Publications by authors named "Cecilia Garmendia-Torres"

9 Publications

  • Page 1 of 1

Multiple inputs ensure yeast cell size homeostasis during cell cycle progression.

Elife 2018 07 4;7. Epub 2018 Jul 4.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.

Coordination of cell growth with division is essential for proper cell function. In budding yeast, although some molecular mechanisms responsible for cell size control during G1 have been elucidated, the mechanism by which cell size homeostasis is established remains to be discovered. Here, we developed a new technique based on quantification of histone levels to monitor cell cycle progression in individual cells with unprecedented accuracy. Our analysis establishes the existence of a mechanism controlling bud size in G2/M that prevents premature onset of anaphase, and controls the overall size variability. While most G1 mutants do not display impaired size homeostasis, mutants in which cyclin B-Cdk regulation is altered display large size variability. Our study thus demonstrates that size homeostasis is not controlled by a G1-specific mechanism alone but is likely to be an emergent property resulting from the integration of several mechanisms that coordinate cell and bud growth with division.
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http://dx.doi.org/10.7554/eLife.34025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085122PMC
July 2018

Independent Origins of Yeast Associated with Coffee and Cacao Fermentation.

Curr Biol 2016 Apr 24;26(7):965-71. Epub 2016 Mar 24.

Pacific Northwest Diabetes Research Institute, Seattle, WA 98122, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA. Electronic address:

Modern transportation networks have facilitated the migration and mingling of previously isolated populations of plants, animals, and insects. Human activities can also influence the global distribution of microorganisms. The best-understood example is yeasts associated with winemaking. Humans began making wine in the Middle East over 9,000 years ago [1, 2]. Selecting favorable fermentation products created specialized strains of Saccharomyces cerevisiae [3, 4] that were transported along with grapevines. Today, S. cerevisiae strains residing in vineyards around the world are genetically similar, and their population structure suggests a common origin that followed the path of human migration [3-7]. Like wine, coffee and cacao depend on microbial fermentation [8, 9] and have been globally dispersed by humans. Theobroma cacao originated in the Amazon and Orinoco basins of Colombia and Venezuela [10], was cultivated in Central America by Mesoamerican peoples, and was introduced to Europeans by Hernán Cortés in 1530 [11]. Coffea, native to Ethiopia, was disseminated by Arab traders throughout the Middle East and North Africa in the 6(th) century and was introduced to European consumers in the 17(th) century [12]. Here, we tested whether the yeasts associated with coffee and cacao are genetically similar, crop-specific populations or genetically diverse, geography-specific populations. Our results uncovered populations that, while defined by niche and geography, also bear signatures of admixture between major populations in events independent of the transport of the plants. Thus, human-associated fermentation and migration may have affected the distribution of yeast involved in the production of coffee and chocolate.
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http://dx.doi.org/10.1016/j.cub.2016.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821677PMC
April 2016

Unidirectional P-body transport during the yeast cell cycle.

PLoS One 2014 11;9(6):e99428. Epub 2014 Jun 11.

Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America; Pacific Northwest Diabetes Research Institute, Seattle, Washington, United States of America.

P-bodies belong to a large family of RNA granules that are associated with post-transcriptional gene regulation, conserved from yeast to mammals, and influence biological processes ranging from germ cell development to neuronal plasticity. RNA granules can also transport RNAs to specific locations. Germ granules transport maternal RNAs to the embryo, and neuronal granules transport RNAs long distances to the synaptic dendrites. Here we combine microfluidic-based fluorescent microscopy of single cells and automated image analysis to follow p-body dynamics during cell division in yeast. Our results demonstrate that these highly dynamic granules undergo a unidirectional transport from the mother to the daughter cell during mitosis as well as a constrained "hovering" near the bud site half an hour before the bud is observable. Both behaviors are dependent on the Myo4p/She2p RNA transport machinery. Furthermore, single cell analysis of cell size suggests that PBs play an important role in daughter cell growth under nutrient limiting conditions.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099428PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053424PMC
February 2015

Identification and characterization of a drug-sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae.

