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Bonnet A, Bluy L, Gress L, Canario L, Ravon L, Sécula A, Billon Y, Liaubet L. Sex and fetal genome influence gene expression in pig endometrium at the end of gestation. BMC Genomics 2024; 25:303. [PMID: 38515025 PMCID: PMC10958934 DOI: 10.1186/s12864-024-10144-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND A fine balance of feto-maternal resource allocation is required to support pregnancy, which depends on interactions between maternal and fetal genetic potential, maternal nutrition and environment, endometrial and placental functions. In particular, some imprinted genes have a role in regulating maternal-fetal nutrient exchange, but few have been documented in the endometrium. The aim of this study is to describe the expression of 42 genes, with parental expression, in the endometrium comparing two extreme breeds: Large White (LW); Meishan (MS) with contrasting neonatal mortality and maturity at two days of gestation (D90-D110). We investigated their potential contribution to fetal maturation exploring genes-fetal phenotypes relationships. Last, we hypothesized that the fetal genome and sex influence their endometrial expression. For this purpose, pure and reciprocally crossbred fetuses were produced using LW and MS breeds. Thus, in the same uterus, endometrial samples were associated with its purebred or crossbred fetuses. RESULTS Among the 22 differentially expressed genes (DEGs), 14 DEGs were differentially regulated between the two days of gestation. More gestational changes were described in LW (11 DEGs) than in MS (2 DEGs). Nine DEGs were differentially regulated between the two extreme breeds, highlighting differences in the regulation of endometrial angiogenesis, nutrient transport and energy metabolism. We identified DEGs that showed high correlations with indicators of fetal maturation, such as ponderal index at D90 and fetal blood fructose level and placental weight at D110. We pointed out for the first time the influence of fetal sex and genome on endometrial expression at D90, highlighting AMPD3, CITED1 and H19 genes. We demonstrated that fetal sex affects the expression of five imprinted genes in LW endometrium. Fetal genome influenced the expression of four genes in LW endometrium but not in MS endometrium. Interestingly, both fetal sex and fetal genome interact to influence endometrial gene expression. CONCLUSIONS These data provide evidence for some sexual dimorphism in the pregnant endometrium and for the contribution of the fetal genome to feto-maternal interactions at the end of gestation. They suggest that the paternal genome may contribute significantly to piglet survival, especially in crossbreeding production systems.
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Affiliation(s)
- Agnes Bonnet
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France.
| | - Lisa Bluy
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Laure Gress
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Laurianne Canario
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Laure Ravon
- GenESI, INRAE, Le Magneraud, 17700, Surgères, France
| | - Aurelie Sécula
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
- Present Address: IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Yvon Billon
- GenESI, INRAE, Le Magneraud, 17700, Surgères, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
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Darnell AM, Subramaniam AR, O'Shea EK. Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell 2019; 71:229-243.e11. [PMID: 30029003 DOI: 10.1016/j.molcel.2018.06.041] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 06/26/2018] [Indexed: 12/22/2022]
Abstract
Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that a selective loss of arginine tRNA charging during limitation for arginine regulates translation through ribosome pausing at two of six arginine codons. Surprisingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevents ribosome pausing, while an insufficient response to arginine limitation leads to loss of tRNA charging and ribosome pausing. Ribosome pausing decreases protein production and triggers premature ribosome termination without reducing mRNA levels. Together, our results suggest that amino acids that are not optimally sensed by the mTORC1 and GCN2 pathways still regulate translation through an evolutionarily conserved mechanism based on codon-specific ribosome pausing.
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Affiliation(s)
- Alicia M Darnell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Program of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Erin K O'Shea
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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3
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Tang X, Keenan MM, Wu J, Lin CA, Dubois L, Thompson JW, Freedland SJ, Murphy SK, Chi JT. Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis. PLoS Genet 2015; 11:e1005158. [PMID: 25849282 PMCID: PMC4388453 DOI: 10.1371/journal.pgen.1005158] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/18/2015] [Indexed: 12/17/2022] Open
Abstract
Besides being building blocks for protein synthesis, amino acids serve a wide variety of cellular functions, including acting as metabolic intermediates for ATP generation and for redox homeostasis. Upon amino acid deprivation, free uncharged tRNAs trigger GCN2-ATF4 to mediate the well-characterized transcriptional amino acid response (AAR). However, it is not clear whether the deprivation of different individual amino acids triggers identical or distinct AARs. Here, we characterized the global transcriptional response upon deprivation of one amino acid at a time. With the exception of glycine, which was not required for the proliferation of MCF7 cells, we found that the deprivation of most amino acids triggered a shared transcriptional response that included the activation of ATF4, p53 and TXNIP. However, there was also significant heterogeneity among different individual AARs. The most dramatic transcriptional response was triggered by methionine deprivation, which activated an extensive and unique response in different cell types. We uncovered that the specific methionine-deprived transcriptional response required creatine biosynthesis. This dependency on creatine biosynthesis was caused by the consumption of S-Adenosyl-L-methionine (SAM) during creatine biosynthesis that helps to deplete SAM under methionine deprivation and reduces histone methylations. As such, the simultaneous deprivation of methionine and sources of creatine biosynthesis (either arginine or glycine) abolished the reduction of histone methylation and the methionine-specific transcriptional response. Arginine-derived ornithine was also required for the complete induction of the methionine-deprived specific gene response. Collectively, our data identify a previously unknown set of heterogeneous amino acid responses and reveal a distinct methionine-deprived transcriptional response that results from the crosstalk of arginine, glycine and methionine metabolism via arginine/glycine-dependent creatine biosynthesis. In order for mammalian cells to live and function, amino acids are required for protein synthesis and the generation of metabolic intermediates. An imbalance or deficiency of amino acids often triggers an “amino acid response” (AAR) to allow cells to adapt to their environment. However, it remains unclear whether the deprivation of any single amino acid leads to similar or different changes compared to the global AAR response or to other single amino acid deficiencies. To answer this question, we removed each or all of the 15 amino acids found in media from cells and comprehensively profiled the resulting changes in their RNA expression. Strikingly, we found a unique and dramatic gene expression program that occurred only when cells were deprived of methionine, but not any other amino acid. We also found that these methionine-specific changes depended on changes in histone modifications and an intact creatine biosynthesis pathway. Methionine deprivation reduced the degree to which histone proteins were indirectly modified by methionine (histone methylation). Creatine biosynthesis consumed methionine’s derivate S-Adenosyl-L-methionine (SAM), contributing to the reduction of histone methylation and an increase in ornithine-mediated signaling. Since methionine restriction may have anti-aging and other medical uses, our findings provide insights that will lead toward a better understanding of the underlying effects of methionine restriction and eventually improve human health.
