Genome-wide analysis of Kluyveromyces lactis in wild-type and rag2 mutant strains

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 970-978 ◽  
Author(s):  
Manuel Becerra ◽  
Nuria Tarrío ◽  
M Isabel González-Siso ◽  
M Esperanza Cerdán
Keyword(s):  
Kluyveromyces Lactis ◽  
Glycolytic Enzyme ◽  
Pentose Phosphate ◽  
Phosphoglucose Isomerase ◽  
Transcriptional Level ◽  
Dna Arrays ◽  
Gene Coding ◽  
Genome Wide ◽  
Rag2 Gene ◽  
Interesting Alternative

The use of heterologous DNA arrays from Saccharomyces cerevisiae has been tested and revealed as a suitable tool to compare the transcriptomes of S. cerevisiae and Kluyveromyces lactis, two yeasts with notable differences in their respirofermentative metabolism. The arrays have also been applied to study the changes in the K. lactis transcriptome owing to mutation in the RAG2 gene coding for the glycolytic enzyme phosphoglucose isomerase. Comparison of the rag2 mutant growing in 2% glucose versus 2% fructose has been used as a model to elucidate the importance of transcriptional regulation of metabolic routes, which may be used to reoxidize the NADPH produced in the pentose phosphate pathway. At this transcriptional level, routes related to the oxidative stress response become an interesting alternative for NADPH use.Key words: Kluyveromyces lactis, transcription, phosphoglucose isomerase, carbohydrate use.

scholarly journals Ribose 5-phosphate isomerase type B from Trypanosoma cruzi: kinetic properties and site-directed mutagenesis reveal information about the reaction mechanism

2006 ◽  
Vol 401 (1) ◽  
pp. 279-285 ◽  
Author(s):  
Ana L. Stern ◽  
Emmanuel Burgos ◽  
Laurent Salmon ◽  
Juan J. Cazzulo
Keyword(s):  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Pentose Phosphate ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Kinetic Properties ◽  
Type B ◽  
Nucleotide Synthesis ◽  
Gene Coding ◽  
Genes Encoding

Trypanosoma cruzi, the human parasite that causes Chagas disease, contains a functional pentose phosphate pathway, probably essential for protection against oxidative stress and also for R5P (ribose 5-phosphate) production for nucleotide synthesis. The haploid genome of the CL Brener clone of the parasite contains one gene coding for a Type B Rpi (ribose 5-phosphate isomerase), but genes encoding Type A Rpis, most frequent in eukaryotes, seem to be absent. The RpiB enzyme was expressed in Escherichia coli as a poly-His tagged active dimeric protein, which catalyses the reversible isomerization of R5P to Ru5P (ribulose 5-phos-phate) with Km values of 4 mM (R5P) and 1.4 mM (Ru5P).4-Phospho-D-erythronohydroxamic acid, an analogue to the reaction intermediate when the Rpi acts via a mechanism involving the formation of a 1,2-cis-enediol, inhibited the enzyme competi-tively, with an IC50 value of 0.7 mM and a Ki of 1.2 mM. Site-directed mutagenesis allowed the demonstration of a role for His102, but not for His138, in the opening of the ribose furanosic ring. A major role in catalysis was confirmed for Cys69, since the C69A mutant was inactive in both forward and reverse directions of the reaction. The present paper contributes to the know-ledge of the mechanism of the Rpi reaction; in addition, the absence of RpiBs in the genomes of higher animals makes this enzyme a possible target for chemotherapy of Chagas disease.

