scholarly journals Amino Acid Starvation Enhances Programmed Ribosomal Frameshift in Metavirus Ty3 of Saccharomyces cerevisiae

2016 ◽  
Vol 2016 ◽  
pp. 1-6
Author(s):  
Sezai Türkel
Keyword(s):  
Amino Acid ◽  
Amino Acid Starvation ◽  
Yeast Cells ◽  
Dependent Manner ◽  
Coding Region ◽  
Coding Regions ◽  
In The Wild ◽  
Amino Acid Depletion ◽  
A Site ◽  
Wild Type Yeast

Ty3 is a retroviral-like element and propagates with a retroviral-like mechanism within the yeast cells. Ty3 mRNA contains two coding regions, which are GAG3 and POL3. The coding region POL3 is translated as a GAG3-POL3 fusion protein by a +1 programmed frameshift. In this study, it was shown that the Ty3 frameshift frequency is significantly increased by amino acid starvation in a Gcn2p complex dependent manner. When the yeast cells were subjected to amino acid starvation, the frameshift frequency of Ty3 increased more than 2-fold in the wild-type yeast cells, mostly independent of Gcn4p. However, Ty3 frameshift frequency remained at basal level in the gcn1, gcn20, or gcn2 mutant yeast cells in amino acid starved yeasts. Gcn1p forms a complex with Gcn2p and Gcn20p and is involved in the sensing of uncharged tRNAs on the ribosomal A-site during translation. Increases in uncharged tRNA levels due to amino acid depletion lead to ribosomal pauses. These ribosomal pauses are significant actors in the regulation of Ty3 frameshift frequency. Results of this research revealed that frameshift frequency in Ty3 is regulated by the Gcn2p complex in response to amino acid starvation in yeast.

scholarly journals Recruitment of folliculin to lysosomes supports the amino acid–dependent activation of Rag GTPases

2013 ◽  
Vol 202 (7) ◽  
pp. 1107-1122 ◽  
Author(s):  
Constance S. Petit ◽  
Agnes Roczniak-Ferguson ◽  
Shawn M. Ferguson
Keyword(s):  
Amino Acid ◽  
Critical Role ◽  
Direct Interaction ◽  
Loss Of Function ◽  
Interacting Protein ◽  
Rag Gtpases ◽  
New Findings ◽  
Pulmonary Cysts ◽  
Amino Acid Depletion ◽  
A Site

Birt-Hogg-Dubé syndrome, a human disease characterized by fibrofolliculomas (hair follicle tumors) as well as a strong predisposition toward the development of pneumothorax, pulmonary cysts, and renal carcinoma, arises from loss-of-function mutations in the folliculin (FLCN) gene. In this study, we show that FLCN regulates lysosome function by promoting the mTORC1-dependent phosphorylation and cytoplasmic sequestration of transcription factor EB (TFEB). Our results indicate that FLCN is specifically required for the amino acid–stimulated recruitment of mTORC1 to lysosomes by Rag GTPases. We further demonstrated that FLCN itself was selectively recruited to the surface of lysosomes after amino acid depletion and directly bound to RagA via its GTPase domain. FLCN-interacting protein 1 (FNIP1) promotes both the lysosome recruitment and Rag interactions of FLCN. These new findings define the lysosome as a site of action for FLCN and indicate a critical role for FLCN in the amino acid–dependent activation of mTOR via its direct interaction with the RagA/B GTPases.

scholarly journals The Osmoregulatory and the Amino Acid-regulated Responses of System A Are Mediated by Different Signal Transduction Pathways

2003 ◽  
Vol 122 (1) ◽  
pp. 5-16 ◽  
Author(s):  
Marta López-Fontanals ◽  
Silvia Rodríguez-Mulero ◽  
F. Javier Casado ◽  
Benoit Dérijard ◽  
Marçal Pastor-Anglada
Keyword(s):  
Signal Transduction ◽  
Amino Acid ◽  
Adaptive Response ◽  
Amino Acid Starvation ◽  
Dominant Negative ◽  
Signal Transduction Pathways ◽  
Mrna Levels ◽  
Dependent Manner ◽  
System A ◽  
Osmotic Response

