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Abrosimov R, Baeken MW, Hauf S, Wittig I, Hajieva P, Perrone CE, Moosmann B. Mitochondrial complex I inhibition triggers NAD +-independent glucose oxidation via successive NADPH formation, "futile" fatty acid cycling, and FADH 2 oxidation. GeroScience 2024; 46:3635-3658. [PMID: 38267672 DOI: 10.1007/s11357-023-01059-y] [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: 07/31/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
Inhibition of mitochondrial complex I (NADH dehydrogenase) is the primary mechanism of the antidiabetic drug metformin and various unrelated natural toxins. Complex I inhibition can also be induced by antidiabetic PPAR agonists, and it is elicited by methionine restriction, a nutritional intervention causing resistance to diabetes and obesity. Still, a comprehensible explanation to why complex I inhibition exerts antidiabetic properties and engenders metabolic inefficiency is missing. To evaluate this issue, we have systematically reanalyzed published transcriptomic datasets from MPP-treated neurons, metformin-treated hepatocytes, and methionine-restricted rats. We found that pathways leading to NADPH formation were widely induced, together with anabolic fatty acid biosynthesis, the latter appearing highly paradoxical in a state of mitochondrial impairment. However, concomitant induction of catabolic fatty acid oxidation indicated that complex I inhibition created a "futile" cycle of fatty acid synthesis and degradation, which was anatomically distributed between adipose tissue and liver in vivo. Cofactor balance analysis unveiled that such cycling would indeed be energetically futile (-3 ATP per acetyl-CoA), though it would not be redox-futile, as it would convert NADPH into respirable FADH2 without any net production of NADH. We conclude that inhibition of NADH dehydrogenase leads to a metabolic shift from glycolysis and the citric acid cycle (both generating NADH) towards the pentose phosphate pathway, whose product NADPH is translated 1:1 into FADH2 by fatty acid cycling. The diabetes-resistant phenotype following hepatic and intestinal complex I inhibition is attributed to FGF21- and GDF15-dependent fat hunger signaling, which remodels adipose tissue into a glucose-metabolizing organ.
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Affiliation(s)
- Roman Abrosimov
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Marius W Baeken
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Samuel Hauf
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ilka Wittig
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
| | - Parvana Hajieva
- Institute for Translational Medicine, MSH Medical School, Hamburg, Germany
| | - Carmen E Perrone
- Orentreich Foundation for the Advancement of Science, Cold Spring-On-Hudson, NY, USA
| | - Bernd Moosmann
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany.
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2
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Lee SH, Rinaudo PF. Metabolic regulation of preimplantation embryo development in vivo and in vitro: Molecular mechanisms and insights. Biochem Biophys Res Commun 2024; 726:150256. [PMID: 38909536 DOI: 10.1016/j.bbrc.2024.150256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
Understanding of embryonic development has led to the clinical application of Assisted Reproductive technologies (ART), with the resulting birth of millions of children. Recent developments in metabolomics, proteomics, and transcriptomics have brought to light new insights into embryonic growth dynamics, with implications spanning reproductive medicine, stem cell research, and regenerative medicine. The review explores the key metabolic processes and molecular pathways active during preimplantation embryo development, including PI3K-Akt, mTOR, AMPK, Wnt/β-catenin, TGF-β, Notch and Jak-Stat signaling pathways. We focused on analyzing the differences occurring in vitro as opposed to in vivo development and we discussed significant physiological and clinical implications.
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Affiliation(s)
- Seok Hee Lee
- Center for Reproductive Sciences, Department of Obstetrics and Gynecology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Paolo F Rinaudo
- Center for Reproductive Sciences, Department of Obstetrics and Gynecology, University of California San Francisco, San Francisco, CA, 94143, USA.
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3
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Georges RN, Ballut L, Aghajari N, Hecquet L, Charmantray F, Doumèche B. Biochemical, Bioinformatic, and Structural Comparisons of Transketolases and Position of Human Transketolase in the Enzyme Evolution. Biochemistry 2024; 63:1460-1473. [PMID: 38767928 DOI: 10.1021/acs.biochem.3c00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Transketolases (TKs) are key enzymes of the pentose phosphate pathway, regulating several other critical pathways in cells. Considering their metabolic importance, TKs are expected to be conserved throughout evolution. However, Tittmann et al. (J Biol Chem, 2010, 285(41): 31559-31570) demonstrated that Homo sapiens TK (hsTK) possesses several structural and kinetic differences compared to bacterial TKs. Here, we study 14 TKs from pathogenic bacteria, fungi, and parasites and compare them with hsTK using biochemical, bioinformatic, and structural approaches. For this purpose, six new TK structures are solved by X-ray crystallography, including the TK of Plasmodium falciparum. All of these TKs have the same general fold as bacterial TKs. This comparative study shows that hsTK greatly differs from TKs from pathogens in terms of enzymatic activity, spatial positions of the active site, and monomer-monomer interface residues. An ubiquitous structural pattern is identified in all TKs as a six-residue histidyl crown around the TK cofactor (thiamine pyrophosphate), except for hsTK containing only five residues in the crown. Residue mapping of the monomer-monomer interface and the active site reveals that hsTK contains more unique residues than other TKs. From an evolutionary standpoint, TKs from animals (including H. sapiens) and Schistosoma sp. belong to a distinct structural group from TKs of bacteria, plants, fungi, and parasites, mostly based on a different linker between domains, raising hypotheses regarding evolution and regulation.
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Affiliation(s)
- Rainier-Numa Georges
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ICBMS UMR5246, 69622 Villeurbanne, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, F-69367 Lyon, France
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, F-69367 Lyon, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand,France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand,France
| | - Bastien Doumèche
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ICBMS UMR5246, 69622 Villeurbanne, France
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Vos WAJW, Vadaq N, Matzaraki V, Otten T, Groenendijk AL, Blaauw MJT, van Eekeren LE, Brinkman K, de Mast Q, Riksen NP, Stalenhoef AFH, van Lunzen J, van der Ven AJAM, Blok WL, Stalenhoef JE. Cardiometabolic Differences in People Living with HIV Receiving Integrase Strand Transfer Inhibitors Compared to Non-nucleoside Reverse Transcriptase Inhibitors: Implications for Current ART Strategies. Viruses 2024; 16:582. [PMID: 38675924 PMCID: PMC11054623 DOI: 10.3390/v16040582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
In people living with HIV (PLHIV), integrase strand transfer inhibitors (INSTIs) are part of the first-line combination antiretroviral therapy (cART), while non-nucleoside reverse transcriptase inhibitor (NNRTI)-based regimens are alternatives. Distinct cART regimens may variably influence the risk for non-AIDS comorbidities. We aimed to compare the metabolome and lipidome of INSTI and NNRTI-based regimens. The 2000HIV study includes asymptomatic PLHIV (n = 1646) on long-term cART, separated into a discovery cohort with 730 INSTI and 617 NNRTI users, and a validation cohort encompassing 209 INSTI and 90 NNRTI users. Baseline plasma samples from INSTI and NNRTI users were compared using mass spectrometry-based untargeted metabolomic (n = 500) analysis. Perturbed metabolic pathways were identified using MetaboAnalyst software. Subsequently, nuclear magnetic resonance spectroscopy was used for targeted lipoprotein and lipid (n = 141) analysis. Metabolome homogeneity was observed between the different types of INSTI and NNRTI. In contrast, higher and lower levels of 59 and 45 metabolites, respectively, were found in the INSTI group compared to NNRTI users, of which 77.9% (81/104) had consistent directionality in the validation cohort. Annotated metabolites belonged mainly to 'lipid and lipid-like molecules', 'organic acids and derivatives' and 'organoheterocyclic compounds'. In pathway analysis, perturbed 'vitamin B1 (thiamin) metabolism', 'de novo fatty acid biosynthesis', 'bile acid biosynthesis' and 'pentose phosphate pathway' were detected, among others. Lipoprotein and lipid levels in NNRTIs were heterogeneous and could not be compared as a group. INSTIs compared to individual NNRTI types showed that HDL cholesterol was lower in INSTIs compared to nevirapine but higher in INSTIs compared to doravirine. In addition, LDL size was lower in INSTIs and nevirapine compared to doravirine. NNRTIs show more heterogeneous cardiometabolic effects than INSTIs, which hampers the comparison between these two classes of drugs. Targeted lipoproteomic and lipid NMR spectroscopy showed that INSTI use was associated with a more unfavorable lipid profile compared to nevirapine, which was shifted to a more favorable profile for INSTI when substituting nevirapine for doravirine, with evidently higher fold changes. The cardiovascular disease risk profile seems more favorable in INSTIs compared to NNRTIs in untargeted metabolomic analysis using mass-spectrometry.
