scholarly journals mTORC1/NF-κB axis controls amino acid catabolism by regulating the expression of the key enzymes in human hepatocytes

2020 ◽  
Author(s):  
Meng Zhang ◽  
Yuting Fu ◽  
Yuhao Chen ◽  
Yuze Ma ◽  
Zhixin Guo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Mrna Level ◽  
Building Blocks ◽  
Human Hepatocytes ◽  
Acid Decarboxylase ◽  
Amino Acid Catabolism ◽  
Qrt Pcr ◽  
Mechanistic Target Of Rapamycin ◽  
Intracellular Content ◽  
Genes Expression

Abstract Background In addition to serving as building blocks for protein synthesis, amino acids also provide energy and precursors that are used by cells through catabolism. Mechanistic target of rapamycin complex 1 (mTORC1) is a central coordinator of cellular metabolism. However, little is known regarding the function of mTORC1 in amino acid catabolism. The aims of this study were to explore the mechanism by which mTORC1 controls the conversion of glutamate to α-ketoglutarate and ornithine to putrescine, and mTORC1 regulates the expression amino acid catabolism-related genes in hepatocyte. Methods HL-7702 hepatocytes were treated with glutamate, ornithine, rapamycin or SC75741, alone or in combination; the plasmids pRNAT-U6.1/Neo-shRaptor and pIRES2-EGFP-Rheb were transfected into HL-7702 cells to silencing Raptor or overexpressing Rheb . The intracellular content of glutamate, oxaloacetate, α-ketoglutaric acid, and aspartic acid, and the intracellular level of aspartate aminotransferase (AST), ornithine decarboxylase (ODC), glutamate dehydrogenase (GDH), and glutamic acid decarboxylase (GAD) were measured by ELISA. The concentrations of intracellular ornithine and putrescine were measured by HPLC. The mRNA level of amino acid catabolism-related genes was detected by qRT-PCR, and the protein level of mTORC1 and NF-κB was investigated by western blot. Results Our data showed that rapamycin inhibits the utilization of glutamate and ornithine in HL-7702 hepatocytes. mTORC1 regulates the expression of AST and ODC through the transcription factor NF-κB in response to glutamate or ornithine. Further, inactivated mTORC1 by Raptor silencing downregulated the expression of AST , ODC , GDH and GAD , while enhanced mTORC1 by Rheb overexpression upregulated NF-κB activation and the indicated genes expression in hepatocytes. Inhibited NF-κB by inhibitor SC75741 decreased the AST , ODC , GDH , and GAD expression. Conclusions Our results demonstrate that mTORC1 regulates amino acid catabolism by inducing the expression of AST , ODC , GDH , and GAD , which is mediated by NF-κB. This finding constitutes a novel mechanism by which amino acid catabolism is regulated in hepatocytes.

scholarly journals Inhibition of the mTORC1/NF-κB Axis Alters Amino Acid Metabolism in Human Hepatocytes

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Meng Zhang ◽  
Yuting Fu ◽  
Yuhao Chen ◽  
Yuze Ma ◽  
Zhixin Guo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Mechanisms ◽  
Building Blocks ◽  
Human Hepatocytes ◽  
Acid Decarboxylase ◽  
Amino Acid Catabolism ◽  
Expression Levels ◽  
Catabolic Genes ◽  
Related Transcription Factor

In addition to serving as the building blocks for protein synthesis, amino acids can be used as an energy source, through catabolism. The transamination, oxidative deamination, and decarboxylation processes that occur during amino acid catabolism are catalyzed by specific enzymes, including aspartate aminotransferase (AST), glutamate dehydrogenase (GDH), glutamic acid decarboxylase (GAD), and ornithine decarboxylase (ODC); however, the overall molecular mechanisms through which amino acid catabolism occurs remain largely unknown. To examine the role of mechanistic target of rapamycin complex 1 (mTORC1) on amino acid catabolism, mTORC1 was inactivated by rapamycin or shRNA targeting Raptor, versus activated by overexpressing Rheb or amino acids in human hepatocytes. The expression of amino acid catabolic genes and related transcription factor was investigated by RT/real-time PCR and western blot analysis. A few types of amino acid metabolite were examined by ELISA and HPLC analysis. The data showed that inactivated mTORC1 resulted in inhibition of NF-κB and the expression of AST, GDH, GAD, and ODC, whereas activated mTORC1 enhanced NF-κB activation and the expression levels of the catabolism-associated genes. Further, inhibition of NF-κB reduced the expression levels of AST, GDH, GAD, and ODC. mTORC1 upregulated NF-κB activation and the expression of AST and ODC in response to glutamate and ornithine treatments, whereas rapamycin inhibited the utilization of glutamate and ornithine in hepatocytes. Taken together, these results indicated that the mTORC1/NF-κB axis modulates the rate of amino acid catabolism by regulating the expression of key catabolic enzymes in hepatocytes.

PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Affan Alim ◽  
Abdul Rafay ◽  
Imran Naseem
Keyword(s):  
Amino Acid ◽  
Dimension Reduction ◽  
Protein Identification ◽  
Cold Water ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antifreeze Proteins ◽  
Building Blocks ◽  
Gradient Boosting ◽  
Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

Axially Chiral Bis(α-amino Acid)s and Their Deamino Analogues. Synthesis and Configurational Assignment

1998 ◽  
Vol 63 (2) ◽  
pp. 211-221 ◽  
Author(s):  
Miloš Tichý ◽  
Luděk Ridvan ◽  
Miloš Buděšínský ◽  
Jiří Závada ◽  
Jaroslav Podlaha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nmr Spectra ◽  
Building Blocks ◽  
X Ray Diffraction ◽  
Amino Groups ◽  
X Ray ◽  
Configurational Assignment ◽  
Symmetry Properties ◽  
Axially Chiral ◽  
Polymeric Structures

The axially chiral bis(α-amino acid)s cis-2 and trans-2 as possible building blocks for polymeric structures of novel type of helicity were prepared. Their configuration has been determined by NMR spectroscopy and, in the case of the trans-isomer, confirmed by single-crystal X-ray diffraction. Analogous pair of stereoisomeric diacids cis-3 and trans-3, devoid of the amino groups, was also prepared and their configuration assigned. The observed differences in the NMR spectra of cis- and trans-isomers of 2 and 3 are discussed from the viewpoint of their different symmetry properties.

Self-assembly of cyclic homo- and hetero-β-peptides with cis- furanoid sugar amino acid and β-hGly as building blocks

2006 ◽  
pp. 4847-4849 ◽  
Author(s):  
Bulusu Jagannadh ◽  
Marepally Srinivasa Reddy ◽  
Chennamaneni Lohitha Rao ◽  
Anabathula Prabhakar ◽  
Bharatam Jagadeesh ◽  
...  
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Building Blocks

scholarly journals AHR-dependent genes and response to MTX therapy in rheumatoid arthritis patients

2021 ◽  
Author(s):  
Anna Wajda ◽  
Ewa Walczuk ◽  
Barbara Stypińska ◽  
Jakub Lach ◽  
Danat Yermakovich ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Lymphoblastic Leukemia ◽  
Mrna Level ◽  
Poor Response ◽  
Evolutionary Analysis ◽  
First Line ◽  
Aryl Hydrocarbon ◽  
First Line Therapy ◽  
Genes Expression ◽  
Ahr Gene

AbstractMethotrexate (MTX) is the first-line therapy for rheumatoid arthritis. Nevertheless, MTX resistance is quite a common issue in clinical practice. There are some premises that aryl hydrocarbon receptor (AhR) gene battery may take part in MTX metabolism. In the present retrospective study, we analyzed genes expression of AHR genes battery associated with MTX metabolism in whole blood of RA patients with good and poor response to MTX treatment. Additionally, sequencing, genotyping and bioinformatics analysis of AHR repressor gene (AHRR) c.565C > G (rs2292596) and c.1933G > C (rs34453673) have been performed. Theoretically, both changes may have an impact on H3K36me3 and H3K27me3. Evolutionary analysis revealed that rs2292596 may be possibly damaging. Allele G in rs2292596 and DAS28 seems to be associated with a higher risk of poor response to MTX treatment in RA. RA patients with poor response to MTX treatment revealed upregulated AhR and SLC19A1 mRNA level. Treatment with IL-6 inhibitor may be helpful to overcome the low-dose MTX resistance. Analysis of gene expression revealed possible another cause of poor response to MTX treatment which is different from that observed in the case of acute lymphoblastic leukemia.

scholarly journals Aromatic L-amino Acid Decarboxylase (AADC) deficiency: results from an Italian modified Delphi consensus

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Carlo Fusco ◽  
◽  
Vincenzo Leuzzi ◽  
Pasquale Striano ◽  
Roberta Battini ◽  
...  
Keyword(s):  
Amino Acid ◽  
Diagnostic Delay ◽  
Steering Committee ◽  
Outcome Data ◽  
Diagnosis And Treatment ◽  
Acid Decarboxylase ◽  
Delphi Consensus ◽  
Amino Acid Decarboxylase ◽  
Modified Delphi ◽  
Number Of Patients

Abstract Background Aromatic L-amino acid decarboxylase (AADC) deficiency is a rare and underdiagnosed neurometabolic disorder resulting in a complex neurological and non-neurological phenotype, posing diagnostic challenges resulting in diagnostic delay. Due to the low number of patients, gathering high-quality scientific evidence on diagnosis and treatment is difficult. Additionally, based on the estimated prevalence, the number of undiagnosed patients is likely to be high. Methods Italian experts in AADC deficiency formed a steering committee to engage clinicians in a modified Delphi consensus to promote discussion, and support research, dissemination and awareness on this disorder. Five experts in the field elaborated six main topics, each subdivided into 4 statements and invited 13 clinicians to give their anonymous feedback. Results 100% of the statements were answered and a consensus was reached at the first round. This enabled the steering committee to acknowledge high rates of agreement between experts on clinical presentation, phenotypes, diagnostic work-up and treatment strategies. A research gap was identified in the lack of standardized cognitive and motor outcome data. The need for setting up an Italian working group and a patients’ association, together with the dissemination of knowledge inside and outside scientific societies in multiple medical disciplines were recognized as critical lines of intervention. Conclusions The panel expressed consensus with high rates of agreement on a series of statements paving the way to disseminate clear messages concerning disease presentation, diagnosis and treatment and strategic interventions to disseminate knowledge at different levels. Future lines of research were also identified.

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