The osmotic response of system A for neutral amino acid transport has been related to the adaptive response of this transport system to amino acid starvation. In a previous study (Ruiz-Montasell, B., M. Gómez-Angelats, F.J. Casado, A. Felipe, J.D. McGivan, and M. Pastor-Anglada. 1994. Proc. Natl. Acad. Sci. USA. 91:9569–9573), a model was proposed in which both responses were mediated by different mechanisms. The recent cloning of several isoforms of system A as well as the elucidation of a variety of signal transduction pathways involved in stress responses allow to test this model. SAT2 mRNA levels increased after amino acid deprivation but not after hyperosmotic shock. Inhibition of p38 activity or transfection with a dominant negative p38 did not alter the response to amino acid starvation but partially blocked the hypertonicity response. Inhibition of the ERK pathway resulted in full inhibition of the adaptive response of system A and no increase in SAT2 mRNA levels, without modifying the response to hyperosmolarity. Similar results were obtained after transfection with a dominant negative JNK1. The CDK2 inhibitor peptide-II decreased the osmotic response in a dose-dependent manner but did not have any effect on the adaptive response of system A. In summary, the previously proposed model of up-regulation of system A after hypertonic shock or after amino acid starvation by separate mechanisms is now confirmed and the two signal transduction pathways have been identified. The involvement of a CDK–cyclin complex in the osmotic response of system A links the activity of this transporter to the increase in cell volume previous to the entry in a new cell division cycle.

scholarly journals Ammonium-Dependent Shortening of CLS in Yeast Cells Starved for Essential Amino Acids Is Determined by the Specific Amino Acid Deprived, through Different Signaling Pathways

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Júlia Santos ◽  
Cecília Leão ◽  
Maria João Sousa
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Essential Amino Acid ◽  
Essential Amino Acids ◽  
Amino Acid Starvation ◽  
Yeast Cells ◽  
Environmental Interventions ◽  
Specific Amino Acid ◽  
Chronological Life Span ◽  
In Cells

Ammonium (NH4+) leads to chronological life span (CLS) shortening inSaccharomyces cerevisiaeBY4742 cells, particularly evident in cells starved for auxotrophy-complementing amino acids (leucine, lysine, and histidine) simultaneously. Here, we report that the effect ofNH4+on aging yeast depends on the specific amino acid they are deprived of. Compared with no amino acid starvation, starvation for leucine alone or in combination with histidine resulted in the most pronouncedNH4+-induced CLS shortening, whereas starvation for lysine, alone or in combination with histidine resulted in the least sensitivity toNH4+. We also show thatNH4+-induced CLS shortening is mainly mediated by Tor1p in cells starved for leucine or histidine but by Ras2p in cells starved for lysine, and in nonstarved cells. Sch9p protected cells from the effect ofNH4+under all conditions tested (starved or nonstarved cells), which was associated with Sch9p-dependent Hog1p phosphorylation. Our data show thatNH4+toxicity can be modulated through manipulation of the specific essential amino acid supplied to cells and of the conserved Ras2p, Tor1p, and Sch9p regulators, thus providing new clues to the development of environmental interventions for CLS extension and to the identification of new therapeutic targets for diseases associated with hyperammonemia.

scholarly journals Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 921-939 ◽  
Author(s):  
J Callis ◽  
T Carpenter ◽  
C W Sun ◽  
R D Vierstra
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Tandem Repeats ◽  
Synonymous Substitution ◽  
Coding Region ◽  
Coding Regions ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
Polyubiquitin Gene ◽  
Polyubiquitin Genes