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Affiliation(s)
- Wilhelm A. J. W. Vos
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Internal Medicine and Infectious Diseases, OLVG, 1091 AC Amsterdam, The Netherlands
| | - Nadira Vadaq
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Twan Otten
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Albert L. Groenendijk
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, ErasmusMC, Erasmus University, 3015 CN Rotterdam, The Netherlands
| | - Marc J. T. Blaauw
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Internal Medicine and Infectious Diseases, Elizabeth-Tweesteden Ziekenhuis, 5022 GC Tilburg, The Netherlands
| | - Louise E. van Eekeren
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Kees Brinkman
- Department of Internal Medicine and Infectious Diseases, OLVG, 1091 AC Amsterdam, The Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Niels P. Riksen
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Anton F. H. Stalenhoef
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Jan van Lunzen
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | - Willem L. Blok
- Department of Internal Medicine and Infectious Diseases, OLVG, 1091 AC Amsterdam, The Netherlands
| | - Janneke E. Stalenhoef
- Department of Internal Medicine and Infectious Diseases, OLVG, 1091 AC Amsterdam, The Netherlands
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Perwad F, Akwo EA, Vartanian N, Suva LJ, Friedman PA, Robinson-Cohen C. Multi-trait Analysis of GWAS for circulating FGF23 Identifies Novel Network Interactions Between HRG-HMGB1 and Cardiac Disease in CKD. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.04.24303051. [PMID: 38496593 PMCID: PMC10942519 DOI: 10.1101/2024.03.04.24303051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Genome-wide association studies (GWAS) have identified numerous genetic loci associated with mineral metabolism (MM) markers but have exclusively focused on single-trait analysis. In this study, we performed a multi-trait analysis of GWAS (MTAG) of MM, exploring overlapping genetic architecture between traits, to identify novel genetic associations for fibroblast growth factor 23 (FGF23). Methods We applied MTAG to genetic variants common to GWAS of 5 genetically correlated MM markers (calcium, phosphorus, FGF23, 25-hydroxyvitamin D (25(OH)D) and parathyroid hormone (PTH)) in European-ancestry subjects. We integrated information from UKBioBank GWAS for blood levels for phosphate, 25(OH)D and calcium (n=366,484), and CHARGE GWAS for PTH (n=29,155) and FGF23 (n=16,624). We then used functional genomics to model interactive and dynamic networks to identify novel associations between genetic traits and circulating FGF23. Results MTAG increased the effective sample size for all MM markers to n=50,325 for FGF23. After clumping, MTAG identified independent genome-wide significant SNPs for all traits, including 62 loci for FGF23. Many of these loci have not been previously reported in single-trait analyses. Through functional genomics we identified Histidine-rich glycoprotein (HRG) and high mobility group box 1(HMGB1) genes as master regulators of downstream canonical pathways associated with FGF23. HRG-HMGB1 network interactions were also highly enriched in left ventricular heart tissue of a cohort of deceased hemodialysis patients. Conclusion Our findings highlight the importance of MTAG analysis of MM markers to boost the number of genome-wide significant loci for FGF23 to identify novel genetic traits. Functional genomics revealed novel networks that inform unique cellular functions and identified HRG-HMGB1 as key master regulators of FGF23 and cardiovascular disease in CKD. Future studies will provide a deeper understanding of genetic signatures associated with FGF23 and its role in health and disease.
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Affiliation(s)
- Farzana Perwad
- University of California San Francisco, San Francisco, CA
| | - Elvis A Akwo
- Vanderbilt University Medical Center, Nashville, TN
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Georges RN, Ballut L, Octobre G, Comte A, Hecquet L, Charmantray F, Doumèche B. Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior. Protein Sci 2024; 33:e4884. [PMID: 38145310 PMCID: PMC10868444 DOI: 10.1002/pro.4884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
Vibrio vulnificus (vv) is a multidrug-resistant human bacterial pathogen whose prevalence is expected to increase over the years. Transketolases (TK), transferases catalyzing two reactions of the nonoxidative branch of the pentose-phosphate pathway and therefore linked to several crucial metabolic pathways, are potential targets for new drugs against this pathogen. Here, the vvTK is crystallized and its structure is solved at 2.1 Å. A crown of 6 histidyl residues is observed in the active site and expected to participate in the thiamine pyrophosphate (cofactor) activation. Docking of fructose-6-phosphate and ferricyanide used in the activity assay, suggests that both substrates can bind vvTK simultaneously. This is confirmed by steady-state kinetics showing a sequential mechanism, on the contrary to the natural transferase reaction which follows a substituted mechanism. Inhibition by the I38-49 inhibitor (2-(4-ethoxyphenyl)-1-(pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine) reveals for the first time a cooperative behavior of a TK and docking experiments suggest a previously undescribed binding site at the interface between the pyrophosphate and pyridinium domains.
