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Barata-Antunes C, Alves R, Talaia G, Casal M, Gerós H, Mans R, Paiva S. Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking. Comput Struct Biotechnol J 2021; 19:1713-37. [PMID: 33897977 DOI: 10.1016/j.csbj.2021.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
Plasma membrane transporters play pivotal roles in the import of nutrients, including sugars, amino acids, nucleobases, carboxylic acids, and metal ions, that surround fungal cells. The selective removal of these transporters by endocytosis is one of the most important regulatory mechanisms that ensures a rapid adaptation of cells to the changing environment (e.g., nutrient fluctuations or different stresses). At the heart of this mechanism lies a network of proteins that includes the arrestin‐related trafficking adaptors (ARTs) which link the ubiquitin ligase Rsp5 to nutrient transporters and endocytic factors. Transporter conformational changes, as well as dynamic interactions between its cytosolic termini/loops and with lipids of the plasma membrane, are also critical during the endocytic process. Here, we review the current knowledge and recent findings on the molecular mechanisms involved in nutrient transporter endocytosis, both in the budding yeast Saccharomyces cerevisiae and in some species of the filamentous fungus Aspergillus. We elaborate on the physiological importance of tightly regulated endocytosis for cellular fitness under dynamic conditions found in nature and highlight how further understanding and engineering of this process is essential to maximize titer, rate and yield (TRY)-values of engineered cell factories in industrial biotechnological processes.
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Key Words
- AAs, amino acids
- ACT, amino Acid/Choline Transporter
- AP, adaptor protein
- APC, amino acid-polyamine-organocation
- Arg, arginine
- Arrestins
- Arts, arrestin‐related trafficking adaptors
- Asp, aspartic acid
- Aspergilli
- Biotechnology
- C, carbon
- C-terminus, carboxyl-terminus
- Cell factories
- Conformational changes
- Cu, copper
- DUBs, deubiquitinating enzymes
- EMCs, eisosome membrane compartments
- ER, endoplasmic reticulum
- ESCRT, endosomal sorting complex required for transport
- Endocytic signals
- Endocytosis
- Fe, iron
- Fungi
- GAAC, general amino acid control
- Glu, glutamic acid
- H+, proton
- IF, inward-facing
- LAT, L-type Amino acid Transporter
- LID, loop Interaction Domain
- Lys, lysine
- MCCs, membrane compartments containing the arginine permease Can1
- MCCs/eisosomes
- MCPs, membrane compartments of Pma1
- MFS, major facilitator superfamily
- MVB, multi vesicular bodies
- Met, methionine
- Metabolism
- Mn, manganese
- N, nitrogen
- N-terminus, amino-terminus
- NAT, nucleobase Ascorbate Transporter
- NCS1, nucleobase/Cation Symporter 1
- NCS2, nucleobase cation symporter family 2
- NH4+, ammonium
- Nutrient transporters
- OF, outward-facing
- PEST, proline (P), glutamic acid (E), serine (S), and threonine (T)
- PM, plasma membrane
- PVE, prevacuolar endosome
- Saccharomyces cerevisiae
- Signaling pathways
- Structure-function
- TGN, trans-Golgi network
- TMSs, transmembrane segments
- TORC1, target of rapamycin complex 1
- TRY, titer, rate and yield
- Trp, tryptophan
- Tyr, tyrosine
- Ub, ubiquitin
- Ubiquitylation
- VPS, vacuolar protein sorting
- W/V, weight per volume
- YAT, yeast Amino acid Transporter
- Zn, Zinc
- fAATs, fungal AA transporters
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Wang D, Li D, Zhang Y, Chen J, Zhang Y, Liao C, Qin S, Tian Y, Zhang Z, Xu F. Functional metabolomics reveal the role of AHR/GPR35 mediated kynurenic acid gradient sensing in chemotherapy-induced intestinal damage. Acta Pharm Sin B 2021; 11:763-80. [PMID: 33777681 DOI: 10.1016/j.apsb.2020.07.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
Intestinal toxicity induced by chemotherapeutics has become an important reason for the interruption of therapy and withdrawal of approved agents. In this study, we demonstrated that chemotherapeutics-induced intestinal damage were commonly characterized by the sharp upregulation of tryptophan (Trp)−kynurenine (KYN)−kynurenic acid (KA) axis metabolism. Mechanistically, chemotherapy-induced intestinal damage triggered the formation of an interleukin-6 (IL-6)−indoleamine 2,3-dioxygenase 1 (IDO1)−aryl hydrocarbon receptor (AHR) positive feedback loop, which accelerated kynurenine pathway metabolism in gut. Besides, AHR and G protein-coupled receptor 35 (GPR35) negative feedback regulates intestinal damage and inflammation to maintain intestinal integrity and homeostasis through gradually sensing kynurenic acid level in gut and macrophage, respectively. Moreover, based on virtual screening and biological verification, vardenafil and linagliptin as GPR35 and AHR agonists respectively were discovered from 2388 approved drugs. Importantly, the results that vardenafil and linagliptin significantly alleviated chemotherapy-induced intestinal toxicity in vivo suggests that chemotherapeutics combined with the two could be a promising therapeutic strategy for cancer patients in clinic. This work highlights GPR35 and AHR as the guardian of kynurenine pathway metabolism and core component of defense responses against intestinal damage.