Yeast 2014 May 19;31(5):167-78. Epub 2014 Mar 19.

Institute for Systems Biology, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.

Puromycin is an aminonucleoside antibiotic with structural similarity to aminoacyl tRNA. This structure allows the drug to bind the ribosomal A site and incorporate into nascent polypeptides, causing chain termination, ribosomal subunit dissociation and widespread translational arrest at high concentrations. In contrast, at sufficiently low concentrations, puromycin incorporates primarily at the C-terminus of proteins. While a number of techniques utilize puromycin incorporation as a tool for probing translational activity in vivo, these methods cannot be applied in yeasts that are insensitive to puromycin. Here, we describe a mutant strain of the yeast Saccharomyces cerevisiae that is sensitive to puromycin and characterize the cellular response to the drug. Puromycin inhibits the growth of yeast cells mutant for erg6∆, pdr1∆ and pdr3∆ (EPP) on both solid and liquid media. Puromycin also induces the aggregation of the cytoplasmic processing body component Edc3 in the mutant strain. We establish that puromycin is rapidly incorporated into yeast proteins and test the effects of puromycin on translation in vivo. This study establishes the EPP strain as a valuable tool for implementing puromycin-based assays in yeast, which will enable new avenues of inquiry into protein production and maturation.
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http://dx.doi.org/10.1002/yea.3007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4013229PMC
May 2014

Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.

G3 (Bethesda) 2013 Dec 9;3(12):2163-71. Epub 2013 Dec 9.

Institute for Systems Biology, Seattle, Washington 98109.

The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site-associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers.
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http://dx.doi.org/10.1534/g3.113.007492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852379PMC
December 2013

Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images.

BMC Bioinformatics 2010 May 13;11:248. Epub 2010 May 13.

Department of Signal Processing, Tampere University of Technology, Tampere, 33101, Finland.

Background: Several algorithms have been proposed for detecting fluorescently labeled subcellular objects in microscope images. Many of these algorithms have been designed for specific tasks and validated with limited image data. But despite the potential of using extensive comparisons between algorithms to provide useful information to guide method selection and thus more accurate results, relatively few studies have been performed.

Results: To better understand algorithm performance under different conditions, we have carried out a comparative study including eleven spot detection or segmentation algorithms from various application fields. We used microscope images from well plate experiments with a human osteosarcoma cell line and frames from image stacks of yeast cells in different focal planes. These experimentally derived images permit a comparison of method performance in realistic situations where the number of objects varies within image set. We also used simulated microscope images in order to compare the methods and validate them against a ground truth reference result. Our study finds major differences in the performance of different algorithms, in terms of both object counts and segmentation accuracies.

Conclusions: These results suggest that the selection of detection algorithms for image based screens should be done carefully and take into account different conditions, such as the possibility of acquiring empty images or images with very few spots. Our inclusion of methods that have not been used before in this context broadens the set of available detection methods and compares them against the current state-of-the-art methods for subcellular particle detection.
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http://dx.doi.org/10.1186/1471-2105-11-248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098061PMC
May 2010

H2O2 activates the nuclear localization of Msn2 and Maf1 through thioredoxins in Saccharomyces cerevisiae.

Eukaryot Cell 2009 Sep 6;8(9):1429-38. Epub 2009 Jul 6.

CEA, IBITECS, SBIGEM, LBI, Gif-sur-Yvette Cedex, France.