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Affiliation(s)
- Xiaohu Tang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Melissa M. Keenan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jianli Wu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Chih-An Lin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Laura Dubois
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Proteomics and Metabolomics Core Facility Duke University Medical Center, Durham, North Carolina, United States of America
| | - J. Will Thompson
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Proteomics and Metabolomics Core Facility Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pharmacology and Cancer Biology Duke University Medical Center, Durham, North Carolina, United States of America
| | - Stephen J. Freedland
- Department of Surgery Duke University Medical Center, Durham, North Carolina, United States of America
| | - Susan K. Murphy
- Department of Surgery Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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4
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Sheng L, Wang L, Sang X, Zhao X, Hong J, Cheng S, Yu X, Liu D, Xu B, Hu R, Sun Q, Cheng J, Cheng Z, Gui S, Hong F. Nano-sized titanium dioxide-induced splenic toxicity: a biological pathway explored using microarray technology. JOURNAL OF HAZARDOUS MATERIALS 2014; 278:180-188. [PMID: 24968254 DOI: 10.1016/j.jhazmat.2014.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 06/01/2014] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
Titanium dioxide nanoparticles (TiO2 NPs) have been widely used in various areas, and its potential toxicity has gained wide attention. However, the molecular mechanisms of multiple genes working together in the TiO2 NP-induced splenic injury are not well understood. In the present study, 2.5, 5, or 10mg/kg body weight TiO2 NPs were administered to the mice by intragastric administration for 90 consecutive days, their immune capacity in the spleen as well as the gene-expressed characteristics in the mouse damaged spleen were investigated using microarray assay. The findings showed that with increased dose, TiO2 NP exposure resulted in the increases of spleen indices, immune dysfunction, and severe macrophage infiltration as well as apoptosis in the spleen. Importantly, microarray data showed significant alterations in the expressions of 1041 genes involved in immune/inflammatory responses, apoptosis, oxidative stress, stress responses, metabolic processes, ion transport, signal transduction, cell proliferation/division, cytoskeleton and translation in the 10 mg/kg TiO2 NP-exposed spleen. Specifically, Cyp2e1, Sod3, Mt1, Mt2, Atf4, Chac1, H2-k1, Cxcl13, Ccl24, Cd14, Lbp, Cd80, Cd86, Cd28, Il7r, Il12a, Cfd, and Fcnb may be potential biomarkers of spleen toxicity following exposure to TiO2 NPs.
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Affiliation(s)
- Lei Sheng
- Medical College of Soochow University, Suzhou 215123, China
| | - Ling Wang
- Library of Soochow University, Suzhou 215123, China
| | - Xuezi Sang
- Medical College of Soochow University, Suzhou 215123, China
| | - Xiaoyang Zhao
- Medical College of Soochow University, Suzhou 215123, China
| | - Jie Hong
- Medical College of Soochow University, Suzhou 215123, China
| | - Shen Cheng
- Medical College of Soochow University, Suzhou 215123, China
| | - Xiaohong Yu
- Medical College of Soochow University, Suzhou 215123, China
| | - Dong Liu
- Medical College of Soochow University, Suzhou 215123, China
| | - Bingqing Xu
- Medical College of Soochow University, Suzhou 215123, China
| | - Renping Hu
- Medical College of Soochow University, Suzhou 215123, China
| | - Qingqing Sun
- Medical College of Soochow University, Suzhou 215123, China
| | - Jie Cheng
- Medical College of Soochow University, Suzhou 215123, China
| | - Zhe Cheng
- Medical College of Soochow University, Suzhou 215123, China
| | - Suxin Gui
- Medical College of Soochow University, Suzhou 215123, China
| | - Fashui Hong
- Medical College of Soochow University, Suzhou 215123, China.
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5
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Lin AH, Chen HW, Liu CT, Tsai CW, Lii CK. Activation of Nrf2 is required for up-regulation of the π class of glutathione S-transferase in rat primary hepatocytes with L-methionine starvation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:6537-6545. [PMID: 22676582 DOI: 10.1021/jf301567m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Numerous genes expression is regulated in response to amino acid shortage, which helps organisms adapt to amino acid limitation. The expression of the π class of glutathione (GSH) S-transferase (GSTP), a highly inducible phase II detoxification enzyme, is regulated mainly by activates activating protein 1 (AP-1) binding to the enhancer I of GSTP (GPEI). Here we show the critical role of nuclear factor erythroid-2-related factor 2 (Nrf2) in up-regulating GSTP gene transcription. Primary rat hepatocytes were cultured in a methionine-restricted medium, and immunoblotting and RT-PCR analyses showed that methionine restriction time-dependently increased GSTP protein and mRNA expression over a 48 h period. Nrf2 translocation to the nucleus, nuclear proteins binding to GPEI, and antioxidant response element (ARE) luciferase reporter activity were increased by methionine restriction as well as by l-buthionine sulfoximine (BSO), a GSH synthesis inhibitor. Transfection with Nrf2 siRNA knocked down Nrf2 expression and reversed the methionine-induced GSTP expression and GPEI binding activity. Chromatin immunoprecipitation assay confirmed the binding of Nrf2 to the GPEI. Phosphorylation of extracellular signal-regulated kinase 2 (ERK2) was increased in methionine-restricted and BSO-treated cells. ERK2 siRNA abolished methionine restriction-induced Nrf2 nuclear translocation, GPEI binding activity, ARE-luciferase reporter activity, and GSTP expression. Our results suggest that the up-regulation of GSTP gene transcription in response to methionine restriction likely occurs via the ERK-Nrf2-GPEI signaling pathway.
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Affiliation(s)
- Ai-Hsuan Lin
- School of Nutrition, Chung Shan Medical University, Taichung 402, Taiwan
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6
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Zhou D, Pan YX. Gestational low protein diet selectively induces the amino acid response pathway target genes in the liver of offspring rats through transcription factor binding and histone modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:549-56. [DOI: 10.1016/j.bbagrm.2011.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 06/27/2011] [Accepted: 07/06/2011] [Indexed: 12/19/2022]
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7
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Corallini S, Taranta A, Bellomo F, Palma A, Pastore A, Emma F. Transcriptional and posttranscriptional regulation of the CTNS gene. Pediatr Res 2011; 70:130-5. [PMID: 21508882 DOI: 10.1203/pdr.0b013e3182200187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cell cysteine (Cys) levels and/or the [Cys/CySS] redox potential have been shown to regulate mRNA levels of the CTNS gene, which encodes for a lysosomal cystine (CySS) carrier that is defective in cystinosis. To investigate the mechanisms involved CTNS mRNA regulation, different portions of the CTNS promotor were cloned into a luciferase vector and transfected in HK2 cells. A 1.5-2.4-fold increase in luciferase activity was observed when cells were incubated in culture medium containing low CySS concentrations. Conversely, CTNS mRNA levels decreased by 47-56% in the presence of N-acetyl-L-cysteine (NAC). Chase experiments with actinomycin D (ActD) demonstrated a 3-fold stabilization of the CTNS mRNA when cells were cultured in low CySS medium for 48 h. Treatment of control cells with cyclohexamide (CHX) increased CTNS mRNA levels, suggesting that CHX blocked the synthesis of proteins involved in mRNA degradation or in repression of the CTNS gene. Finally, in vitro binding assays showed increased binding (30-110%) of the Sp-1 transcription factor to two regions of the CTNS promotor when cells were incubated in low CySS medium. These results indicate that the CTNS gene is actively regulated at the transcriptional and posttranscriptional levels and suggest that CTNS plays a pivotal role in regulating cell thiol concentrations.