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Key Words
- 1-MT, 1-methyl-tryptophan
- AG, AG490
- AHR
- AHR, aryl hydrocarbon receptor
- ARNT, aryl hydrocarbon receptor nuclear translocator
- BCA, bicinchoninic acid
- BSA, bovine serum albumin
- CH, CH223191
- CPT-11, irinotecan
- CYP1A1, cytochrome P450 1A1
- DAI, disease activity index
- DMSO, dimethyl sulfoxide
- DPP-4, dipeptidyl peptidase-4
- DRE, dioxin response elements
- DSS, dextran sulphate sodium
- Dens-Cl, N-diethyl-amino naphthalene-1-sulfonyl chloride
- Dns-Cl, N-dimethyl-amino naphthalene-1-sulfonyl chloride
- ECL, enhanced chemiluminescence
- ELISA, enzyme-linked immunosorbent assay
- ERK1/2, extracellular regulated protein kinases 1/2
- ESI, electrospray ionization
- FBS, fetal bovine serum
- GE, gastric emptying
- GFP, green fluorescence protein
- GI, gastrointestinal transit
- GPR35
- GPR35, G protein-coupled receptor 35
- Gradually sensing
- HE, hematoxylin and eosin
- HRP, horseradish peroxi-dase
- IBD, inflammatory bowel disease
- IDO1, indoleamine 2,3-dioxygenase 1
- IL-6, interleukin-6
- IS, internal standard
- Intestinal toxicity
- JAK2, janus kinase 2
- KA, kynurenic acid
- KAT, kynurenine aminotransferase
- KYN, kynurenine
- Kynurenine pathway
- LC–MS, liquid chromatography–mass spectrometry
- LPS, lipopolysaccharides
- Linag, linagliptin
- MOE, molecular operating environment
- MOI, multiplicity of infection
- MRM, multiple-reaction monitoring
- MTT, thiazolyl blue tetrazolium bromide
- PBS, phosphate buffer saline
- PDB, protein data bank
- PDE5, phosphodiesterase type-5
- PF, PF-04859989
- PMA, phorbol 12-myristate 13-acetate
- PMSF, phenylmethylsulfonyl fluoride
- RIPA, radioimmunoprecipitation
- RPKM, reads per kilobase per million mapped reads
- RPMI 1640, Roswell Park Memorial Institute 1640
- RT-PCR, real-time polymerase chain reaction
- STAT3, signal transducer and activator of transcription 3
- Trp, tryptophan
- VCR, vincristine
- Vard, vardenafil
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Gao Y, Li W, Chen J, Wang X, Lv Y, Huang Y, Zhang Z, Xu F. Pharmacometabolomic prediction of individual differences of gastrointestinal toxicity complicating myelosuppression in rats induced by irinotecan. Acta Pharm Sin B 2019; 9:157-166. [PMID: 30766787 PMCID: PMC6362258 DOI: 10.1016/j.apsb.2018.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/21/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022] Open
Abstract
Pharmacometabolomics has been already successfully used in toxicity prediction for one specific adverse effect. However in clinical practice, two or more different toxicities are always accompanied with each other, which puts forward new challenges for pharmacometabolomics. Gastrointestinal toxicity and myelosuppression are two major adverse effects induced by Irinotecan (CPT-11), and often show large individual differences. In the current study, a pharmacometabolomic study was performed to screen the exclusive biomarkers in predose serums which could predict late-onset diarrhea and myelosuppression of CPT-11 simultaneously. The severity and sensitivity differences in gastrointestinal toxicity and myelosuppression were judged by delayed-onset diarrhea symptoms, histopathology examination, relative cytokines and blood cell counts. Mass spectrometry-based non-targeted and targeted metabolomics were conducted in sequence to dissect metabolite signatures in predose serums. Eventually, two groups of metabolites were screened out as predictors for individual differences in late-onset diarrhea and myelosuppression using binary logistic regression, respectively. This result was compared with existing predictors and validated by another independent external validation set. Our study indicates the prediction of toxicity could be possible upon predose metabolic profile. Pharmacometabolomics can be a potentially useful tool for complicating toxicity prediction. Our findings also provide a new insight into CPT-11 precision medicine.