DNase I sensitive domain of the gene coding for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase

Biochemistry ◽  
1984 ◽  
Vol 23 (10) ◽  
pp. 2309-2314 ◽  
Author(s):  
Martin C. Alevy ◽  
Ming Jer Tsai ◽  
Bert W. O'Malley
Keyword(s):  
Glycolytic Enzyme ◽  
Dnase I ◽  
Gene Coding

scholarly journals Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route

2020 ◽  
Author(s):  
Lehai Zhang ◽  
Shifu Wang ◽  
Qian Ren ◽  
Junjie Yang ◽  
Yanqin Lu ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Detection Efficiency ◽  
Evolutionary Relationship ◽  
Clinical Manifestations ◽  
Coding Region ◽  
Gene Coding ◽  
Genome Wide ◽  
Group A ◽  
Group B ◽  
Relationship Of

AbstractIn the epidemic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the issues of mutation, origin, typing and the effect of mutation on molecular detection remain to be unrevealed. In order to identify the evolutionary relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are currently used in different countries, we retrieved genomic sequences of 373 SARS-CoV-2 strains from multiple databases and performed genome-wide variation analysis. According to the nucleotide C28144T variation, the SARS-CoV-2 can be divided into group A (117 strains) and group B (256 strains). The spike protein gene (S gene) coding region 1841 (total 23403) A1841G, formed a B1 subgroup (40 strains) in group B, of which 30 strains were from European and American countries in March (especially Washington, USA). These mutations are likely to be influenced by the environment or the immunization selection pressure of different populations. Although the mutation is not in the receptor binding region (RBD) and alkaline cleavage region, it may also affect the ability of transmission and pathogenicity; however, the significance is not yet clear. As the ratio of A / B strains in the epidemic months showed an increasing trend (0.35: 1 in January, 0.62: 1 in February and 0.76: 1 in March), it seems that the transmissibility of group A strains becomes stronger with time. Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. By comparing the detection capabilities of primers in different countries, the SARS-CoV-2 nucleotide variation may only affect molecular detection of very few strains. The differences in the transmissibility, pathogenicity and clinical manifestations of different types of strains require further investigations.

scholarly journals Epigenomics of Plant’s Responses to Environmental Stress

2017 ◽  
Author(s):  
Suresh Kumar
Keyword(s):  
Gene Expression ◽  
Nuclear Dna ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Epigenetic Changes ◽  
Post Translational Modifications ◽  
Genome Wide ◽  
A Cell ◽  
Non Coding Rnas ◽  
Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

scholarly journals Investigation of Heterologously Expressed Glucose-6-Phosphate Dehydrogenase Genes in a Yeast zwf1 Deletion

2020 ◽  
Vol 8 (4) ◽  
pp. 546 ◽  
Author(s):  
Jürgen J. Heinisch ◽  
Johannes Knuesting ◽  
Renate Scheibe
Keyword(s):  
Kluyveromyces Lactis ◽  
Expression System ◽  
Disulfide Bridge ◽  
Pentose Phosphate ◽  
Yeast Saccharomyces Cerevisiae ◽  
Physiological Properties ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Synthetic Media ◽  
Glucose 6 Phosphate Dehydrogenase

Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme of the oxidative part of the pentose phosphate pathway and serves as the major source of NADPH for metabolic reactions and oxidative stress response in pro- and eukaryotic cells. We here report on a strain of the model yeast Saccharomyces cerevisiae which lacks the G6PD-encoding ZWF1 gene and displays distinct growth retardation on rich and synthetic media, as well as a strongly reduced chronological lifespan. This strain was used as a recipient to introduce plasmid-encoded heterologous G6PD genes, synthesized in the yeast codon usage and expressed under the control of the native PFK2 promotor. Complementation of the hypersensitivity of the zwf1 mutant towards hydrogen peroxide to different degrees was observed for the genes from humans (HsG6PD1), the milk yeast Kluyveromyces lactis (KlZWF1), the bacteria Escherichia coli (EcZWF1) and Leuconostoc mesenteroides (LmZWF1), as well as the genes encoding three different plant G6PD isoforms from Arabidopsis thaliana (AtG6PD1, AtG6PD5, AtG6PD6). The plastidic AtG6PD1 isoform retained its redox-sensitive activity when produced in the yeast as a cytosolic enzyme, demonstrating the suitability of this host for determination of its physiological properties. Mutations precluding the formation of a disulfide bridge in AtG6PD1 abolished its redox-sensitivity but improved its capacity to complement the yeast zwf1 deletion. Given the importance of G6PD in human diseases and plant growth, this heterologous expression system offers a broad range of applications.