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Affiliation(s)
- Serena Corallini
- Division of Nephrology and Dialysis, Bambino Gesù Children's Hospital and Research Institute, 00165 Rome, Italy
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8
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Leucine nutrition in animals and humans: mTOR signaling and beyond. Amino Acids 2011; 41:1185-93. [DOI: 10.1007/s00726-011-0983-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Accepted: 06/15/2011] [Indexed: 12/14/2022]
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9
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Sikalidis AK, Lee JI, Stipanuk MH. Gene expression and integrated stress response in HepG2/C3A cells cultured in amino acid deficient medium. Amino Acids 2011; 41:159-71. [PMID: 20361218 PMCID: PMC3119335 DOI: 10.1007/s00726-010-0571-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 03/16/2010] [Indexed: 12/11/2022]
Abstract
The integrated stress response (ISR), a defense mechanism cells employ when under stress (e.g., amino acid deprivation), causes suppression of global protein synthesis along with the paradoxical increased expression of a host of proteins that are useful in combating various stresses. Genes that were similarly differentially expressed under conditions of either leucine- or cysteine-depletion were identified. Many of the genes known to contain an amino acid response element and to be induced in response to eIF2α phosphorylation and ATF4 heterodimer binding (ATF3, C/EBPβ, SLC7A1, SLC7A11, and TRIB3), as well as others shown to be induced downstream of eIF2α phosphorylation (C/EBPγ, CARS, SARS, CLCN3, CBX4, and PPP1R15A) were among the upregulated genes. Evidence for the induction of the ISR in these cells also included the increased phosphorylation of eIF2α and increased protein abundance of ATF4, ATF3, and ASNS in cysteine- and leucine-depleted cells. Based on genes highly differentially expressed in both leucine- and cysteine-deficient cells, a list of 67 downregulated and 53 upregulated genes is suggested as likely targets of essential amino acid deprivation in mammalian cells.
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Filiputti E, Rafacho A, Araújo EP, Silveira LR, Trevisan A, Batista TM, Curi R, Velloso LA, Quesada I, Boschero AC, Carneiro EM. Augmentation of insulin secretion by leucine supplementation in malnourished rats: possible involvement of the phosphatidylinositol 3-phosphate kinase/mammalian target protein of rapamycin pathway. Metabolism 2010; 59:635-44. [PMID: 19913855 DOI: 10.1016/j.metabol.2009.09.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 09/03/2009] [Accepted: 09/04/2009] [Indexed: 01/01/2023]
Abstract
A regimen of low-protein diet induces a reduction of pancreatic islet function that is associated with development of metabolic disorders including diabetes and obesity afterward. In the present study, the influence of leucine supplementation on metabolic parameters, insulin secretion to glucose and to amino acids, as well as the levels of proteins that participate in the phosphatidylinositol 3-phosphate kinase (PI3K) pathway was investigated in malnourished rats. Four groups were fed with different diets for 12 weeks: a normal protein diet (17%) without (NP) or with leucine supplementation (NPL) or a low (6%)-protein diet without (LP) or with leucine supplementation (LPL). Leucine was given in the drinking water during the last 4 weeks. As indicated by the intraperitoneal glucose tolerance test, LPL rats exhibited increased glucose tolerance as compared with NPL group. Both NPL and LPL rats had higher circulating insulin levels than controls. The LPL rats also showed increased insulin secretion by pancreatic islets in response to glucose or arginine compared with those observed in islets from LP animals. Glucose oxidation was significantly reduced in NPL, LP, and LPL isolated islets as compared with NP; but no alteration was observed for leucine and glutamate oxidation among the 4 groups. Western blotting analysis demonstrated increased PI3K and mammalian target protein of rapamycin protein contents in LPL compared with LP islets. A significant increase in insulin-induced insulin receptor substrate 1-associated PI3K activation was also observed in LPL compared with LP islets. These findings indicate that leucine supplementation can augment islet function in malnourished rats and that activation of the PI3K/mammalian target protein of rapamycin pathway may play a role in this process.
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Affiliation(s)
- Eliane Filiputti
- Department of Anatomy, Cell Biology and Physiology and Biophysics, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil
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Chaveroux C, Lambert-Langlais S, Cherasse Y, Averous J, Parry L, Carraro V, Jousse C, Maurin AC, Bruhat A, Fafournoux P. Molecular mechanisms involved in the adaptation to amino acid limitation in mammals. Biochimie 2010; 92:736-45. [PMID: 20188139 DOI: 10.1016/j.biochi.2010.02.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 02/16/2010] [Indexed: 12/15/2022]
Abstract
In mammals, metabolic adaptations are required to cope with episodes of protein deprivation and malnutrition. Consequently, mammals have to adjust physiological functions involved in the adaptation to amino acid availability. Part of this regulation involves the modulation of the expression of numerous genes. In particular, it has been shown that amino acids by themselves can modify the expression of target genes. This review describes the regulation of amino acids homeostasis and the their role as signal molecules. The recent advances in the understanding of the molecular mechanisms involved in the control of mammalian gene expression in response to amino acid limitation will be described.
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Affiliation(s)
- Cédric Chaveroux
- Unité de Nutrition Humaine, UMR 1019, INRA de Theix, 63122 Saint Genès Champanelle, France
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Amino acid deprivation induces CREBZF/Zhangfei expression via an AARE-like element in the promoter. Biochem Biophys Res Commun 2010; 391:1352-7. [DOI: 10.1016/j.bbrc.2009.12.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 12/10/2009] [Indexed: 11/18/2022]
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13
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Bruhat A, Chérasse Y, Chaveroux C, Maurin AC, Jousse C, Fafournoux P. Amino acids as regulators of gene expression in mammals: molecular mechanisms. Biofactors 2009; 35:249-57. [PMID: 19415732 DOI: 10.1002/biof.40] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In mammals, the impact of nutrients on gene expression has become an important area of research. Because amino acids have multiple and important functions, their homeostasis has to be finely maintained. However, amino acidemia can be affected in some nutritional conditions and by various forms of stress. Consequently, mammals have to adjust physiological functions involved in the adaptation to amino acid availability. Part of this regulation involves the modulation of numerous gene expression. It has been shown that amino acids by themselves can modify the expression of target genes. This review focuses on the recent advances in the understanding of the mechanisms involved in the control of mammalian gene expression in response to amino acid limitation.
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Affiliation(s)
- Alain Bruhat
- UMR 1019, Unité de Nutrition Humaine, INRA de Theix, 63122 Saint Genès Champanelle, France.
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Deval C, Chaveroux C, Maurin AC, Cherasse Y, Parry L, Carraro V, Milenkovic D, Ferrara M, Bruhat A, Jousse C, Fafournoux P. Amino acid limitation regulates the expression of genes involved in several specific biological processes through GCN2-dependent and GCN2-independent pathways. FEBS J 2008; 276:707-18. [PMID: 19120448 DOI: 10.1111/j.1742-4658.2008.06818.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Evidence has accumulated that amino acids play an important role in controlling gene expression. Nevertheless, two components of the amino acid control of gene expression are not yet completely understood in mammals: (a) the target genes and biological processes regulated by amino acid availability, and (b) the signaling pathways that mediate the amino acid response. Using large-scale analysis of gene expression, the objective of this study was to gain a better understanding of the control of gene expression by amino acid limitation. We found that a 6 h period of leucine starvation regulated the expression of a specific set of genes: 420 genes were up-regulated by more than 1.8-fold and 311 genes were down-regulated. These genes were involved in the control of several biological processes, such as amino acid metabolism, lipid metabolism and signal regulation. Using GCN2-/- cells and rapamycin treatment, we checked for the role of mGCN2 and mTORC1 kinases in this regulation. We found that (a) the GCN2 pathway was the major, but not unique, signaling pathway involved in the up- and down-regulation of gene expression in response to amino acid starvation, and (b) that rapamycin regulates the expression of a set of genes that only partially overlaps with the set of genes regulated by leucine starvation.
