative growth to respiration during diauxic shift, by tightly coordinating energy- and biomass-producing pathways. Although leucine other components of branched-chain amino acid (BCAA) are known regulators, how BCAA is controlled across this influences crosstalk between central carbon metabolism remains unclear. By integrating high-throughput flow cytometry untargeted LC-MS metabolomics into a...
Overlapped genes originate by a) loss of a stop codon among contiguous coded in different frames; b) shift to an upstream initiation one the genes; or c) overprinting, whereby novel open reading frame originates through point mutation inside existing gene. Although overlapped are common viruses, it is not clear whether overprinting has led new prokaryotes. Here we report origin gene Escherichia coli K12. The htgA coding for positive regulator sigma 32 heat shock promoter arose 123/213 phase...
The mitochondrial proteome is mostly composed of nuclear-encoded proteins. Such polypeptides are synthesized with signals that guide their intracellular transport to the surface organelle and later within different subcompartments until they reach functional destination. It has been suggested nascent-polypeptide associated complex (NAC) - a cytosolic chaperone recognizes nascent chains on translationally active ribosomes role in import However, molecular mechanisms regulate NAC-mediated...
A single gene can partake in several biological processes, and therefore deletions lead to different-sometimes unexpected-phenotypes. However, it is not always clear whether such pleiotropy reflects the loss of a unique molecular activity involved different processes or multifunctional protein. Here, using Saccharomyces cerevisiae metabolism as model, we systematically test null hypothesis that enzyme phenotypes depend on annotated function, namely their catalysis. We screened set carefully...
Abstract Yeasts are a diverse group of fungal microorganisms that widely used to produce fermented foods and beverages. In Mexico, open fermentations obtain spirits from agave plants. Despite the prevalence this traditional practice throughout country, yeasts have only been isolated studied limited number distilleries. To systematically describe diversity yeast species fermentations, here we generate YMX‐1.0 culture collection by isolating 4524 strains 68 sites with climatic, geographical,...
In the yeast Saccharomyces cerevisiae, first committed step of lysine biosynthetic pathway is catalysed by two homocitrate synthases encoded LYS20 and LYS21. We undertook a study duplicate to analyse whether their retention presumable specialization have affected efficiency biosynthesis in yeast. Our results show that during growth on ethanol, mainly synthesized through Lys21p, while under fermentative metabolism, Lys20p Lys21p play redundant roles. Furthermore, presented this paper indicate...
Production of α-isopropylmalate (α-IPM) is critical for leucine biosynthesis and the global control metabolism. The budding yeast Saccharomyces cerevisiae has two paralogous genes, LEU4 LEU9, that encode α-IPM synthase (α-IPMS) isozymes. Little known about biochemical differences between these α-IPMS isoenzymes. Here, we show Leu4 homodimer a leucine-sensitive isoform, while Leu9 resistant to such feedback inhibition. leu4Δ mutant, which expresses only feedback-resistant homodimer, grows...