A New Role of Phosphoglucose Isomerase. Involvement of the Glycolytic Enzyme in Aldehyde Metabolism

2005 ◽  
Vol 70 (11) ◽  
pp. 1251-1255 ◽  
Author(s):  
Z. S. Agadjanyan ◽  
L. F. Dmitriev ◽  
S. F. Dugin
Keyword(s):  
Glycolytic Enzyme ◽  
Phosphoglucose Isomerase

scholarly journals Phosphofructokinase deficiency impairs ATP generation, autophagy, and redox balance in rheumatoid arthritis T cells

2013 ◽  
Vol 210 (10) ◽  
pp. 2119-2134 ◽  
Author(s):  
Zhen Yang ◽  
Hiroshi Fujii ◽  
Shalini V. Mohan ◽  
Jorg J. Goronzy ◽  
Cornelia M. Weyand
Keyword(s):  
Rheumatoid Arthritis ◽  
T Cells ◽  
Cd4 T Cells ◽  
Redox Balance ◽  
Glycolytic Enzyme ◽  
Pentose Phosphate ◽  
Glycolytic Flux ◽  
Alternative Means ◽  
Atp Generation ◽  
Phosphofructokinase Deficiency

In the HLA class II–associated autoimmune syndrome rheumatoid arthritis (RA), CD4 T cells are critical drivers of pathogenic immunity. We have explored the metabolic activity of RA T cells and its impact on cellular function and fate. Naive CD4 T cells from RA patients failed to metabolize equal amounts of glucose as age-matched control cells, generated less intracellular ATP, and were apoptosis-susceptible. The defect was attributed to insufficient induction of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), a regulatory and rate-limiting glycolytic enzyme known to cause the Warburg effect. Forced overexpression of PFKFB3 in RA T cells restored glycolytic flux and protected cells from excessive apoptosis. Hypoglycolytic RA T cells diverted glucose toward the pentose phosphate pathway, generated more NADPH, and consumed intracellular reactive oxygen species (ROS). PFKFB3 deficiency also constrained the ability of RA T cells to resort to autophagy as an alternative means to provide energy and biosynthetic precursor molecules. PFKFB3 silencing and overexpression identified a novel extraglycolytic role of the enzyme in autophagy regulation. In essence, T cells in RA patients, even those in a naive state, are metabolically reprogrammed with insufficient up-regulation of the glycolytic activator PFKFB3, rendering them energy-deprived, ROS- and autophagy-deficient, apoptosis-sensitive, and prone to undergo senescence.

SHQ1 Regulates MYC mRNA Splicing and Promotes T Cell Leukemogenesis

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 440-440
Author(s):  
Hexiu Su ◽  
Yufeng Hu ◽  
Jue Jiang ◽  
Zhichao Chen ◽  
Hudan Liu
Keyword(s):  
Cell Proliferation ◽  
T Cell ◽  
Functional Role ◽  
Conflicts Of Interest ◽  
Mrna Splicing ◽  
Transcriptional Level ◽  
Normal Peripheral Blood ◽  
Genome Wide ◽  
T Cell Leukemogenesis