Abstract The Arabidopsis thaliana ecotype Columbia ubiquitin gene family consists of 14 members that can be divided into three types of ubiquitin genes; polyubiquitin genes, ubiquitin-like genes and ubiquitin extension genes. The isolation and characterization of eight ubiquitin sequences, consisting of four polyubiquitin genes and four ubiquitin-like genes, are described here, and their relationships to each other and to previously identified Arabidopsis ubiquitin genes were analyzed. The polyubiquitin genes, UBQ3, UBQ10, UBQ11 and UBQ14, contain tandem repeats of the 228-bp ubiquitin coding region. Together with a previously described polyubiquitin gene, UBQ4, they differ in synonymous substitutions, number of ubiquitin coding regions, number and nature of nonubiquitin C-terminal amino acid(s) and chromosomal location, dividing into two subtypes; the UBQ3/UBQ4 and UBQ10/UBQ11/UBQ14 subtypes. Ubiquitin-like genes, UBQ7, UBQ8, UBQ9 and UBQ12, also contain tandem repeats of the ubiquitin coding region, but at least one repeat per gene encodes a protein with amino acid substitutions. Nucleotide comparisons, Ks value determinations and neighbor-joining analyses were employed to determine intra- and intergenic relationships. In general, the rate of synonymous substitution is too high to discern related repeats. Specific exceptions provide insight into gene relationships. The observed nucleotide relationships are consistent with previously described models involving gene duplications followed by both unequal crossing-over and gene conversion events.

scholarly journals General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4

2018 ◽  
Vol 115 (8) ◽  
pp. E1829-E1838 ◽  
Author(s):  
Caia D. S. Duncan ◽  
María Rodríguez-López ◽  
Phil Ruis ◽  
Jürg Bähler ◽  
Juan Mata
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Amino Acid ◽  
Fission Yeast ◽  
Transcriptional Response ◽  
Amino Acid Starvation ◽  
Ribosome Profiling ◽  
Transcriptional Networks ◽  
Dependent Manner ◽  
Zip Family

Eukaryotes respond to amino acid starvation by enhancing the translation of mRNAs encoding b-ZIP family transcription factors (GCN4 in Saccharomyces cerevisiae and ATF4 in mammals), which launch transcriptional programs to counter this stress. This pathway involves phosphorylation of the eIF2 translation factor by Gcn2-protein kinases and is regulated by upstream ORFs (uORFs) in the GCN4/ATF4 5′ leaders. Here, we present evidence that the transcription factors that mediate this response are not evolutionarily conserved. Although cells of the fission yeast Schizosaccharomyces pombe respond transcriptionally to amino acid starvation, they lack clear Gcn4 and Atf4 orthologs. We used ribosome profiling to identify mediators of this response in S. pombe, looking for transcription factors that behave like GCN4. We discovered a transcription factor (Fil1) translationally induced by amino acid starvation in a 5′ leader and Gcn2-dependent manner. Like Gcn4, Fil1 is required for the transcriptional response to amino acid starvation, and Gcn4 and Fil1 regulate similar genes. Despite their similarities in regulation, function, and targets, Fil1 and Gcn4 belong to different transcription factor families (GATA and b-ZIP, respectively). Thus, the same functions are performed by nonorthologous proteins under similar regulation. These results highlight the plasticity of transcriptional networks, which maintain conserved principles with nonconserved regulators.

Role of a PDZ1 domain of NHERF1 in the binding of airway epithelial RACK1 to NHERF1

2004 ◽  
Vol 286 (5) ◽  
pp. C1037-C1044 ◽  
Author(s):  
Carole M. Liedtke ◽  
Viswanathan Raghuram ◽  
C. Chris Yun ◽  
Xiangyun Wang
Keyword(s):  
Amino Acid ◽  
Solid Phase ◽  
Binding Constants ◽  
Dependent Manner ◽  
Airway Epithelial ◽  
Binding Assays ◽  
Glutathione S Transferase ◽  
Cell Lysate ◽  
A Site