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Affiliation(s)
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, Lyon, France
| | | | - Arnaud Comte
- Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), Clermont-Ferrand, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), Clermont-Ferrand, France
| | - Bastien Doumèche
- Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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Mukhopadhyay A, Karu K, Dalby PA. Two-substrate enzyme engineering using small libraries that combine the substrate preferences from two different variant lineages. Sci Rep 2024; 14:1287. [PMID: 38218974 PMCID: PMC10787763 DOI: 10.1038/s41598-024-51831-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Improving the range of substrates accepted by enzymes with high catalytic activity remains an important goal for the industrialisation of biocatalysis. Many enzymes catalyse two-substrate reactions which increases the complexity in engineering them for the synthesis of alternative products. Often mutations are found independently that can improve the acceptance of alternatives to each of the two substrates. Ideally, we would be able to combine mutations identified for each of the two alternative substrates, and so reprogramme new enzyme variants that synthesise specific products from their respective two-substrate combinations. However, as we have previously observed for E. coli transketolase, the mutations that improved activity towards aromatic acceptor aldehydes, did not successfully recombine with mutations that switched the donor substrate to pyruvate. This likely results from several active site residues having multiple roles that can affect both of the substrates, as well as structural interactions between the mutations themselves. Here, we have designed small libraries, including both natural and non-natural amino acids, based on the previous mutational sites that impact on acceptance of the two substrates, to achieve up to 630× increases in kcat for the reaction with 3-formylbenzoic acid (3-FBA) and pyruvate. Computational docking was able to determine how the mutations shaped the active site to improve the proximity of the 3-FBA substrate relative to the enamine-TPP intermediate, formed after the initial reaction with pyruvate. This work opens the way for small libraries to rapidly reprogramme enzyme active sites in a plug and play approach to catalyse new combinations of two-substrate reactions.
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Affiliation(s)
- Arka Mukhopadhyay
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Kersti Karu
- Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
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Zhang J, Lin XT, Yu HQ, Fang L, Wu D, Luo YD, Zhang YJ, Xie CM. Elevated FBXL6 expression in hepatocytes activates VRK2-transketolase-ROS-mTOR-mediated immune evasion and liver cancer metastasis in mice. Exp Mol Med 2023; 55:2162-2176. [PMID: 37653031 PMCID: PMC10618235 DOI: 10.1038/s12276-023-01060-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/15/2023] [Accepted: 05/25/2023] [Indexed: 09/02/2023] Open
Abstract
Metastatic hepatocellular carcinoma (HCC) is the most lethal malignancy and lacks effective treatment. FBXL6 is overexpressed in human hepatocellular carcinoma (HCC), but whether this change drives liver tumorigenesis and lung metastasis in vivo remains unknown. In this study, we aimed to identify FBXL6 (F-Box and Leucine Rich Repeat Protein 6) as a key driver of HCC metastasis and to provide a new paradigm for HCC therapy. We found that elevated FBXL6 expression in hepatocytes drove HCC lung metastasis and was a much stronger driver than Kras mutation (KrasG12D/+;Alb-Cre), p53 haploinsufficiency (p53+/-) or Tsc1 loss (Tsc1fl/fl;Alb-Cre). Mechanistically, VRK2 promoted Thr287 phosphorylation of TKT and then recruited FBXL6 to promote TKT ubiquitination and activation. Activated TKT further increased PD-L1 and VRK2 expression via the ROS-mTOR axis, leading to immune evasion and HCC metastasis. Targeting or knockdown of TKT significantly blocked FBXL6-driven immune evasion and HCC metastasis in vitro and in vivo. Notably, the level of active TKT (p-Thr287 TKT) was increased and was positively correlated with the FBXL6 and VRK2 expression levels in HCC patients. Our work provides novel mechanistic insights into FBXL6-driven HCC metastasis and suggests that targeting the TKT-ROS-mTOR-PD-L1/VRK2 axis is a new paradigm for treating patients with metastatic HCC with high FBXL6 expression.
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Affiliation(s)
- Jie Zhang
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Xiao-Tong Lin
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Hong-Qiang Yu
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Lei Fang
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Di Wu
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yuan-Deng Luo
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yu-Jun Zhang
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Chuan-Ming Xie
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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Huang H, Wu H, Qi M, Wang H, Lu Z. Thiamine-Mediated Microbial Interaction between Auxotrophic Rhodococcus ruber ZM07 and Prototrophic Cooperators in the Tetrahydrofuran-Degrading Microbial Community H-1. Microbiol Spectr 2023; 11:e0454122. [PMID: 37125924 PMCID: PMC10269752 DOI: 10.1128/spectrum.04541-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
As a crucial growth factor, thiamine can regulate functional microbial communities; however, our current understanding of its effect on bioremediation is lacking. Using metatranscriptome and 16S rRNA gene sequencing, we explored the mechanism of response of an efficient tetrahydrofuran (THF)-degrading microbial culture, designated H-1, to exogenous thiamine. Rhodococcus ruber ZM07, a strain performing the THF degradation function in H-1, is a thiamine-auxotrophic bacterium. Furthermore, thiamine affected the microbial community structure of H-1 by altering resource and niche distributions. A microbial co-occurrence network was constructed to help us identify and isolate the cooperators of strain ZM07 in the microbial community. Based on the prediction of the network, two non-THF-degrading bacteria, Hydrogenophaga intermedia ZM11 and Pigmentiphaga daeguensis ZM12, were isolated. Our results suggest that strain ZM11 is a good cooperator of ZM07, and it might be more competitive than other cooperators (e.g., ZM12) in cocultured systems. Additionally, two dominant strains in our microbial culture displayed a "seesaw" pattern, and they showed completely different responses to exogenous thiamine. The growth of the THF degrader ZM07 was spurred by additional thiamine (with an increased relative abundance and significant upregulation of most metabolic pathways), while the growth of the cooperator ZM11 was obviously suppressed under the same circumstances. This relationship was the opposite without thiamine addition. Our study reveals that exogenous thiamine can affect the interaction patterns between THF- and non-THF-degrading microorganisms and provides new insight into the effects of micronutrients on the environmental microbial community. IMPORTANCE Auxotrophic microorganisms play important roles in the biodegradation of pollutants in nature. Exploring the interspecies relationship between auxotrophic THF-degrading bacteria and other microbes is helpful for the efficient utilization of auxotrophic functional microorganisms. Herein, the thiamine-auxotrophic THF-degrading bacterium ZM07 was isolated from the microbial culture H-1, and the effect of thiamine on the structure of H-1 during THF bioremediation was studied. Thiamine may help ZM07 occupy more niches and utilize more resources, thus improving THF degradation efficiency. This research provides a new strategy to improve the THF or other xenobiotic compound biodegradation performance of auxotrophic functional microorganisms/microbial communities by artificially adding special micronutrients. Additionally, the "seesaw" relationship between the thiamine-auxotrophic strain ZM07 and its prototrophic cooperator ZM11 during THF bioremediation could be changed by exogenous thiamine. This study reveals the effect of micronutrients on microbial interactions and provides an effective way to regulate the pollutant biodegradation efficiency of microbial communities.
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Affiliation(s)
- Hui Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Minbo Qi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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10
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Yue Z, Liu Y, Chen Y, Chen C, Zhang J, He L, Ma K. Comprehensive Genomics and Proteomics Analysis Reveals the Multiple Response Strategies of Endophytic Bacillus sp. WR13 to Iron Limitation. Microorganisms 2023; 11:microorganisms11020367. [PMID: 36838332 PMCID: PMC9961900 DOI: 10.3390/microorganisms11020367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Iron (Fe) is an important metal element for the growth of bacteria. Many bacteria respond to Fe limitation through a variety of strategies. We previously isolated an endophyte Bacillus sp. WR13 from wheat root. However, whether and how this strain can cope with Fe-deficient environments remains unclear. In this study, the growth of WR13 under Fe starvation was investigated, and the underlying mechanisms of WR13 in response to Fe starvation were elucidated via genomics and iTRAQ-based proteomics. Under Fe limitation, WR13 showed a growth pattern similar to that of Fe sufficiency. Genomics analysis demonstrated that WR13 had gene clusters related to siderophore synthesis (dhbACEBF), transportation (bcbE), uptake (feuABC-yusV) and hydrolysis (besA). These genes were significantly up-regulated in Fe-starved WR13, which resulted in more siderophore production. Proteomics data revealed that many Fe-containing proteins such as ACO, HemQ, ferredoxin, CNP, and SufD were significantly reduced under Fe limitation. Meanwhile, significant decreases in many proteins involved in glycolysis, TCA cycle, pentose phosphate pathway; asparagine, glutamine, methionine, and serine metabolism; and phospholipid hydrolysis were also observed. Overall, this study shows that Bacillus sp. WR13 was able to respond to Fe limitation via multiple strategies and provides a theoretical basis for the application of WR13 in Fe-deficient soil.
