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Lei Shi, Xiaolong Wang, Jinjia Wang, Ping Zhang, Fei Qi, Menghao Cai, Yuanxing Zhang, Xiangshan Zhou
Two catabolite repressor genes (MIG1 and MIG2) were previously identified in Pichia pastoris, and the derepression of alcohol oxidase (AOX) expression was realized in Δmig1 or Δmig1Δmig2 mutants grown in glycerol, but not in glucose. In this study, genome-wide RNA-seq analysis of Δmig1Δmig2 and the wild-type strain grown in glycerol revealed that the expression of numerous genes was greatly altered. Nearly 7% (357 genes) of approximately 5276 genes annotated in P. pastoris were significantly upregulated, with at least a two-fold differential expression in Δmig1Δmig2; the genes were mainly related to cell metabolism...
April 2018: Genes & Genomics
Dakshayini G Chandrashekarappa, Rhonda R McCartney, Allyson F O'Donnell, Martin C Schmidt
Saccharomyces cerevisiae express three isoforms of Snf1 kinase that differ by which β subunit is present, Gal83, Sip1 or Sip2. Here we investigate the abundance, activation, localization and signaling specificity of the three Snf1 isoforms. The relative abundance of these isoforms was assessed by quantitative immunoblotting using two different protein extraction methods and by fluorescence microscopy. The Gal83 containing isoform is the most abundant in all assays while the abundance of the Sip1 and Sip2 isoforms is typically underestimated especially in glass-bead extractions...
December 2016: Cellular Signalling
Marc-Andre Comeau, Daniel A Lafontaine, Sherif Abou Elela
Members of the ribonuclease III (RNase III) family regulate gene expression by triggering the degradation of double stranded RNA (dsRNA). Hundreds of RNase III cleavage targets have been identified and their impact on RNA maturation and stability is now established. However, the mechanism defining substrates' reactivity remains unclear. In this study, we developed a real-time FRET assay for the detection of dsRNA degradation by yeast RNase III (Rnt1p) and characterized the kinetic bottlenecks controlling the reactivity of different substrates...
September 19, 2016: Nucleic Acids Research
Montserrat Vega, Alberto Riera, Alejandra Fernández-Cid, Pilar Herrero, Fernando Moreno
Hexokinase 2 (Hxk2) fromSaccharomyces cerevisiaeis a bi-functional enzyme, being both a catalyst in the cytosol and an important regulator of the glucose repression signal in the nucleus. Despite considerable recent progress, little is known about the regulatory mechanism that controls nuclear Hxk2 association with theSUC2promoter chromatin and how this association is necessary forSUC2gene repression. Our data indicate that in theSUC2promoter context, Hxk2 functions through a variety of structurally unrelated factors, mainly the DNA-binding Mig1 and Mig2 repressors and the regulatory Snf1 and Reg1 factors...
April 1, 2016: Journal of Biological Chemistry
Karen L Hinkle, Chad C Anderson, Blake Forkey, Jacob Griffin, Kelsey Cone, Carl Vitzthum, Darlene Olsen
The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) is used to control sea lamprey (Petromyzon marinus) populations in freshwater lakes. Although TFM can have sublethal and lethal effects, little is known about gene expression changes with TFM exposure. Microarray analysis was used to determine differential gene expression over 4 h of exposure in Saccharomyces cerevisiae. Among the most significantly up-regulated genes were regulators of carbohydrate transport, including HXT1, HXT3, HXT4, IMA5, MIG2, and YKR075C...
July 2016: Environmental Toxicology and Chemistry
Albert Serra-Cardona, Silvia Petrezsélyová, David Canadell, José Ramos, Joaquín Ariño
The yeast Saccharomyces cerevisiae has two main high-affinity inorganic phosphate (Pi) transporters, Pho84 and Pho89, that are functionally relevant at acidic/neutral pH and alkaline pH, respectively. Upon Pi starvation, PHO84 and PHO89 are induced by the activation of the PHO regulon by the binding of the Pho4 transcription factor to specific promoter sequences. We show that PHO89 and PHO84 are induced by alkalinization of the medium with different kinetics and that the network controlling Pho89 expression in response to alkaline pH differs from that of other members of the PHO regulon...
December 2014: Molecular and Cellular Biology
Vasiliki Gkretsi, Vassilis Papanikolaou, Lefteris C Zacharia, Evangelos Athanassiou, Chuanyue Wu, Aspasia Tsezou
BACKGROUND: Cell adhesion proteins that connect each cell to neighboring cells and the extracellular matrix play a fundamental role in metastasis. Mitogen-inducible gene-2 (MIG2), is a cell-matrix adhesion protein, which through migfilin, interacts with filamin-A, being linked to actin cytoskeleton. AIM: Recent studies have implicated both MIG2 and migfilin in cancer, but little is known regarding their expression in breast cancer. In this study, we investigated this topic...