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Affiliation(s)
- Christiane Deval
- Unité de Nutrition Humaine, Equipe Génes-Nutriments, Saint Genès Champanelle, France
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15
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Role of sulfur amino acids in controlling nutrient metabolism and cell functions: implications for nutrition. Br J Nutr 2008; 101:1132-9. [PMID: 19079841 DOI: 10.1017/s0007114508159025] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein synthesis is affected when an insufficient level of sulfur amino acids is available. This defect may originate from dietary amino acid deficiency and/or excessive amino acid utilisation for other purposes such as the synthesis of glutathione and acute-phase proteins during catabolic stress. Sulfur amino acids are recognised to exert other significant functions since they are precursors of essential molecules, are involved in the methylation process, participate in the control of oxidative status, and may act as mediators affecting metabolism and cell functions. Despite this increased understanding of the role of sulfur amino acids, many questions still remain unanswered due to the complexity of the mechanisms involved. Moreover, surprising effects of dietary sulfur amino acids have been reported, with the development of disorders in cases of both deficiency and excess. These findings indicate the importance of defining adequate levels of intake and providing a rationale for nutritional advice. The aim of the present review is to provide an overview on the roles of sulfur amino acids as regulators of nutrient metabolism and cell functions, with emphasis placed on the implications for nutrition.
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Specificity of amino acid regulated gene expression: analysis of genes subjected to either complete or single amino acid deprivation. Amino Acids 2008; 37:79-88. [PMID: 19009228 DOI: 10.1007/s00726-008-0199-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 10/17/2008] [Indexed: 12/20/2022]
Abstract
Amino acid deprivation activates the amino acid response (AAR) pathway that enhances transcription of genes containing an amino acid response element (AARE). The present data reveal a quantitative difference in the response to deprivation of individual amino acids. The AAR leads to increased eukaryotic initiation factor 2alpha (eIF2alpha) phosphorylation and ATF4 translation. When HepG2 cells were deprived of an individual essential amino acid, p-eIF2alpha and activating transcription factor 4 were increased, but the correlation was relatively weak. Complete amino acid starvation in either Earle's balanced salt solution or Krebs-Ringer bicarbonate buffer (KRB) resulted in activation of transcription driven by a SNAT2 genomic fragment that contained an AARE. However, for the KRB, a proportion of the transcription was AARE-independent suggesting that amino acid-independent mechanisms were responsible. Therefore, activation of AARE-driven transcription is triggered by a deficiency in any one of the essential amino acids, but the response is not uniform. Furthermore, caution must be exercised when using a medium completely devoid of amino acids.
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17
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Impaired insulin secretion and decreased expression of the nutritionally responsive ribosomal kinase protein S6K-1 in pancreatic islets from malnourished rats. Life Sci 2008; 82:542-8. [DOI: 10.1016/j.lfs.2007.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 09/25/2007] [Accepted: 12/15/2007] [Indexed: 11/21/2022]
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18
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Kilberg MS, Pan YX, Chen H, Leung-Pineda V. Nutritional control of gene expression: how mammalian cells respond to amino acid limitation. Annu Rev Nutr 2005; 25:59-85. [PMID: 16011459 PMCID: PMC3600373 DOI: 10.1146/annurev.nutr.24.012003.132145] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The amino acid response (AAR) pathway in mammalian cells is designed to detect and respond to amino acid deficiency. Limiting any essential amino acid initiates this signaling cascade, which leads to increased translation of a "master regulator," activating transcription factor (ATF) 4, and ultimately, to regulation of many steps along the pathway of DNA to RNA to protein. These regulated events include chromatin remodeling, RNA splicing, nuclear RNA export, mRNA stabilization, and translational control. Proteins that are increased in their expression as targets of the AAR pathway include membrane transporters, transcription factors from the basic region/leucine zipper (bZIP) superfamily, growth factors, and metabolic enzymes. Significant progress has been achieved in understanding the molecular mechanisms by which amino acids control the synthesis and turnover of mRNA and protein. Beyond gaining additional knowledge of these important regulatory pathways, further characterization of how these processes contribute to the pathology of various disease states represents an interesting aspect of future research in molecular nutrition.
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Affiliation(s)
- M S Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, USA.
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19
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Tsai CW, Chen HW, Yang JJ, Liu KL, Lii CK. Sulfur amino acid restriction induces the pi class of glutathione S-transferase expression in primary rat hepatocytes. J Nutr 2005; 135:1034-9. [PMID: 15867277 DOI: 10.1093/jn/135.5.1034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The regulation of genes by amino acids is attracting increasing attention. In the present study, we investigated the restriction of expression of the pi class of glutathione S-transferase (GST Yp) by sulfur amino acids. Hepatocytes isolated from male Sprague-Dawley rats were cultured with L-15-based medium containing low (LSAA; 0.1 mmol/L L-methionine and 0.1 mmol/L L-cysteine) or high (HSAA; 0.5 mmol/L L-methionine and 0.2 mmol/L L-cysteine) amounts of sulfur amino acids for up to 6 d. Cellular protein contents did not differ between LSAA- and HSAA-treated cells over the entire period. In contrast, glutathione concentrations were suppressed by the LSAA medium and on d 6 were only 20% of those of HSAA-treated cells (P < 0.05). As shown by immunoblot analysis, GST Yp protein levels were greater in LSAA-treated cells than in HSAA-treated cells (P < 0.05). The induction of GST Yp by L-methionine and L-cysteine restriction was not affected by insulin and dexamethasone, but the latter suppressed GST Yp expression (P < 0.05). LSAA increased GST Yp mRNA levels and GST activity toward ethacrynic acid (P < 0.05). GST Yp induction occurred only in cells with a limited supply of L-methionine; restriction of L-isoleucine, L-leucine, L-lysine, and L-phenylalanine had no significant effect. In contrast with the induction of GST Yp, the expression of the GST isoforms Ya and Yb was not changed by amino acid restriction. In conclusion, hepatic GST Yp gene expression is upregulated by a limited availability of sulfur amino acids.
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Affiliation(s)
- Chia-Wen Tsai
- Department of Nutrition, Chung Shan Medical University, Taichung, Taiwan
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20
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Ronchi VP, Conde RD, Guillemot JC, Sanllorenti PM. The mouse liver content of carbonic anhydrase III and glutathione S-tranferases A3 and P1 depend on dietary supply of methionine and cysteine. Int J Biochem Cell Biol 2005; 36:1993-2004. [PMID: 15203113 DOI: 10.1016/j.biocel.2004.02.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2003] [Revised: 02/20/2004] [Accepted: 02/25/2004] [Indexed: 11/23/2022]
Abstract
The contents of glutathione S-transferase (GST) subunits, carbonic anhydrase III (CAIII), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a 230 kDa protein are affected by protein deprivation in mouse liver. In order to know if particular amino acids control these contents, the effects of feeding for 5 days with diets containing different amino acids were examined. After an exploration using SDS-PAGE analysis, the action of selected diets was further examined by distinct techniques. The 230 kDa protein was identified as fatty acid synthase (FAS) by both mass spectrometry and amino acid sequence analyses. Dietary tests showed that: (1) a protein-free diet (PFD) increased the content of glutathione S-transferases P1 and M1, and glyceraldehyde-3-phosphate dehydrogenase, while the content of glutathione S-transferase A3, fatty acid synthase and carbonic anhydrase III decreased; (2) a protein-free diet having either methionine or cysteine preserved the normal contents of glutathione S-transferases P1, A3, M1 and carbonic anydrase III; (3) a protein-free diet having threonine preserved partially the normal contents of glutathione S-transferases P1, A3, M1 and carbonic anhydrase III; (4) a protein-free diet having methionine, threonine and cysteine prevented in part the loss of fatty acid synthase; and (5) the glyceraldehyde-3-phosphate dehydrogenase content was controlled by increased carbohydrate level and/or by lower amino acid content of diets, but not by any specific amino acid. These data indicate that methionine and cysteine exert a main role on the control of liver glutathione S-transferases A3 and P1, and carbonic anhydrase III. Thus, they emerge necessary to prevent unsafe alterations of liver metabolism caused by protein deprivation.