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Affiliation(s)
- Zonghao Yue
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
| | - Yongchuang Liu
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
| | - Yanjuan Chen
- School of Mechanical and Electrical Engineering, Zhoukou Normal University, Zhoukou 466001, China
| | - Can Chen
- Henan Key Laboratory of Plant Molecular Breeding and Bioreactor, Zhoukou 466001, China
| | - Ju Zhang
- Henan Key Laboratory of Plant Molecular Breeding and Bioreactor, Zhoukou 466001, China
| | - Le He
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
| | - Keshi Ma
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
- Correspondence: ; Tel.: +86-158-9672-0176
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11
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Solovjeva ON. New Role of Water in Transketolase Catalysis. Int J Mol Sci 2023; 24:ijms24032068. [PMID: 36768400 PMCID: PMC9917271 DOI: 10.3390/ijms24032068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Transketolase catalyzes the interconversion of keto and aldo sugars. Its coenzyme is thiamine diphosphate. The binding of keto sugar with thiamine diphosphate is possible only after C2 deprotonation of its thiazole ring. It is believed that deprotonation occurs due to the direct transfer of a proton to the amino group of its aminopyrimidine ring. Using mass spectrometry, it is shown that a water molecule is directly involved in the deprotonation process. After the binding of thiamine diphosphate with transketolase and its subsequent cleavage, a thiamine diphosphate molecule is formed with a mass increased by one oxygen molecule. After fragmentation, a thiamine diphosphate molecule is formed with a mass reduced by one and two hydrogen atoms, that is, HO and H2O are split off. Based on these data, it is assumed that after the formation of holotransketolase, water is covalently bound to thiamine diphosphate, and carbanion is formed as a result of its elimination. This may be a common mechanism for other thiamine enzymes. The participation of a water molecule in the catalysis of the one-substrate transketolase reaction and a possible reason for the effect of the acceptor substrate on the affinity of the donor substrate for active sites are also shown.
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Affiliation(s)
- Olga N Solovjeva
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia
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12
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Kareem O, Nisar S, Tanvir M, Muzaffer U, Bader GN. Thiamine deficiency in pregnancy and lactation: implications and present perspectives. Front Nutr 2023; 10:1080611. [PMID: 37153911 PMCID: PMC10158844 DOI: 10.3389/fnut.2023.1080611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/03/2023] [Indexed: 05/10/2023] Open
Abstract
During pregnancy, many physiologic changes occur in order to accommodate fetal growth. These changes require an increase in many of the nutritional needs to prevent long-term consequences for both mother and the offspring. One of the main vitamins that are needed throughout the pregnancy is thiamine (vitamin B1) which is a water-soluble vitamin that plays an important role in many metabolic and physiologic processes in the human body. Thiamine deficiency during pregnancy can cause can have many cardiac, neurologic, and psychological effects on the mother. It can also dispose the fetus to gastrointestinal, pulmonological, cardiac, and neurologic conditions. This paper reviews the recently published literature about thiamine and its physiologic roles, thiamine deficiency in pregnancy, its prevalence, its impact on infants and subsequent consequences in them. This review also highlights the knowledge gaps within these topics.
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Affiliation(s)
- Ozaifa Kareem
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, India
- *Correspondence: Ozaifa Kareem, ,
| | - Sobia Nisar
- Department of Medicine, Government Medical College, Srinagar, India
| | - Masood Tanvir
- Department of Medicine, Government Medical College, Srinagar, India
| | - Umar Muzaffer
- Department of Medicine, Government Medical College, Srinagar, India
| | - G. N. Bader
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, India
- G. N. Bader,
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13
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O'Brien NL, Quadri G, Lightley I, Sharp SI, Guerrini I, Smith I, Heydtmann M, Morgan MY, Thomson AD, Bass NJ, McHugh PC, McQuillin A. SLC19A1 Genetic Variation Leads to Altered Thiamine Diphosphate Transport: Implications for the Risk of Developing Wernicke-Korsakoff's Syndrome. Alcohol Alcohol 2022; 57:581-588. [PMID: 35952336 DOI: 10.1093/alcalc/agac032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 04/29/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022] Open
Abstract
AIMS Wernicke-Korsakoff syndrome (WKS) is commonly associated with chronic alcohol misuse, a condition known to have multiple detrimental effects on thiamine metabolism. This study was conducted to identify genetic variants that may contribute to the development of WKS in individuals with alcohol dependence syndrome through alteration of thiamine transport into cells. METHODS Exome sequencing data from a panel of genes related to alcohol metabolism and thiamine pathways were analysed in a discovery cohort of 29 individuals with WKS to identify possible genetic risk variants associated with its development. Variant frequencies in this discovery cohort were compared with European frequencies in the Genome Aggregation Database browser, and those present at significantly higher frequencies were genotyped in an additional cohort of 87 alcohol-dependent cases with WKS and 197 alcohol-dependent cognitively intact controls. RESULTS Thirty non-synonymous variants were identified in the discovery cohort and, after filtering, 23 were taken forward and genotyped in the case-control cohort. Of these SLC19A1:rs1051266:G was nominally associated with WKS. SLC19A1 encodes the reduced folate carrier, a major transporter for physiological folate in plasma; rs1051266 is reported to impact folate transport. Thiamine pyrophosphate (TPP) efflux was significantly decreased in HEK293 cells, stably transfected with rs1051266:G, under thiamine deficient conditions when compared with the efflux from cells transfected with rs1051266:A (P = 5.7 × 10-11). CONCLUSION This study provides evidence for the role of genetic variation in the SLC19A1 gene, which may contribute to the development of WKS in vivo through modulation of TPP transport in cells.