May 2013: Anticancer Research
Alejandra Fernández-Cid, Montserrat Vega, Pilar Herrero, Fernando Moreno
BACKGROUND: Mig2 has been described as a transcriptional factor that in the absence of Mig1 protein is required for glucose repression of the SUC2 gene. Recently it has been reported that Mig2 has two different subcellular localizations. In high-glucose conditions it is a nuclear modulator of several Mig1-regulated genes, but in low-glucose most of the Mig2 protein accumulates in mitochondria. Thus, the Mig2 protein enters and leaves the nucleus in a glucose regulated manner. However, the mechanism by which Mig2 enters into the nucleus was unknown until now...
2012: BMC Cell Biology
Sheelarani Karunanithi, Paul J Cullen
In the budding yeast S. cerevisiae, nutrient limitation induces a MAPK pathway that regulates filamentous growth and biofilm/mat formation. How nutrient levels feed into the regulation of the filamentous growth pathway is not entirely clear. We characterized a newly identified MAPK regulatory protein of the filamentous growth pathway, Opy2. A two-hybrid screen with the cytosolic domain of Opy2 uncovered new interacting partners including a transcriptional repressor that functions in the AMPK pathway, Mig1, and its close functional homolog, Mig2...
November 2012: Genetics
Alejandra Fernández-Cid, Alberto Riera, Pilar Herrero, Fernando Moreno
Mig2 has been described as a transcriptional factor that in the absence of Mig1 protein is required for glucose repression of the SUC2 gene. Thus, until now, the main role assigned to Mig2 has been the functional redundancy to Mig1. In this study, we report that Mig2 has a double subcellular localization. As expected, in high-glucose conditions it is accumulated in the nucleus but in low-glucose conditions Mig2 has an unexpected mitochondrial localization and role in mitochondrial morphology. We describe that Mig2 physically interacts with the mitochondrial protein Ups1 in a glucose-dependent manner...
May 2012: Mitochondrion
Mei Kee Lim, Wee Leng Siew, Jin Zhao, Ywee Chieh Tay, Edwin Ang, Norbert Lehming
Skp1 an essential component of the SCF (Skp1/cullin/F-box) E3 ubiquitin ligases, which target proteins for degradation by the 26S proteasome. We generated a skp1dM mutant strain that is defective for galactose induction of the GAL1 gene and we have found that galactose-induced protein degradation of the repressor Mig2 is defective in this strain. Mig2 degradation was also abolished in cells lacking the protein kinase Snf1 and the F-box protein Das1, suggesting that Snf1 triggers galactose-induced protein degradation of Mig2 by SCFDas1...
May 1, 2011: Biochemical Journal
Hailong Cao, Min Yue, Shuguang Li, Xuefang Bai, Xiaoming Zhao, Yuguang Du
The zinc finger proteins Mig1 and Mig2 play important roles in glucose repression of Saccharomyces cerevisiae. To investigate whether the alleviation of glucose effect would result in an increase in aerobic succinate production, MIG1 and/or MIG2 were disrupted in a succinate dehydrogenase (SDH)-negative S. cerevisiae strain. Moreover, their impacts on physiology of the SDH-negative S. cerevisiae strain were studied under fully aerobic conditions when glucose was the sole carbon source. Our results showed that the succinate production for the SDH-negative S...
February 2011: Applied Microbiology and Biotechnology
Sooraj Kuttykrishnan, Jeffrey Sabina, Laura L Langton, Mark Johnston, Michael R Brent
The ability to design and engineer organisms demands the ability to predict kinetic responses of novel regulatory networks built from well-characterized biological components. Surprisingly, few validated kinetic models of complex regulatory networks have been derived by combining models of the network components. A major bottleneck in producing such models is the difficulty of measuring in vivo rate constants for components of complex networks. We demonstrate that a simple, genetic approach to measuring rate constants in vivo produces an accurate kinetic model of the complex network that Saccharomyces cerevisiae employs to regulate the expression of genes encoding glucose transporters...
September 21, 2010: Proceedings of the National Academy of Sciences of the United States of America
Jakub Orzechowski Westholm, Niklas Nordberg, Eva Murén, Adam Ameur, Jan Komorowski, Hans Ronne
BACKGROUND: Expression of a large number of yeast genes is repressed by glucose. The zinc finger protein Mig1 is the main effector in glucose repression, but yeast also has two related proteins: Mig2 and Mig3. We have used microarrays to study global gene expression in all possible combinations of mig1, mig2 and mig3 deletion mutants. RESULTS: Mig1 and Mig2 repress a largely overlapping set of genes on 2% glucose. Genes that are upregulated in a mig1 mig2 double mutant were grouped according to the contribution of Mig2...