Abstract T-acute lymphoblastic leukemias (T-ALLs) are aggressive hematologic tumors resulting from the malignant transformation of T cell progenitors. In this context, constitutive activation of NOTCH1 signaling is the most prominent oncogenic pathway in T cell transformation. Yet functional role(s) of NOTCH1 in T-ALL pathogenesis and precise mechanism(s) of action remain to be fully determined. SHQ1 is an essential assembly factor for H/ACA ribonucleoproteins which are required for spliceosomal small nuclear RNA (snRNA) maturation. We here identify SHQ1 as a NOTCH1 downstream target that plays a pivotal role in maintaining MYC splicing fidelity and promoting T-ALL cell proliferation in vitro and in vivo. We identified SHQ1 as a NOTCH1-regulated gene from multiple human T-ALL genome-wide expression studies. To validate this finding, we analyzed SHQ1 expression in a spectrum of human T-ALL cells upon NOTCH1 pathway inhibition. NOTCH1 inactivation caused a marked downregulation of SHQ1 in all T-ALL cell lines tested. We further demonstrated NOTCH1 bound to the canonical CSL binding sites in the SHQ1 promoter and directly activated the transcription. We next systematically analyzed the SHQ1 expression in 174 T-ALL primary samples and found that SHQ1 expression was significantly elevated in T-ALL compared with normal peripheral blood. To explore the functional role of SHQ1, we knocked it down in T-ALL using specific shRNAs. SHQ1 depletion profoundly inhibited T-ALL cell proliferation and induced massive apoptotic cell death. Consistent with these in vitro findings, SHQ1 depletion in a human T-ALL xenograft significantly delayed leukemia onset and prolonged survival. To decipher the molecular mechanism whereby SHQ1 contributes to T cell leukemogenesis, we performed genome-wide RNA-Seq and analyzed alternative splicing across the genome. Approximately 70% of genes exhibited abnormal intron retention upon SHQ1 depletion. Among those whose expression levels and mRNA splicing were prominently altered by SHQ1, MYC gained our attention because of its vital role in T-ALL. Depletion of SHQ1 resulted in marked downregulation of mature MYC mRNA and protein. Endogenous mRNA analysis and mini-gene experiments showed aberrant accumulation of MYC pre-mRNA in SHQ1-depleted cells. Expectedly, SHQ1 knockdown had minimal effects on T-ALL cells constitutively expressing a human MYC protein. In addition to the well-documented transcriptional control of MYC by NOTCH1, we herein report a previously unsuspected mechanism in which NOTCH1 modulates MYC splicing by activation of SHQ1. Our findings not only shed new insights in the molecular pathology of NOTCH1-induced T-ALL but also provide a new layer of regulation of oncogene MYC at the post-transcriptional level, mechanism of which may apply to other MYC involved tumors. Disclosures No relevant conflicts of interest to declare.

scholarly journals Cu, Zn Superoxide Dismutase and NADP(H) Homeostasis Are Required for Tolerance of Endoplasmic Reticulum Stress inSaccharomyces cerevisiae

2009 ◽  
Vol 20 (5) ◽  
pp. 1493-1508 ◽  
Author(s):  
Shi-Xiong Tan ◽  
Mariati Teo ◽  
Yuen T. Lam ◽  
Ian W. Dawes ◽  
Gabriel G. Perrone
Keyword(s):  
Endoplasmic Reticulum ◽  
Superoxide Dismutase ◽  
Er Stress ◽  
Stress Sensitivity ◽  
Pentose Phosphate ◽  
Unfolded Protein ◽  
Genome Wide ◽  
The Unfolded Protein Response ◽  
Protein Response

Genome-wide screening for sensitivity to chronic endoplasmic reticulum (ER) stress induced by dithiothreitol and tunicamycin (TM) identified mutants deleted for Cu, Zn superoxide dismutase (SOD) function (SOD1, CCS1) or affected in NADPH generation via the pentose phosphate pathway (TKL1, RPE1). TM-induced ER stress led to an increase in cellular superoxide accumulation and an increase in SOD1 expression and Sod1p activity. Prior adaptation of the hac1 mutant deficient in the unfolded protein response (UPR) to the superoxide-generating agent paraquat reduced cell death under ER stress. Overexpression of the ER oxidoreductase Ero1p known to generate hydrogen peroxide in vitro, did not lead to increased superoxide levels in cells subjected to ER stress. The mutants lacking SOD1, TKL1, or RPE1 exhibited decreased UPR induction under ER stress. Sensitivity of the sod1 mutant to ER stress and decreased UPR induction was partially rescued by overexpression of TKL1 encoding transketolase. These data indicate an important role for SOD and cellular NADP(H) in cell survival during ER stress, and it is proposed that accumulation of superoxide affects NADP(H) homeostasis, leading to reduced UPR induction during ER stress.

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