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Affiliation(s)
- Niamh L O'Brien
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Giorgia Quadri
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Iain Lightley
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, UK
| | - Sally I Sharp
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Irene Guerrini
- Erith Health Centre, South London and Maudsley NHS Foundation Trust, London, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - Iain Smith
- Alcohol Related Brain Injury Team, Stirling, UK
| | - Mathis Heydtmann
- Department of Gastroenterology, Dumfries & Galloway Royal Infirmary, Cargenbridge, Dumfries, UK
| | - Marsha Y Morgan
- UCL Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, UK
| | - Allan D Thomson
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - Nicholas J Bass
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Patrick C McHugh
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
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14
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Shcherbakova TA, Baldin SM, Shumkov MS, Gushchina IV, Nilov DK, Švedas VK. Isolation and Biochemical Characterization of Recombinant Transketolase from Mycobacterium tuberculosis. Acta Naturae 2022; 14:93-97. [PMID: 35923567 PMCID: PMC9307985 DOI: 10.32607/actanaturae.11713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Transketolase, an enzyme of the pentose phosphate pathway, plays an important
role in the functioning of mycobacteria. Using plasmid pET-19b carrying the
Rv1449c gene of transketolase from Mycobacterium
tuberculosis and an additional histidine tag, we isolated and purified
recombinant transketolase and determined the conditions for obtaining the
apoform of the protein. The Michaelis constants were evaluated for the thiamine
diphosphate cofactor in the presence of magnesium and calcium ions. We found
that the affinity of mycobacterial transketolase for thiamine diphosphate is by
three orders of magnitude lower than that of the human enzyme. Analysis of the
structural organization of the active centers of homologous enzymes showed that
this difference is due to a replacement of lysine residues by less polar amino
acid residues.
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Affiliation(s)
- T. A. Shcherbakova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
| | - S. M. Baldin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
| | - M. S. Shumkov
- Federal Research Centre «Fundamentals of Biotechnology», Russian Academy of Sciences, Moscow, 119071 Russia
| | - I. V. Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991 Russia
| | - D. K. Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
| | - V. K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991 Russia
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15
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L-tyrosine-bound ThiH structure reveals C-C bond break differences within radical SAM aromatic amino acid lyases. Nat Commun 2022; 13:2284. [PMID: 35477710 PMCID: PMC9046217 DOI: 10.1038/s41467-022-29980-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/05/2022] [Indexed: 11/08/2022] Open
Abstract
2-iminoacetate synthase ThiH is a radical S-adenosyl-L-methionine (SAM) L-tyrosine lyase and catalyzes the L-tyrosine Cα-Cβ bond break to produce dehydroglycine and p-cresol while the radical SAM L-tryptophan lyase NosL cleaves the L-tryptophan Cα-C bond to produce 3-methylindole-2-carboxylic acid. It has been difficult to understand the features that condition one C-C bond break over the other one because the two enzymes display significant primary structure similarities and presumably similar substrate-binding modes. Here, we report the crystal structure of L-tyrosine bound ThiH from Thermosinus carboxydivorans revealing an unusual protonation state of L-tyrosine upon binding. Structural comparison of ThiH with NosL and computational studies of the respective reactions they catalyze show that substrate activation is eased by tunneling effect and that subtle structural changes between the two enzymes affect, in particular, the hydrogen-atom abstraction by the 5´-deoxyadenosyl radical species, driving the difference in reaction specificity.
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16
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Transketolase promotes colorectal cancer metastasis through regulating AKT phosphorylation. Cell Death Dis 2022; 13:99. [PMID: 35110545 PMCID: PMC8810869 DOI: 10.1038/s41419-022-04575-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/09/2022] [Accepted: 01/19/2022] [Indexed: 01/05/2023]
Abstract
Transketolase (TKT) which is an important metabolic enzyme in the pentose phosphate pathway (PPP) participates in maintaining ribose 5-phosphate levels. TKT is necessary for maintaining cell growth. However, we found that in addition to this, TKT can also affect tumor progression through other ways. Our previous study indicate that TKT could promote the development of liver cancer by affecting bile acid metabolism. And in this study, we discovered that TKT expression was remarkably upregulated in colorectal cancer, abnormal high expression of TKT is associated with poor prognosis of colorectal cancer. Additionally, TKT promoted colorectal cancer cell growth and metastasis. Further study demonstrated that TKT interacted with GRP78 and promoted colorectal cancer cell glycolysis through increasing AKT phosphorylation, thereby enhancing colorectal cancer cell metastasis. Thus, TKT is expected to become an indicator for judging the prognosis of colorectal cancer, and provide a theoretical basis for drug development of new treatment targets for colorectal cancer.
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17
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Biological Properties of Vitamins of the B-Complex, Part 1: Vitamins B1, B2, B3, and B5. Nutrients 2022; 14:nu14030484. [PMID: 35276844 PMCID: PMC8839250 DOI: 10.3390/nu14030484] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
This review summarizes the current knowledge on essential vitamins B1, B2, B3, and B5. These B-complex vitamins must be taken from diet, with the exception of vitamin B3, that can also be synthetized from amino acid tryptophan. All of these vitamins are water soluble, which determines their main properties, namely: they are partly lost when food is washed or boiled since they migrate to the water; the requirement of membrane transporters for their permeation into the cells; and their safety since any excess is rapidly eliminated via the kidney. The therapeutic use of B-complex vitamins is mostly limited to hypovitaminoses or similar conditions, but, as they are generally very safe, they have also been examined in other pathological conditions. Nicotinic acid, a form of vitamin B3, is the only exception because it is a known hypolipidemic agent in gram doses. The article also sums up: (i) the current methods for detection of the vitamins of the B-complex in biological fluids; (ii) the food and other sources of these vitamins including the effect of common processing and storage methods on their content; and (iii) their physiological function.
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18
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Choppin M, Feldmeyer B, Foitzik S. Histone acetylation regulates the expression of genes involved in worker reproduction in the ant Temnothorax rugatulus. BMC Genomics 2021; 22:871. [PMID: 34861814 PMCID: PMC8642982 DOI: 10.1186/s12864-021-08196-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/12/2021] [Indexed: 12/29/2022] Open
Abstract
Background In insect societies, queens monopolize reproduction while workers perform tasks such as brood care or foraging. Queen loss leads to ovary development and lifespan extension in workers of many ant species. However, the underlying molecular mechanisms of this phenotypic plasticity remain unclear. Recent studies highlight the importance of epigenetics in regulating plastic traits in social insects. Thus, we investigated the role of histone acetylation in regulating worker reproduction in the ant Temnothorax rugatulus. We removed queens from their colonies to induce worker fecundity, and either fed workers with chemical inhibitors of histone acetylation (C646), deacetylation (TSA), or the solvent (DMSO) as control. We monitored worker number for six weeks after which we assessed ovary development and sequenced fat body mRNA. Results Workers survived better in queenless colonies. They also developed their ovaries after queen removal in control colonies as expected, but not in colonies treated with the chemical inhibitors. Both inhibitors affected gene expression, although the inhibition of histone acetylation using C646 altered the expression of more genes with immunity, fecundity, and longevity functionalities. Interestingly, these C646-treated workers shared many upregulated genes with infertile workers from queenright colonies. We also identified one gene with antioxidant properties commonly downregulated in infertile workers from queenright colonies and both C646 and TSA-treated workers from queenless colonies. Conclusion Our results suggest that histone acetylation is involved in the molecular regulation of worker reproduction, and thus point to an important role of histone modifications in modulating phenotypic plasticity of life history traits in social insects. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08196-8.
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Affiliation(s)
- Marina Choppin
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany.