2008: BMC Genomics
Chris Hlynialuk, Ryan Schierholtz, Amanda Vernooy, George van der Merwe
In Saccharomyces cerevisiae, fermentable carbon sources such as glucose and fructose are preferred and elicit glucose repression of genes needed to metabolize non-fermentable carbon sources such as glycerol, ethanol and acetate. Different sets of transcription factors are needed to adjust to specific carbon conditions. For example, Mig1 and Mig2 repress the transcription of gluconeogenic and respiratory genes in the presence of abundant glucose, while the transcriptional activation of these genes depends on transcription factors such as Adr1 and Cat8...
August 2008: Microbiology
Yan Zheng, Jan Kief, Kathrin Auffarth, Jan W Farfsing, Michael Mahlert, Fernanda Nieto, Christoph W Basse
The smut fungus Ustilago maydis establishes a biotrophic relationship with its host plant maize to progress through sexual development. Here, we report the identification and characterization of the Cys(2)His(2)-type zinc finger protein Mzr1 that functions as a transcriptional activator during host colonization. Expression of the U. maydis mig2 cluster genes is tightly linked to this phase. Upon conditional overexpression, Mzr1 confers induction of a subset of mig2 genes during vegetative growth and this requires the same promoter elements that confer inducible expression in planta...
June 2008: Molecular Microbiology
Amélie Avet-Rochex, Jackie Perrin, Evelyne Bergeret, Marie-Odile Fauvarque
Pathogen recognition and engulfment by phagocytic cells of the blood cell lineage constitute the first line of defense against invading pathogens. This cellular immune response is conserved throughout evolution and depends strictly on cytoskeletal changes regulated by the RhoGTPases family. Many pathogens have developed toxins modifying RhoGTPases activity to their own benefit. In particular, the Exoenzyme S (ExoS) toxin of the Gram-negative bacteria Pseudomonas aeruginosa is directly injected into the host cell cytoplasm and contains a GAP domain (ExoSGAP) targeting RhoGTPases...
October 2007: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Joseph M Gozgit, Brian T Pentecost, Sharon A Marconi, Christopher N Otis, Chuanyue Wu, Kathleen F Arcaro
An estrogen receptor-negative variant of the MCF-7 breast cancer cell line, TMX2-28, was used as a model in which to study breast cancer cell invasion. Using a reconstituted basement membrane (Matrigel) assay to evaluate cell invasion, we determined that TMX2-28 cells are more invasive than MCF-7 cells and that the invasiveness of TMX2-28 is similar to that of the aggressive MDA-MB-231 breast cancer cell line. TMX2-28 cells displayed a rounded, epithelial cell-like morphology, suggesting an amoeboid mode of cell invasion, in contrast to the mesenchymal mode of invasion characteristic of spindle-shaped, fibroblast-like MDA-MB-231 cells...
December 2006: Molecular Cancer Research: MCR
Maria Platara, Amparo Ruiz, Raquel Serrano, Aarón Palomino, Fernando Moreno, Joaquín Ariño
Adaptive response of the yeast Saccharomyces cerevisiae to environmental alkalinization results in remodeling of gene expression. A key target is the gene ENA1, encoding a Na(+)-ATPase, whose induction by alkaline pH has been shown to involve calcineurin and the Rim101/Nrg1 pathway. Previous functional analysis of the ENA1 promoter revealed a calcineurin-independent pH responsive region (ARR2, 83 nucleotides). We restrict here this response to a small (42 nucleotides) ARR2 5.-region, named MCIR (minimum calcineurin independent response), which contains a MIG element, able to bind Mig1,2 repressors...
December 1, 2006: Journal of Biological Chemistry
Yuan Qi, Alex Rolfe, Kenzie D MacIsaac, Georg K Gerber, Dmitry Pokholok, Julia Zeitlinger, Timothy Danford, Robin D Dowell, Ernest Fraenkel, Tommi S Jaakkola, Richard A Young, David K Gifford
Direct physical information that describes where transcription factors, nucleosomes, modified histones, RNA polymerase II and other key proteins interact with the genome provides an invaluable mechanistic foundation for understanding complex programs of gene regulation. We present a method, joint binding deconvolution (JBD), which uses additional easily obtainable experimental data about chromatin immunoprecipitation (ChIP) to improve the spatial resolution of the transcription factor binding locations inferred from ChIP followed by DNA microarray hybridization (ChIP-Chip) data...
August 2006: Nature Biotechnology
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