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Affiliation(s)
- Virginia Paola Ronchi
- Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, C.C. 1245, B7600GTQ Mar del Plata, Argentina.
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21
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Humphrey BD, Stephensen CB, Calvert CC, Klasing KC. Glucose and cationic amino acid transporter expression in growing chickens (Gallus gallus domesticus). Comp Biochem Physiol A Mol Integr Physiol 2004; 138:515-25. [PMID: 15369841 DOI: 10.1016/j.cbpb.2004.06.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Revised: 06/23/2004] [Accepted: 06/23/2004] [Indexed: 11/25/2022]
Abstract
Tissue glucose transporter (GLUT1-3) and cationic amino acid transporter (CAT1-3) mRNA expression was determined in growing broiler chicks posthatch. In two experiments, tissues were either collected on days 1, 3 and 7 or days 1 and 14 posthatch. Heart and liver were the only tissues expressing a GLUT isoform on day 1. All tissues expressed a GLUT isoform on day 7 except for the thymus. Most tissues expressing a CAT isoform on day 1 decreased mRNA levels through day 7 (P<0.05), except for bursa CAT-1 which tended to increase (P=0.05). The thymus and spleen did not express any CAT isoform mRNA until day 7. The liver was the only tissue expressing GLUT-2 mRNA through day 14. On day 14, GLUT-1, CAT-1 and CAT-2 mRNA were differentially expressed across tissues (P<0.05). High-affinity GLUT and CAT mRNA expression was highest in the heart and bursa, respectively (P<0.05). Total CAT mRNA expression was greatest in the bursa (P<0.05). The thymus had the lowest high affinity GLUT and total CAT mRNA expression on day 14 posthatch. Therefore, T lymphocytes within the thymus may be most susceptible to glucose and cationic amino acid supply.
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Affiliation(s)
- Brooke D Humphrey
- Department of Animal Science, University of California, 1 Shields Avenue, Davis, CA 95616, USA
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22
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Gietzen DW, Ross CM, Hao S, Sharp JW. Phosphorylation of eIF2alpha is involved in the signaling of indispensable amino acid deficiency in the anterior piriform cortex of the brain in rats. J Nutr 2004; 134:717-23. [PMID: 15051816 DOI: 10.1093/jn/134.4.717] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Sensing of indispensable amino acid (IAA) deficiency, an acute challenge to protein homeostasis, is demonstrated by rats as rejection of IAA-deficient diets within 20 min. The anterior piriform cortex (APC) of the brain in rats and birds is essential for this nutrient sensing, and is activated by IAA deficiency. Yet the mechanisms that sense and transduce IAA reduction to signaling in the APC, or indeed in any animal cells, are unknown. Because rejection of a deficient diet within 20 min is too rapid to be explained by transcription-derived signals, brain tissue was taken from rats after 20 min access to either a threonine-basal, -devoid, or -corrected diet and examined for proteins associated with early signaling of IAA deficiency in the yeast model. Western blots and immunohistochemistry showed that the phosphorylation of eukaryotic initiation factor 2-alpha (p-eIF2alpha[Ser51]) and translation of its downstream product, c-Jun, were increased (47%, P < 0.005, and 55%, P < 0.025, respectively) in APC from rats offered devoid, but not corrected diets, compared with those offered basal diets. This was not seen in other brain areas. In cells intensely labeled for cytoplasmic p-eIF2alpha, there was intense fluorescence for c-Jun in the nucleus. Thus, p-eIF2alpha, which is pivotal in the initiation of global protein translation, and its downstream product, the leucine zipper protein, c-Jun, are increased in the mammalian APC within the time frame necessary for the behavioral response. We suggest that p-eIF2alpha and c-Jun participate in signaling nutrient deficiency in the IAA-sensitive neurons of the APC.
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Affiliation(s)
- Dorothy W Gietzen
- Department of Anatomy, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA.
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23
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Ferreira F, Barbosa HCL, Stoppiglia LF, Delghingaro-Augusto V, Pereira EA, Boschero AC, Carneiro EM. Decreased insulin secretion in islets from rats fed a low protein diet is associated with a reduced PKAalpha expression. J Nutr 2004; 134:63-7. [PMID: 14704294 DOI: 10.1093/jn/134.1.63] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A low protein diet has been shown to affect the amount and activity of several enzymes and to decrease insulin secretion by islets isolated from rats fed such a diet. To understand the mechanisms involved in this phenomenon, we investigated the effects of forskolin, a stimulator of adenylyl cyclase, on insulin secretion by pancreatic islets from rats fed a normal (17%; NP) or low (6%; LP) protein diet for 8 wk. Isolated islets were incubated for 1 h in Krebs-bicarbonate solution containing 8.3 mmol glucose/L, with or without 10 micromol forskolin/L. The forskolin-induced insulin secretion was higher in islets from NP rats than in those from LP rats (P<0.05). Western blotting revealed that the amount of the alpha catalytic subunit of protein kinase A (PKAalpha) was 35% lower in islets from LP rats than in islets from NP rats (P<0.05). Moreover, PKAalpha mRNA expression was reduced by 30% in islets from LP rats (P<0.05). Our results indicated a possible relationship between a low protein diet and a reduction in PKAalpha expression. These alterations in PKAalpha may be responsible in part for the decreased insulin secretion by islets from rats fed a low protein diet.
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Affiliation(s)
- Fabiano Ferreira
- Departamento de Fisiologia e Biofísica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
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24
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Jousse C, Averous J, Bruhat A, Carraro V, Mordier S, Fafournoux P. Amino acids as regulators of gene expression: molecular mechanisms. Biochem Biophys Res Commun 2004; 313:447-52. [PMID: 14684183 DOI: 10.1016/j.bbrc.2003.07.020] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Regulation of gene expression by nutrients in mammals is an important mechanism allowing them to adapt their physiological functions according to the supply of nutrient in the diet. It has been shown recently that amino acids are able to regulate by themselves the expression of numerous genes. CHOP, asparagine synthetase, and IGFBP-1 regulation following AA starvation will be described in this review with special interest in the molecular mechanisms involved.
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Affiliation(s)
- Céline Jousse
- Unité de Nutrition et Métabolisme Protéique, Institut National de la Recherche Agronomique de Theix, 63122 Saint Genès Champanelle, France
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25
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Affiliation(s)
- R Pieters
- University Medical Center Rotterdam, Sophia Childrens Hospital, Pediatric Oncology/Hematology, Rotterdam, The Netherlands.