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Senckenberg, Frankfurt, Germany
| | - Susanne Foitzik
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
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19
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Fúster Fernández I, Hecquet L, Fessner W. Transketolase Catalyzed Synthesis of
N
‐Aryl Hydroxamic Acids. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Inés Fúster Fernández
- Institut für Organische Chemie und Biochemie Technische Universität Darmstadt Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Laurence Hecquet
- Institut de Chimie de Clermont-Ferrand CNRS Auvergne Clermont INP Université Clermont Auverne 63000 Clermont-Ferrand France
| | - Wolf‐Dieter Fessner
- Institut für Organische Chemie und Biochemie Technische Universität Darmstadt Alarich-Weiss-Str. 4 64287 Darmstadt Germany
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20
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Fernández-Pombo A, Rodríguez-Carnero G, Castro AI, Cantón-Blanco A, Seoane LM, Casanueva FF, Crujeiras AB, Martínez-Olmos MA. Relevance of nutritional assessment and treatment to counteract cardiac cachexia and sarcopenia in chronic heart failure. Clin Nutr 2021; 40:5141-5155. [PMID: 34461588 DOI: 10.1016/j.clnu.2021.07.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 12/18/2022]
Abstract
Chronic heart failure (CHF) is frequently associated with the involuntary loss of body weight and muscle wasting, which can determine the course of the disease and its prognosis. While there is no gold standard malnutrition screening tool for their detection in the CHF population, several bioelectrical and imaging methods have been used to assess body composition in these patients (such as Dual Energy X-Ray Absorptiometry and muscle ultrasound, among other techniques). In addition, numerous nutritional biomarkers have been found to be useful in the determination of the nutritional status. Nutritional considerations include the slow and progressive supply of nutrients, avoiding high volumes, which could ultimately lead to refeeding syndrome and worsen the clinical picture. If oral feeding is insufficient, hypercaloric and hyperproteic supplementation should be considered. β-Hydroxy-β-methylbutyrate and omega-3 polyunsaturated fatty acid administration prove to be beneficial in certain patients with CHF, and several interventional studies with micronutrient supplementation have also described their possible role in these subjects. Taking into account that CHF is sometimes associated with gastrointestinal dysfunction, parenteral nutritional support may be required in selected cases. In addition, potential therapeutic options regarding nutritional state and muscle wasting have also been tested in clinical studies. This review summarises the scientific evidence that demonstrates the necessity to carry out a careful nutritional evaluation and nutritional treatment to prevent or improve cardiac cachexia and sarcopenia in CHF, as well as improve its course.
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Affiliation(s)
- Antía Fernández-Pombo
- Division of Endocrinology and Nutrition, Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Gemma Rodríguez-Carnero
- Division of Endocrinology and Nutrition, Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain; Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Ana I Castro
- Division of Endocrinology and Nutrition, Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Ana Cantón-Blanco
- Division of Endocrinology and Nutrition, Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain; Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Luisa M Seoane
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain; Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Felipe F Casanueva
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain; Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.
| | - Miguel A Martínez-Olmos
- Division of Endocrinology and Nutrition, Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain; Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain; Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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21
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Qiu L, Ma Y, Chen X, Zhou L, Zhang H, Zhong G, Zhang L, Tang J. Heparin-binding growth factor (HDGF) drives radioresistance in breast cancer by activating the STAT3 signaling pathway. J Transl Med 2021; 19:344. [PMID: 34376200 PMCID: PMC8353798 DOI: 10.1186/s12967-021-03021-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Although reports implicate radioresistance as an important obstacle for the management of breast cancer, its molecular mechanism is elusive. Herein, we found that high HDGF levels are expressed significantly in breast cancer and exhibit a positive association with poor survival prognosis. Heparin-binding growth factor (HDGF) was upregulated in radioresistant breast cancer cells, however, its knockdown could reduce breast cancer radioresistant both in vitro and in vivo. Additionally, the binding of RXRα to HDGF promoter blocked HDGF transcriptional activity, consequently inhibiting breast cancer radioresistance. The enhanced radioresistant activity of HDGF is induced by TKT and STAT3, impacting the STAT3-Tyr705 and STAT3-Ser727 phosphorylation and STAT3 transcriptional activity. Notably, HDGF depletion renders radioresistant hypersensitive to the drug that targets STAT3 phosphorylation. This article demonstrates the novel function of HDGF as a promising molecular target for predicting radioresistance in breast cancer.
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Affiliation(s)
- Lingyun Qiu
- Oncology Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Yan Ma
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Xiaohua Chen
- Department of Radiation Oncology, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Liheng Zhou
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People's Republic of China
| | - Haibo Zhang
- Oncology Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Guansheng Zhong
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, People's Republic of China
| | - Lei Zhang
- Department of Radiation Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People's Republic of China.
| | - Jianming Tang
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
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22
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Cárdenas-Fernández M, Subrizi F, Dobrijevic D, Hailes HC, Ward JM. Characterisation of a hyperthermophilic transketolase from Thermotoga maritima DSM3109 as a biocatalyst for 7-keto-octuronic acid synthesis. Org Biomol Chem 2021; 19:6493-6500. [PMID: 34250527 PMCID: PMC8317047 DOI: 10.1039/d1ob01237a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/21/2022]
Abstract
Transketolase (TK) is a fundamentally important enzyme in industrial biocatalysis which carries out a stereospecific carbon-carbon bond formation, and is widely used in the synthesis of prochiral ketones. This study describes the biochemical and molecular characterisation of a novel and unusual hyperthermophilic TK from Thermotoga maritima DSM3109 (TKtmar). TKtmar has a low protein sequence homology compared to the already described TKs, with key amino acid residues in the active site highly conserved. TKtmar has a very high optimum temperature (>90 °C) and shows pronounced stability at high temperature (e.g. t1/2 99 and 9.3 h at 50 and 80 °C, respectively) and in presence of organic solvents commonly used in industry (DMSO, acetonitrile and methanol). Substrate screening showed activity towards several monosaccharides and aliphatic aldehydes. In addition, for the first time, TK specificity towards uronic acids was achieved with TKtmar catalysing the efficient conversion of d-galacturonic acid and lithium hydroxypyruvate into 7-keto-octuronic acid, a very rare C8 uronic acid, in high yields (98%, 49 mM).
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Affiliation(s)
- Max Cárdenas-Fernández
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK. and School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Fabiana Subrizi
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Dragana Dobrijevic
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK.
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK.
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Ocal N, Lagarde A, L'enfant M, Charmantray F, Hecquet L. High-Throughput Solid-Phase Assay for Substrate Profiling and Directed Evolution of Transketolase. Chembiochem 2021; 22:2814-2820. [PMID: 34289225 DOI: 10.1002/cbic.202100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 11/10/2022]
Abstract
Thiamine diphosphate-dependent enzymes, and specifically transketolases, form one of the most important families of biocatalytic tools for enantioselective carbon-carbon bond formation yielding various hydroxyketones of biological interest. To enable substrate profiling of transketolases for acceptance of different donors and acceptors, a simple, direct colorimetric assay based on pH reaction variation was developed to establish a high-throughput solid-phase assay. This assay reduces the screening effort in the directed evolution of transketolases, as only active variants are selected for further analysis. Transketolase activity is detected as bicarbonate anions released from the α-ketoacid donor substrate, which causes the pH to rise. A pH indicator, bromothymol blue, which changes color from yellow to blue in alkaline conditions, was used to directly detect, with the naked eye, clones expressing active transketolase variants, obviating enzyme extraction.