The cellular response to hydrogen peroxide (H(2)O(2)) is characterized by a repression of growth-related processes and an enhanced expression of genes important for cell defense. In budding yeast, this response requires the activation of a set of transcriptional effectors. Some of them, such as the transcriptional activator Yap1, are specific to oxidative stress, and others, such as the transcriptional activators Msn2/4 and the negative regulator Maf1, are activated by a wide spectrum of stress conditions. How these general effectors are activated in response to oxidative stress remains an open question. In this study, we demonstrate that the two cytoplasmic thioredoxins, Trx1 and Trx2, are essential to trigger the nuclear accumulation of Msn2/4 and Maf1, specifically under H(2)O(2) treatment. Contrary to the case with many stress conditions previously described for yeast, the H(2)O(2)-induced nuclear accumulation of Msn2 and Maf1 does not correlate with the downregulation of PKA kinase activity. Nevertheless, we show that PP2A phosphatase activity is essential for driving Maf1 dephosphorylation and its subsequent nuclear accumulation in response to H(2)O(2) treatment. Interestingly, under this condition, the lack of PP2A activity has no impact on the subcellular localization of Msn2, demonstrating that the H(2)O(2) signaling pathways share a common route through the thioredoxin system and then diverge to activate Msn2 and Maf1, the final integrators of these pathways.
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http://dx.doi.org/10.1128/EC.00106-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747830PMC
September 2009

Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation.

Curr Biol 2007 Jun;17(12):1044-9

Université de Paris-Sud, Unité Mixte de Recherche 8621, Centre National de la Recherche Scientifique, Orsay, F-91405, France.

At intermediate intensities, stress induces oscillations in the nucleocytoplasmic shuttling of the transcription factor Msn2 in budding yeast. Activation by stress results in a reversible translocation of Msn2 from the cytoplasm to the nucleus. This translocation is negatively controlled by the cAMP-PKA pathway through Msn2 phosphorylation. Here we show that the nuclear localization signal (NLS) of Msn2 is necessary and sufficient to promote the nucleocytoplasmic oscillations of the transcription factor. Because the NLS is controlled by protein kinase A (PKA) phosphorylation, we use a computational model to investigate the possibility that the cAMP-PKA pathway could function as an oscillator driving the periodic shuttling of Msn2. The model indicates that sustained oscillations of cAMP can indeed occur in a range bounded by two critical values of stress intensity, owing to the negative feedback exerted by PKA on cAMP accumulation. We verify the predictions of the model in mutants by showing that suppressing this negative-feedback loop prevents the oscillatory shuttling but still promotes the stress-induced nuclear localization of Msn2. The physiological significance of Msn2 oscillations is discussed in the light of the frequency encoding of cellular rhythms.
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http://dx.doi.org/10.1016/j.cub.2007.05.032DOI Listing
June 2007

Role of Gal11, a component of the RNA polymerase II mediator in stress-induced hyperphosphorylation of Msn2 in Saccharomyces cerevisiae.

Mol Microbiol 2006 Oct;62(2):438-52

Laboratoire Polarité cellulaire, Traffic membranaire & Signalisation, UMR 6061 CNRS, Université Rennes 1, Faculté de Médecine, 2 Avenue du Pr Léon Bernard, CS 34317, 35043 Rennes Cedex, France.

In the yeast Saccharomyces cerevisiae, the Msn2 transcription factor is a key element in mediating the environmental stress response (ESR), leading to the induction of 100-200 genes through the cis-acting Stress Response Element (STRE) in response to various physico-chemical stresses and nutritional variations. This activation is accompanied by a stress-induced hyperphosphorylation of Msn2. By a systematic screening we identified two proteins essential in this process: (i) the cyclin-dependent Ssn3/Srb10 protein kinase, part of a module of the RNA polymerase II mediator, which has already been shown to be involved in hyperphosphorylation and degradation of Msn2 upon stress, and (ii) Gal11, a component of the mediator. In a gal11 mutant, stress-induced hyperphosphorylation of Msn2 is abolished, stress-induced transcription of Msn2-dependent genes is decreased and Msn2 degradation is impaired. Rgr1, another component of the mediator, is also critical for this hyperphosphorylation, indicating that the integrity of the mediator is required for this process. Moreover the transactivating region of Msn2 interacts in vitro with the N-terminal domain of Gal11. These results point out the role of the mediator, especially its Gal11 subunit, in the hyperphosphorylation and degradation of Msn2 during stress response.
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http://dx.doi.org/10.1111/j.1365-2958.2006.05363.xDOI Listing
October 2006