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26
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Claeyssens S, Gangneux C, Brasse-Lagnel C, Ruminy P, Aki T, Lavoinne A, Salier JP. Amino acid control of the human glyceraldehyde 3-phosphate dehydrogenase gene transcription in hepatocyte. Am J Physiol Gastrointest Liver Physiol 2003; 285:G840-9. [PMID: 12842822 DOI: 10.1152/ajpgi.00060.2003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Glutamine (Gln) is the most potent of the amino acids (AAs) that regulate liver anabolism, and its effect is similar to that of insulin in peripheral tissues. However, the influence of AAs on regulation of metabolic enzyme-encoding genes is not known at the molecular level in liver. We now report that Gln and some essential AAs activate the human GAPDH gene that codes for GAPDH, a central enzyme of glycolysis and a target for insulin regulation. In HepG2 cells, Gln upregulated the GAPDH mRNA level, and this effect was additive to that of insulin. Transient transfection of GAPDH promoter/cat constructs demonstrated that a gene-specific and insulin-independent transcriptional step is involved in the Gln responsiveness of GAPDH. Transfected HepG2 cells challenged with various AAs, Gln metabolites or inhibitors of Gln metabolism showed that the Gln-induced effect is similar to that of some essential AAs and that Gln metabolism is a necessary step for GAPDH activation. Deletion mutants and site-directed mutagenesis of the GAPDH promoter indicated that the Gln responsiveness is mediated by a sequence that is distinct from insulin-responsive elements and from positively acting elements previously described in this promoter. This motif located at -126/-118 clearly differs from AA-responsive elements recently identified in other genes. Electromobility shift assay and supershifts showed that the transcription factors bound to the Gln-responsive element in the GAPDH promoter are C/EBPalpha and -delta. This finding is consistent with the role of C/EBP family members in controlling the hepatic expression of genes involved in nutrient metabolism.
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Affiliation(s)
- Sophie Claeyssens
- Faculté de Médecine-Pharmacie, 22 Bvd Gambetta, 76183 Rouen cedex, France.
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27
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Pan Y, Chen H, Siu F, Kilberg MS. Amino acid deprivation and endoplasmic reticulum stress induce expression of multiple activating transcription factor-3 mRNA species that, when overexpressed in HepG2 cells, modulate transcription by the human asparagine synthetase promoter. J Biol Chem 2003; 278:38402-12. [PMID: 12881527 DOI: 10.1074/jbc.m304574200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription from the ASNS (asparagine synthetase) gene is increased in response to either amino acid (amino acid response) or glucose (endoplasmic reticulum stress response) deprivation. These two independent pathways converge on the same set of genomic cis-elements within the ASNS promoter, referred to as nutrient-sensing response element-1 and -2. Chromatin immunoprecipitation analysis provides the first in vivo evidence for activating transcription factor (ATF)-3 binding to the proximal ASNS promoter containing the nutrient-sensing response element-1 sequence. Overexpression of the full-length ATF3 protein caused a concentration-dependent biphasic response in ASNS promoter-driven transcription. Both amino acid limitation and activation of the endoplasmic reticulum stress response by glucose deprivation caused an increase in ATF3 mRNA content. However, reverse transcriptase-PCR analysis revealed that the increase in the ATF3 mRNA species detected by Northern analysis actually encoded both full-length ATF3 and two predicted truncated ATF3 isoforms (ATF3deltaZip2c and ATF3deltaZip3). Based on sequence analysis, one of the predicted truncated proteins (ATF3deltaZip3) is likely incapable of binding DNA; and yet, exogenous expression of the cDNA enhanced starvation-induced or ATF4-activated ASNS transcription, possibly by sequestering corepressor proteins. Collectively, the results provide evidence for a potential role of multiple predicted ATF3 isoforms in the transcriptional regulation of the ASNS gene in response to nutrient deprivation.
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Affiliation(s)
- YuanXiang Pan
- Department of Biochemistry and Molecular Biology, Centers for Mammalian Genetics and Nutritional Sciences, University of Florida College of Medicine, Gainesville, Florida 32610-0245, USA
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28
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Blais A, Huneau JF, Magrum LJ, Koehnle TJ, Sharp JW, Tomé D, Gietzen DW. Threonine deprivation rapidly activates the system A amino acid transporter in primary cultures of rat neurons from the essential amino acid sensor in the anterior piriform cortex. J Nutr 2003; 133:2156-64. [PMID: 12840171 DOI: 10.1093/jn/133.7.2156] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Omnivores show recognition of essential (indispensable) amino acid deficiency by changing their feeding behavior within 20 min, yet the cellular mechanisms of amino acid sensation in eukaryotes are poorly understood. The anterior piriform cortex (APC) of the brain in rats or its analog in birds likely houses the in vivo amino acid chemosensor. Because amino acid transporters adapt rapidly to essential amino acid deficiency in several cell models, we hypothesized that activation of electrogenic amino acid transport in APC neurons might contribute to the function of the amino acid sensor. We evaluated transport systems in primary cultures of neurons from the APC, hippocampus and cerebellum, or glia, incubated in complete or threonine-devoid (deficient) medium. After 10 min in deficient medium, uptake of threonine or a system A-selective substrate, methyl amino-isobutyric acid, was increased 60% in APC neurons only (P < 0.05). These results demonstrated upregulation of system A, an electrogenic amino acid-sodium symporter. This depletion-induced activation required sodium, intact intracellular trafficking, and phosphorylation of signal transduction-related kinases. Efflux studies showed that other transporter types were functional in the APC; they appeared to be altered dynamically in threonine-deficient cells in response to rapid increases in system A activity. The present data provided support for the chemical sensitivity of the APC and its role as the brain area housing the indispensable amino acid chemosensor. They also showed a region-specific, phosphorylation-dependent activation of the system A transporter in the brain in response to threonine deficiency.
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Affiliation(s)
- Anne Blais
- Institut National de la Research Agronomique, Unité de Physiologie de la Nutrition et du Comportement Alimentaire, Paris, France
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29
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Averous J, Bruhat A, Mordier S, Fafournoux P. Recent advances in the understanding of amino acid regulation of gene expression. J Nutr 2003; 133:2040S-2045S. [PMID: 12771362 DOI: 10.1093/jn/133.6.2040s] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In mammals, the impact of nutrients on gene expression has become an important area of research. Because amino acids have multiple and important functions, their homeostasis has to be finely maintained. However, amino acidemia can be affected by certain nutritional conditions or various forms of stress. Consequently, mammals must adjust several of the physiological functions involved in the adaptation to amino acid availability by regulating expression of numerous genes. It has been shown that amino acids alone can modify the expression of target genes. However, understanding of amino acid-dependent control of gene expression has just started to emerge. This review focuses on recent advances in the understanding of mechanisms involved in the amino acid control of gene expression.