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Affiliation(s)
- Nazim Ocal
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Aurélie Lagarde
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Mélanie L'enfant
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, Auvergne Clermont INP, ICCF, 63000, Clermont-Ferrand, France
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The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis. Biomolecules 2021; 11:biom11050725. [PMID: 34065948 PMCID: PMC8151747 DOI: 10.3390/biom11050725] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023] Open
Abstract
The pentose phosphate pathway (PPP) is a route that can work in parallel to glycolysis in glucose degradation in most living cells. It has a unidirectional oxidative part with glucose-6-phosphate dehydrogenase as a key enzyme generating NADPH, and a non-oxidative part involving the reversible transketolase and transaldolase reactions, which interchange PPP metabolites with glycolysis. While the oxidative branch is vital to cope with oxidative stress, the non-oxidative branch provides precursors for the synthesis of nucleic, fatty and aromatic amino acids. For glucose catabolism in the baker’s yeast Saccharomyces cerevisiae, where its components were first discovered and extensively studied, the PPP plays only a minor role. In contrast, PPP and glycolysis contribute almost equally to glucose degradation in other yeasts. We here summarize the data available for the PPP enzymes focusing on S. cerevisiae and Kluyveromyces lactis, and describe the phenotypes of gene deletions and the benefits of their overproduction and modification. Reference to other yeasts and to the importance of the PPP in their biotechnological and medical applications is briefly being included. We propose future studies on the PPP in K. lactis to be of special interest for basic science and as a host for the expression of human disease genes.
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Mouillot T, Brindisi MC, Chambrier C, Audia S, Brondel L. [Refeeding syndrome]. Rev Med Interne 2021; 42:346-354. [PMID: 33549330 DOI: 10.1016/j.revmed.2020.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 11/22/2020] [Accepted: 12/26/2020] [Indexed: 10/22/2022]
Abstract
Refeeding syndrome (RS) is a rare but severe condition that is poorly understood, often under-diagnosed and can lead to death. It occurs within 5 days after refeeding in patients after prolonged fasting or in a context of undernutrition. As a consequence of the abrupt transition from catabolism to anabolism, RS is defined as a decrease in plasma levels of phosphorus, potassium and/or magnesium, whether or not associated with organ dysfunction resulting from a decrease in one of the electrolytes or a thiamine deficiency, after refeeding. The clinical symptoms are varied and non-specific and are related to hydro electrolyte disorders, sodium-hydroxide retention or failure of one or more organs. Patient management should be appropriate with regular clinical examination and careful biological monitoring, including hydro electrolyte monitoring. The correction of hydroelectrolytic disorders and systematic thiamine supplementation are essential during refeeding, that must be done carefully and very progressively, whatever its form (oral, enteral or parenteral). The severity of the refeeding syndrome indicates that its prevention and screening are the corners of its management in at-risk patients.
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Affiliation(s)
- T Mouillot
- Service d'hépato-gastro-entérologie, CHU F.-Mitterrand, 21000 Dijon, France; AgroSup Dijon, CNRS, Inrae, centre des sciences du goût et de l'alimentation, université Bourgogne Franche-Comté, 21000 Dijon, France.
| | - M-C Brindisi
- AgroSup Dijon, CNRS, Inrae, centre des sciences du goût et de l'alimentation, université Bourgogne Franche-Comté, 21000 Dijon, France; Service d'endocrinologie et diabétologie, CHU F.-Mitterrand, 21000 Dijon, France
| | - C Chambrier
- Service de nutrition clinique intensive, hospices civils de Lyon, hôpital Lyon sud, 69495 Pierre-Bénite, France
| | - S Audia
- Service de médecine interne 1, CHU F.-Mitterrand, 21000 Dijon, France
| | - L Brondel
- Service d'hépato-gastro-entérologie, CHU F.-Mitterrand, 21000 Dijon, France; AgroSup Dijon, CNRS, Inrae, centre des sciences du goût et de l'alimentation, université Bourgogne Franche-Comté, 21000 Dijon, France
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26
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Labuschagne P, Divol B. Thiamine: a key nutrient for yeasts during wine alcoholic fermentation. Appl Microbiol Biotechnol 2021; 105:953-973. [PMID: 33404836 DOI: 10.1007/s00253-020-11080-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 12/27/2020] [Indexed: 12/27/2022]
Abstract
Alcoholic fermentation is a crucial step of winemaking, during which yeasts convert sugars to alcohol and also produce or biotransform numerous flavour compounds. In this context, nutrients are essential compounds to support yeast growth and ultimately ensure complete fermentation, as well as optimized production of flavour compounds over that of off-flavour compounds. In particular, the vitamin thiamine not only plays an essential cofactor role for several enzymes involved in various metabolic pathways, including those leading to the production of wine-relevant flavour compounds, but also aids yeast survival via thiamine-dependent stress protection functions. Most yeast species are able to both assimilate exogenous thiamine into the cell and synthesize thiamine de novo. However, the mechanism and level of thiamine accumulation depend on several factors. This review provides an in-depth overview of thiamine utilization and metabolism in the model yeast species Saccharomyces cerevisiae, as well as the current knowledge on (1) the intracellular functions of thiamine, (2) the balance between and regulation of uptake and synthesis of thiamine and (3) the multitude of factors influencing thiamine availability and utilization. For the latter, a particular emphasis is placed on conditions occurring during wine fermentation. The adequacy of thiamine concentration in grape must to ensure successful fermentation is discussed together with the effect of thiamine concentration on fermentation kinetics and on wine sensory properties. This knowledge may serve as a resource to optimise thiamine concentrations for optimal industrial application of yeasts. KEY POINTS: • Thiamine uptake is preferred over biosynthesis and is transcriptionally repressed. • Multiple factors affect thiamine synthesis, availability and uptake for wine yeast. • Thiamine availability impacts fermentation kinetics and wine's sensory properties.
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Affiliation(s)
- Pwj Labuschagne
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Private Bag X1, Matieland, 7602, South Africa
| | - B Divol
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Private Bag X1, Matieland, 7602, South Africa.
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Bajpai VK, Sonwal S, Hwang SK, Shukla S, Khan I, Dey DK, Chen L, Simal-Gandara J, Xiao J, Huh YS, Han YK. Sugiol, a diterpenoid: Therapeutic actions and molecular pathways involved. Pharmacol Res 2021; 163:105313. [PMID: 33246173 DOI: 10.1016/j.phrs.2020.105313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 02/08/2023]
Abstract
Understanding how the natural products structural diversity interacts with cellular metabolism and infectious disease targets remains a challenge. Inflammation is an important process in the human healing response in which the tissues respond to injuries induced by many agents, including pathogens. In recent years, several drugs derived from plant products have been developed, and current drug research is actively investigating the pharmacotherapeutic role of natural products in advanced multimodal inflammatory disease targeting. Sugiol, a diterpenoid, can act as an antimicrobial, antioxidant, anti-inflammatory, anti-carcinoma, antiviral, and cardiovascular agent. Until now, there have been no updates on the pharmacotherapeutic advancement of sugiol. Herein, we correlate the diverse molecular pathways in disease prevention involving sugiol. We also discuss the origins of its structural diversity and summarize new research directions toward exploring its novel effective future uses. Despite much evidence of its efficacy and safety, the sugiol has not yet been approved as a therapeutic agent due to its low bioavailability, and insolubility in an aqueous environment. The aim of this review is to renew and update noteworthy information on the pharmacotherapeutic characteristics of sugiol to approach different advanced strategies employed in the context of natural nurturing-based biomedicine.