In past studies, we demonstrated regulation of CFTR Cl channel function by protein kinase C (PKC)-ϵ through the binding of PKC-ϵ to RACK1 (a receptor for activated C-kinase) and of RACK1 to human Na+/H+ exchanger regulatory factor (NHERF1). In this study, we investigated the site of RACK1 binding on NHERF1 using solid-phase and solution binding assays and pulldown, immunoprecipitation, and 36Cl efflux experiments. Recombinant RACK1 binding to glutathione S-transferase (GST)-tagged PDZ1 domain of NHERF1 was 10-fold higher than its binding to GST-tagged PDZ2 domain of NHERF1. PDZ1 binds to RACK1 in a dose-dependent manner and vice versa, with similar binding constants of 1.67 and 1.26 μg, respectively. Interaction of the PDZ1 domain with RACK1 was not blocked by binding of activated PKC-ϵ to RACK1. A GST-tagged PDZ1 domain pulled down endogenous RACK1 from Calu-3 cell lysate. An internal 11-amino acid motif embedding the GYGF carboxylate binding loop of PDZ1 binds to RACK1, inhibits binding of recombinant NHERF1 and RACK1, pulls down endogenous RACK1 from Calu-3 cell lysate, and blocks coimmunoprecipitation of endogenous RACK1 with endogenous NHERF1 but does not affect cAMP-dependent activation of CFTR. A similar amino acid sequence in the PDZ2 domain did not bind RACK1. Our results indicate binding of Calu-3 RACK1 predominantly to the PDZ1 domain of NHERF1 at a site encompassing the GYGF loop of the PDZ1 domain and a site on RACK1 distinct from a PKC-ϵ binding site. CFTR activation by cAMP-generating agent is not affected by loss of RACK1-NHERF1 interaction.

scholarly journals CRISPR/Transposon gene integration (CRITGI) can manage gene expression in a retrotransposon-dependent manner

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Miki Hanasaki ◽  
Hiroshi Masumoto
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Consensus Sequence ◽  
Marker Gene ◽  
Gene Activation ◽  
Fine Tuning ◽  
Selection Marker ◽  
Regulation System ◽  
Dependent Manner ◽  
Amino Acid Depletion

Abstract The fine-tuning of gene expression contributes to both basic science and applications. Here, we develop a novel gene expression technology termed CRITGI (CRISPR/Transposon gene integration). CRITGI uses CRISPR/Cas9 to integrate multiple copies of the plasmid pTy1 into Ty1 loci, budding yeast retrotransposons. The pTy1 plasmid harbors a Ty1 consensus sequence for integration, a gene of interest with its own promoter and a selection marker gene. Interestingly, the expression of the pTy1 gene in Ty1 loci could be induced in synthetic complete amino acid depletion medium, which could activate the selection marker gene on pTy1. The induction or repression of the gene on pTy1 depended on Ty1 transcription. Activation of the selection marker gene on pTy1 triggered Ty1 transcription, which led to induction of the gene on pTy1. The gene on pTy1 was not transcribed with Ty1 mRNA; the transcription required its own promoter. Furthermore, the trimethylation of histone H3 on lysine 4, a landmark of transcriptionally active chromatin, accumulated at the 5′ end of the gene on pTy1 following selection marker gene activation. Thus, CRITGI is a unique gene regulation system to induce the genes on pTy1 in amino acid depletion medium and utilizes Ty1 transcription to create a chromatin environment favorable for the transcription of the genes on pTy1.

scholarly journals New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1232
Author(s):  
Mariola Dutkiewicz ◽  
Jakub Kuczynski ◽  
Michal Jarzab ◽  
Aleksandra Stachowiak ◽  
Agata Swiatkowska
Keyword(s):  
Protein Interactions ◽  
Rna Structure ◽  
Magnesium Concentration ◽  
Dependent Manner ◽  
Structural Elements ◽  
Coding Region ◽  
Virus Propagation ◽  
Concentration Dependent Manner ◽  
Computer Prediction ◽  
Coding Regions