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Affiliation(s)
- Julien Averous
- Unité de Nutrition et Métabolisme Protéique, Institut National de la Recherche Agronomique de Theix, 63122 Saint Genès Champanelle, France
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30
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Zhong C, Chen C, Kilberg MS. Characterization of the nutrient-sensing response unit in the human asparagine synthetase promoter. Biochem J 2003; 372:603-9. [PMID: 12628003 PMCID: PMC1223424 DOI: 10.1042/bj20030076] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2003] [Revised: 02/25/2003] [Accepted: 03/10/2003] [Indexed: 11/17/2022]
Abstract
Transcription from the human asparagine synthetase (A.S.) gene is increased in response to either amino acid (amino acid response) or glucose (endoplasmic reticulum stress response) deprivation. These two independent nutrient-sensing pathways converge on the same set of genomic cis -elements, referred to as nutrient sensing-response elements (NSREs) 1 and 2, within the A.S. promoter. The present report uses single-nucleotide mutagenesis to confirm that both NSRE-1 and NSRE-2 are absolutely required for gene activation and to identify the boundaries of each binding site. The core sequence of the NSRE-1 site is contained within nucleotides -68 to -60 and the NSRE-2 core sequence is within nucleotides -48 to -43. Through insertion or deletion of 5-10 nucleotides in the intervening sequence between NSRE-1 and NSRE-2, transient transfection studies with an A.S. promoter/reporter gene construct showed that the 11 bp distance between these two elements is critical. These results document that the optimal configuration is with both binding sites on the same side of the DNA helix, only one helical turn away from each other and the data provide support for the hypothesis that a larger multi-protein complex exists between the binding proteins for NSRE-1 and NSRE-2. The data also illustrate that the combination of NSRE-1 and NSRE-2, referred to as the nutrient-sensing response unit (NSRU), has enhancer activity in that it functions in an orientation- and position-independent manner, and conveys nutrient-dependent transcriptional control to a heterologous promoter.
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Affiliation(s)
- Can Zhong
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Box 100245, Gainesville 32610-0245, USA
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31
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Bruhat A, Averous J, Carraro V, Zhong C, Reimold AM, Kilberg MS, Fafournoux P. Differences in the molecular mechanisms involved in the transcriptional activation of the CHOP and asparagine synthetase genes in response to amino acid deprivation or activation of the unfolded protein response. J Biol Chem 2002; 277:48107-14. [PMID: 12351626 DOI: 10.1074/jbc.m206149200] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A promoter element called the amino acid response element (AARE), which is essential for the induction of CHOP (a CCAAT/enhancer-binding protein-related gene) transcription by amino acid depletion, has been previously characterized. Conversely, the human asparagine synthetase (AS) promoter contains two cis-acting elements termed nutrient-sensing response elements (NSRE-1 and NSRE-2) that are required to activate the gene by either amino acid deprivation or the endoplasmic reticulum stress response. The results reported here document the comparison between CHOP and AS transcriptional control elements used by the amino acid pathway. We first establish that the AS NSRE-1 sequence shares nucleotide sequence and functional similarities with the CHOP AARE. However, we demonstrate that the CHOP AARE can function independently, whereas AS NSRE-1 is functionally weak by itself and instead requires the presence of NSRE-2. Furthermore, AS NSRE-2 can confer endoplasmic reticulum stress responsiveness to the CHOP AARE. Using activating transcription factor-2-deficient mouse embryonic fibroblasts, we also show that lack of this transcription factor does not abolish the amino acid inducibility of AS transcription, but this transcription factor is necessary to obtain the full AS response to amino acid starvation. Collectively, these results document that there are significant differences in the molecular mechanisms involved in the transcriptional activation of CHOP and AS by amino acid limitation.
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Affiliation(s)
- Alain Bruhat
- Unité de Nutrition et Métabolisme Protéique, Institut National de la Recherche Agronomique de Theix, 63122 Saint Genès Champanelle, France.
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32
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Schwerin M, Dorroch U, Beyer M, Swalve H, Metges CC, Junghans P. Dietary protein modifies hepatic gene expression associated with oxidative stress responsiveness in growing pigs. FASEB J 2002; 16:1322-4. [PMID: 12154008 DOI: 10.1096/fj.01-0734fje] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Understanding the basis for differences in nutrient requirements and for nutrient effects on health and performance requires an appreciation of the links between nutrition and gene expression. We developed and applied molecular probes to characterize diet-associated postabsorptive hepatic gene expression in growing pigs chronically fed protein-restricted diets based on either casein (CAS) or soy protein isolate (SPI). Eighty-eight expressed sequence tags (ESTs) were identified on the basis of diet-related changes in expression, by using an mRNA differential display method. Expression profiling based on transcription analysis by real-time reverse transcriptase-polymerase chain reaction showed that the SPI diet significantly changed the pattern of gene expression as compared with the CAS diet and allowed identification of coregulated genes. The expression of six genes involved in the metabolism of stress response (glutathione S-transferase, peptide methionine sulfoxide reductase, apolipoprotein A-I, organic anion transport polypeptide 2, calnexin, heat shock transcription factor 1) exhibited significant changes in the transcription level and indicated an increased oxidative stress response in pigs fed the SPI diet. Hierarchical clustering of gene expression data of all 33 ESTs analyzed across 14 pigs fed the two different diets resulted in clustering of genes related to the oxidative stress response with genes related to the regulation of gene expression and neuronal signaling.
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Affiliation(s)
- Manfred Schwerin
- Research Units Molecular Biology, Research Institute for the Biology of Farm Animals, D-18196 Dummerstorf; Germany.
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33
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Siu F, Bain PJ, LeBlanc-Chaffin R, Chen H, Kilberg MS. ATF4 is a mediator of the nutrient-sensing response pathway that activates the human asparagine synthetase gene. J Biol Chem 2002; 277:24120-7. [PMID: 11960987 DOI: 10.1074/jbc.m201959200] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription from the asparagine synthetase (A.S.) gene is increased in response to either amino acid (amino acid response) or glucose (endoplasmic reticulum stress response) deprivation. These two independent pathways converge on the same set of genomic cis-elements within the A.S. promoter referred to as nutrient-sensing response elements (NSRE) 1 and 2, both of which are necessary for gene activation. The NSRE-1 sequence was used to screen ATF/CREB family members by electrophoresis mobility shift assays and supershift by specific antibodies. The results indicated that ATF4 binds to the NSRE-1 sequence and that the amount of the ATF4 complex was increased when extracts from amino acid-deprived or glucose-deprived cells were tested. Using electrophoresis mobility shift assay experiments and a probe that contained both NSRE-1 and NSRE-2, mutation of the NSRE-1 sequence completely prevented formation of the ATF4-containing complexes, whereas mutation of the NSRE-2 sequence did not. Overexpression of ATF4 increased A.S. promoter-driven transcription, whereas an inhibitory dominant negative ATF4 mutant blocked both basal and starvation-enhanced transcription. Collectively, the results provide both in vitro and in vivo evidence for a role of ATF4 in the transcriptional activation of the A.S. gene in response to nutrient deprivation.
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Affiliation(s)
- Fai Siu
- Department of Biochemistry and Molecular Biology, Center for Mammalian Genetics, and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, Florida 32610-0245, USA
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Rodriguez PC, Zea AH, Culotta KS, Zabaleta J, Ochoa JB, Ochoa AC. Regulation of T cell receptor CD3zeta chain expression by L-arginine. J Biol Chem 2002; 277:21123-9. [PMID: 11950832 DOI: 10.1074/jbc.m110675200] [Citation(s) in RCA: 350] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
L-Arg plays a central role in the normal function of several organ systems including the immune system. L-Arg can be depleted by arginase I produced by macrophages and hepatocytes in several disease states such as trauma and sepsis and following liver transplantation. The decrease in L-Arg levels induces a profound decrease in T cell function through mechanisms that have remained unclear. The data presented here demonstrate that Jurkat T cells cultured in medium without L-Arg (L-Arg-free RPMI) have a rapid decrease in the expression of the T cell antigen receptor zeta chain (CD3zeta), the principal signal transduction element in this receptor, and a decrease in T cell proliferation. This phenomenon is completely reversed by the replenishment of L-Arg but not other amino acids. These changes are not caused by cell apoptosis; instead, the diminished expression of CD3zeta protein is paralleled by a decrease in CD3zeta mRNA. This change in CD3zeta mRNA expression is not caused by a decrease in the transcription rate but rather by a significantly shorter CD3zeta mRNA half-life. This mechanism is sensitive to cycloheximide. Therefore, the regulation of L-Arg concentration in the microenvironment could represent an important mechanism to modulate the expression of CD3zeta and the T cell receptor and consequently of T cell function.