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Key Words
- AUC-ROC, area under receiver operating characteristic
- BHB, β-hydroxybutyric acid
- Biomarkers
- C, control group
- CA, cholic acid
- CPT-11, irinotecan
- Complicating toxicity
- DBIL, direct bilirubin
- DCA, deoxycholic acid
- Diarrhea
- FDR, false discovery rate
- GCA, glycocholic acid
- Gastrointestinal toxicity
- IBIL, indirect bilirubin
- IT-TOF/MS, ion trap/time-offlight hybrid mass spectrometry
- Individual differences
- Irinotecan
- Lys, lysine
- MSTFA, N-methyl-N-trifluoroacetamide
- Metabolomics
- NS, non-sensitive group
- NSgt, non-sensitive for gastrointestinal toxicity
- NSmt, non-sensitive for myelosuppression toxicity
- OPLS-DA, orthogonal partial least-squares-discriminant analysis
- PCA, principal component analysis
- PLS-DA, partial least-squares-discriminant analysis
- Phe, phenylalanine
- Prediction
- QC, quality control
- RSD, relative standard deviation
- S, sensitive group
- Sgt, sensitive for gastrointestinal toxicity
- Smt, sensitive for myelosuppression toxicity
- T, CPT-11 treated group
- Trp, tryptophan
- UFLC, ultrafast liquid chromatography
- VIP, variable importance in the projection
- pFDR, false-discovery-rate-adjusted P value
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Affiliation(s)
- Yiqiao Gao
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Wei Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Jiaqing Chen
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Xu Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Yingtong Lv
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Yin Huang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Zunjian Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
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Abstract
Preclinical and clinical studies have shown bidirectional interactions within the brain-gut-microbiome axis. Gut microbes communicate to the central nervous system through at least 3 parallel and interacting channels involving nervous, endocrine, and immune signaling mechanisms. The brain can affect the community structure and function of the gut microbiota through the autonomic nervous system, by modulating regional gut motility, intestinal transit and secretion, and gut permeability, and potentially through the luminal secretion of hormones that directly modulate microbial gene expression. A systems biological model is proposed that posits circular communication loops amid the brain, gut, and gut microbiome, and in which perturbation at any level can propagate dysregulation throughout the circuit. A series of largely preclinical observations implicates alterations in brain-gut-microbiome communication in the pathogenesis and pathophysiology of irritable bowel syndrome, obesity, and several psychiatric and neurologic disorders. Continued research holds the promise of identifying novel therapeutic targets and developing treatment strategies to address some of the most debilitating, costly, and poorly understood diseases.
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Key Words
- 2BA, secondary bile acid
- 5-HT, serotonin
- ANS, autonomic nervous system
- ASD, autism spectrum disorder
- BBB, blood-brain barrier
- BGM, brain-gut-microbiome
- CNS, central nervous system
- ECC, enterochromaffin cell
- EEC, enteroendocrine cell
- FFAR, free fatty acid receptor
- FGF, fibroblast growth factor
- FXR, farnesoid X receptor
- GF, germ-free
- GI, gastrointestinal
- GLP-1, glucagon-like peptide-1
- GPR, G-protein–coupled receptor
- IBS, irritable bowel syndrome
- Intestinal Permeability
- Irritable Bowel Syndrome
- LPS, lipopolysaccharide
- SCFA, short-chain fatty acid
- SPF, specific-pathogen-free
- Serotonin
- Stress
- TGR5, G protein-coupled bile acid receptor
- Trp, tryptophan
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Affiliation(s)
| | | | | | - Emeran A. Mayer
- Correspondence Address correspondence to: Emeran A. Mayer, MD, G. Oppenheimer Center for Neurobiology of Stress and Resilience, University of California at Los Angeles, MC737818-10833 Le Conte Avenue, Los Angeles, California 90095-7378. fax: (310) 825-1919.
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