Here we present a set of new structural elements formed within the open reading frame of the virus, which are highly probable, evolutionarily conserved and may interact with host proteins. This work focused on the coding regions of the CVB3 genome (particularly the V4-, V1-, 2C-, and 3D-coding regions), which, with the exception of the cis-acting replication element (CRE), have not yet been subjected to experimental analysis of their structures. The SHAPE technique, chemical modification with DMS and RNA cleavage with Pb2+, were performed in order to characterize the RNA structure. The experimental results were used to improve the computer prediction of the structural models, whereas a phylogenetic analysis was performed to check universality of the newly identified structural elements for twenty CVB3 genomes and 11 other enteroviruses. Some of the RNA motifs turned out to be conserved among different enteroviruses. We also observed that the 3′-terminal region of the genome tends to dimerize in a magnesium concentration-dependent manner. RNA affinity chromatography was used to confirm RNA–protein interactions hypothesized by database searches, leading to the discovery of several interactions, which may be important for virus propagation.

scholarly journals Class III phosphoinositide 3-kinase–Beclin1 complex mediates the amino acid-dependent regulation of autophagy in C2C12 myotubes

2003 ◽  
Vol 376 (3) ◽  
pp. 577-586 ◽  
Author(s):  
Amina TASSA ◽  
Marie Paule ROUX ◽  
Didier ATTAIX ◽  
Daniel M. BECHET
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Glycogen Synthase ◽  
Amino Acid Starvation ◽  
Class I ◽  
C2c12 Myotubes ◽  
Dependent Manner ◽  
Class Iii ◽  
Mitogen Activated Protein ◽  
Phosphoinositide 3 Kinase

Increased proteolysis contributes to muscle atrophy that prevails in many diseases. Elucidating the signalling pathways responsible for this activation is of obvious clinical importance. Autophagy is a ubiquitous degradation process, induced by amino acid starvation, that delivers cytoplasmic components to lysosomes. Starvation markedly stimulates autophagy in myotubes, and the present studies investigate the mechanisms of this regulation. In C2C12 myotubes incubated with serum growth factors, amino acid starvation stimulated autophagic proteolysis independently of p38 and p42/p44 mitogen-activated protein kinases, but in a PI3K (phosphoinositide 3-kinase)-dependent manner. Starvation, however, did not alter activities of class I and class II PI3Ks, and was not sufficient to affect major signalling proteins downstream from class I PI3K (glycogen synthase kinase, Akt/protein kinase B and protein S6). In contrast, starvation increased class III PI3K activity in whole-myotube extracts. In fact, this increase was most pronounced for a population of class III PI3K that coimmunoprecipitated with Beclin1/Apg6 protein, a major determinant in the initiation of autophagy. Stimulation of proteolysis was reproduced by feeding myotubes with synthetic dipalmitoyl-PtdIns3P, the class III PI3K product. Conversely, protein transfection of anti-class III PI3K inhibitory antibody into starved myotubes inverted the induction of proteolysis. Therefore, independently of class I PI3K/Akt, protein S6 and mitogen-activated protein kinase pathways, amino acid starvation stimulates proteolysis in myotubes by regulating class III PI3K–Beclin1 autophagic complexes.

scholarly journals Predicting and Clustering Plant CLE Genes with a New Method Developed Specifically for Short Amino Acid Sequences

2020 ◽  
Author(s):  
Zhe Zhang ◽  
Lei Liu ◽  
Melis Kucukoglu ◽  
Dongdong Tian ◽  
Robert M. Larkin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
Sequence Similarity ◽  
Gene Prediction ◽  
Cell Communication ◽  
Amino Acid Sequences ◽  
Evolutionary Analysis ◽  
Dependent Manner ◽  
Amino Acid Residues ◽  
A Site

Abstract Background: The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results: We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions: Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.

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