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Affiliation(s)
- Paulo C Rodriguez
- Tumor Immunology Program, Stanley S. Scott Cancer Center and Department of Pediatrics, Louisiana State University, Health Sciences Center, New Orleans, Louisiana 70112, USA
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Mordier S, Bruhat A, Averous J, Fafournoux P. Cellular Adaptation to Amino Acid Availability: Mechanisms Involved in the Regulation of Gene Expression and Protein Metabolism. CELL AND MOLECULAR RESPONSE TO STRESS 2002. [DOI: 10.1016/s1568-1254(02)80015-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Siu F, Chen C, Zhong C, Kilberg MS. CCAAT/enhancer-binding protein-beta is a mediator of the nutrient-sensing response pathway that activates the human asparagine synthetase gene. J Biol Chem 2001; 276:48100-7. [PMID: 11677247 DOI: 10.1074/jbc.m109533200] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription from the human asparagine synthetase (AS) gene is increased in response to either amino acid (amino acid response) or glucose (unfolded protein response) deprivation. These two independent pathways converge on the same set of genomic cis-elements within the AS promoter, which are referred to as nutrient-sensing response element (NSRE)-1 and -2, both of which are absolutely necessary for gene activation. The NSRE-1 sequence was used to identify the corresponding transcription factor by yeast one-hybrid screening. Based on those results, electrophoretic mobility shift assays for individual CCAAT/enhancer-binding protein-beta (C/EBP) family members were performed to test for supershifting of complexes by specific antibodies. The results indicated that of all the family members, C/EBPbeta bound to the NSRE-1 sequence to the greatest extent and that the absolute amount of this complex was increased when extracts from amino acid- or glucose-deprived cells were tested. Using electrophoretic mobility shift assays, mutation of the NSRE-1 sequence completely prevented formation of the C/EBPbeta-containing complexes. In contrast, mutation of the NSRE-2 sequence did not block C/EBPbeta binding. Overexpression in HepG2 hepatoma cells of the activating isoform of C/EBPbeta increased AS promoter-driven transcription, whereas the inhibitory dominant-negative isoform of C/EBPbeta blocked enhanced transcription following amino acid or glucose deprivation. Collectively, the results provide both in vitro and in vivo evidence for a role of C/EBPbeta in the transcriptional activation of the AS gene in response to nutrient deprivation.
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Affiliation(s)
- F Siu
- Department of Biochemistry, Centers for Mammalian Genetics and Nutritional Sciences, University of Florida College of Medicine, Gainesville, Florida 32610-0245, USA
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Bruhat A, Fafournoux P. Recent advances on molecular mechanisms involved in amino acid control of gene expression. Curr Opin Clin Nutr Metab Care 2001; 4:439-43. [PMID: 11568507 DOI: 10.1097/00075197-200109000-00016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In mammals, the impact of nutrients on gene expression has become an important area of research. Because amino acids have multiple and important functions, their homeostasis has to be finely maintained. However, amino acidaemia can be affected by certain nutritional conditions or various forms of aggression. It follows that mammals have to adjust several of their physiological functions involved in the adaptation to amino acid availability by regulating the expression of numerous genes. It has been shown that amino acids by themselves can modify the expression of target genes. However, the current understanding of amino acid-dependent control of gene expression has just started to emerge. This review focuses on the recent advances on mechanisms involved in the amino acids control of gene expression. Several examples discussed in this paper demonstrate that amino acids regulate gene expression at the level of transcription, messenger RNA stability and translation.
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Affiliation(s)
- A Bruhat
- Unité de Nutrition Cellulaire et Moléculaire, INRA de Theix, 63122 Saint Genès Champanelle, France
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Franchi-Gazzola R, Visigalli R, Dall'Asta V, Sala R, Woo SK, Kwon HM, Gazzola GC, Bussolati O. Amino acid depletion activates TonEBP and sodium-coupled inositol transport. Am J Physiol Cell Physiol 2001; 280:C1465-74. [PMID: 11350742 DOI: 10.1152/ajpcell.2001.280.6.c1465] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The expression of the osmosensitive sodium/myo-inositol cotransporter (SMIT) is regulated by multiple tonicity-responsive enhancers (TonEs) in the 5'-flanking region of the gene. In response to hypertonicity, the nuclear abundance of the transcription factor TonE-binding protein (TonEBP) is increased, and the transcription of the SMIT gene is induced. Transport system A for neutral amino acids, another osmosensitive mechanism, is progressively stimulated if amino acid substrates are not present in the extracellular compartment. Under this condition, as in hypertonicity, cells shrink and mitogen-activated protein kinases are activated. We demonstrate here that a clear-cut nuclear redistribution of TonEBP, followed by SMIT expression increase and inositol transport activation, is observed after incubation of cultured human fibroblasts in Earle's balanced salts (EBSS), an isotonic, amino acid-free saline. EBSS-induced SMIT stimulation is prevented by substrates of system A, although these compounds do not compete with inositol for transport through SMIT. We conclude that the incubation in isotonic, amino acid-free saline triggers an osmotic stimulus and elicits TonEBP-dependent responses like hypertonic treatment.
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Affiliation(s)
- R Franchi-Gazzola
- Dipartimento di Medicina Sperimentale, Sezione di Patologia Generale e Clinica, Università degli Studi di Parma, Via Volturna, 39, 43100 Parma, Italy.
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Abstract
The impact of nutrients on gene expression in mammals has become an important area of research. Nevertheless, the current understanding of the amino acid-dependent control of gene expression is limited. Because amino acids have multiple and important functions, their homoeostasis has to be finely maintained. However, amino-acidaemia can be affected by certain nutritional conditions or various forms of stress. It follows that mammals have to adjust several of their physiological functions involved in the adaptation to amino acid availability by regulating the expression of numerous genes. The aim of the present review is to examine the role of amino acids in regulating mammalian gene expression and protein turnover. It has been reported that some genes involved in the control of growth or amino acid metabolism are regulated by amino acid availability. For instance, limitation of several amino acids greatly increases the expression of the genes encoding insulin-like growth factor binding protein-1, CHOP (C/EBP homologous protein, where C/EBP is CCAAT/enhancer binding protein) and asparagine synthetase. Elevated mRNA levels result from both an increase in the rate of transcription and an increase in mRNA stability. Several observations suggest that the amino acid regulation of gene expression observed in mammalian cells and the general control process described in yeast share common features. Moreover, amino acid response elements have been characterized in the promoters of the CHOP and asparagine synthetase genes. Taken together, the results discussed in the present review demonstrate that amino acids, by themselves, can, in concert with hormones, play an important role in the control of gene expression.
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Affiliation(s)
- P Fafournoux
- Unité de Nutrition Cellulaire et Moléculaire, INRA de Theix, 63122 Saint Genès Champanelle, France.
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