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Affiliation(s)
- Vivek K Bajpai
- Department of Energy and Materials Engineering, Dongguk University, 30 Pildong-ro 1-gil, Seoul, 04620, South Korea
| | - Sonam Sonwal
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, Incheon 22212, Republic of Korea
| | - Seung-Kyu Hwang
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, Incheon 22212, Republic of Korea
| | - Shruti Shukla
- Department of Food Science and Technology, National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Sonipat, Haryana, 131028, India
| | - Imran Khan
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Debasish Kumar Dey
- Department of Biotechnology, Daegu University, Jillyang, Naeri-ri, Gyeongsan, Gyeongbuk, 38453, South Korea
| | - Lei Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo - Ourense Campus, E-32004 Ourense, Spain
| | - Jianbo Xiao
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo - Ourense Campus, E-32004 Ourense, Spain.
| | - Yun Suk Huh
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, Incheon 22212, Republic of Korea.
| | - Young-Kyu Han
- Department of Energy and Materials Engineering, Dongguk University, 30 Pildong-ro 1-gil, Seoul, 04620, South Korea.
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Mizukami H, Osonoi S. Pathogenesis and Molecular Treatment Strategies of Diabetic Neuropathy Collateral Glucose-Utilizing Pathways in Diabetic Polyneuropathy. Int J Mol Sci 2020; 22:ijms22010094. [PMID: 33374137 PMCID: PMC7796340 DOI: 10.3390/ijms22010094] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
Diabetic polyneuropathy (DPN) is the most common neuropathy manifested in diabetes. Symptoms include allodynia, pain, paralysis, and ulcer formation. There is currently no established radical treatment, although new mechanisms of DPN are being vigorously explored. A pathophysiological feature of DPN is abnormal glucose metabolism induced by chronic hyperglycemia in the peripheral nerves. Particularly, activation of collateral glucose-utilizing pathways such as the polyol pathway, protein kinase C, advanced glycation end-product formation, hexosamine biosynthetic pathway, pentose phosphate pathway, and anaerobic glycolytic pathway are reported to contribute to the onset and progression of DPN. Inhibitors of aldose reductase, a rate-limiting enzyme involved in the polyol pathway, are the only compounds clinically permitted for DPN treatment in Japan, although their efficacies are limited. This may indicate that multiple pathways can contribute to the pathophysiology of DPN. Comprehensive metabolic analysis may help to elucidate global changes in the collateral glucose-utilizing pathways during the development of DPN, and highlight therapeutic targets in these pathways.
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Affiliation(s)
- Hiroki Mizukami
- Department Pathology and Molecular Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan;
- Correspondence: ; Tel.: +81-172-39-5025
| | - Sho Osonoi
- Department Pathology and Molecular Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan;
- Department of Endocrinology and Metabolism, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
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29
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Runthala A, Sai TH, Kamjula V, Phulara SC, Rajput VS, Sangapillai K. Excavating the functionally crucial active-site residues of the DXS protein of Bacillus subtilis by exploring its closest homologues. J Genet Eng Biotechnol 2020; 18:76. [PMID: 33242110 PMCID: PMC7691408 DOI: 10.1186/s43141-020-00087-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/21/2020] [Indexed: 11/10/2022]
Abstract
Abstract
Background
To achieve a high yield of terpenoid-based therapeutics, 1-deoxy-d-xylulose-5-phosphate (DXP) pathway has been significantly exploited for the production of downstream enzymes. The DXP synthase (DXS) enzyme, the initiator of this pathway, is pivotal for the convergence of carbon flux, and is computationally studied well for the industrially utilized generally regarded as safe (GRAS) bacterium Bacillus subtilis to decode its vital regions for aiding the construction of a functionally improved mutant library.
Results
For the 546 sequence dataset of DXS sequences, a representative set of 108 sequences is created, and it shows a significant evolutionary divergence across different species clubbed into 37 clades, whereas three clades are observed for the 76 sequence dataset of Bacillus subtilis. The DXS enzyme, sharing a statistically significant homology to transketolase, is shown to be evolutionarily too distant. By the mutual information-based co-evolutionary network and hotspot analysis, the most crucial loci within the active site are deciphered. The 650-residue representative structure displays a complete conservation of 114 loci, and only two co-evolving residues ASP154 and ILE371 are found to be the conserved ones. Lastly, P318D is predicted to be the top-ranked mutation causing the increase in the thermodynamic stability of 6OUW.
Conclusion
The study excavates the vital functional, phylogenetic, and conserved residues across the active site of the DXS protein, the key rate-limiting controller of the entire pathway. It would aid to computationally understand the evolutionary landscape of this industrially useful enzyme and would allow us to widen its substrate repertoire to increase the enzymatic yield of unnatural molecules for in vivo and in vitro applications.
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30
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Boateng RA, Tastan Bishop Ö, Musyoka TM. Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study. Malar J 2020; 19:442. [PMID: 33256744 PMCID: PMC7756947 DOI: 10.1186/s12936-020-03512-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodial transketolase (PTKT) enzyme is one of the novel pharmacological targets being explored as potential anti-malarial drug target due to its functional role and low sequence identity to the human enzyme. Despite this, features contributing to such have not been exploited for anti-malarial drug design. Additionally, there are no anti-malarial drugs targeting PTKTs whereas the broad activity of these inhibitors against PTKTs from other Plasmodium spp. is yet to be reported. This study characterises different PTKTs [Plasmodium falciparum (PfTKT), Plasmodium vivax (PvTKT), Plasmodium ovale (PoTKT), Plasmodium malariae (PmTKT) and Plasmodium knowlesi (PkTKT) and the human homolog (HsTKT)] to identify key sequence and structural based differences as well as the identification of selective potential inhibitors against PTKTs. METHODS A sequence-based study was carried out using multiple sequence alignment, phylogenetic tree calculations and motif discovery analysis. Additionally, TKT models of PfTKT, PmTKT, PoTKT, PmTKT and PkTKT were modelled using the Saccharomyces cerevisiae TKT structure as template. Based on the modelled structures, molecular docking using 623 South African natural compounds was done. The stability, conformational changes and detailed interactions of selected compounds were accessed viz all-atom molecular dynamics (MD) simulations and binding free energy (BFE) calculations. RESULTS Sequence alignment, evolutionary and motif analyses revealed key differences between plasmodial and the human TKTs. High quality homodimeric three-dimensional PTKTs structures were constructed. Molecular docking results identified three compounds (SANC00107, SANC00411 and SANC00620) which selectively bind in the active site of all PTKTs with the lowest (better) binding affinity ≤ - 8.5 kcal/mol. MD simulations of ligand-bound systems showed stable fluctuations upon ligand binding. In all systems, ligands bind stably throughout the simulation and form crucial interactions with key active site residues. Simulations of selected compounds in complex with human TKT showed that ligands exited their binding sites at different time steps. BFE of protein-ligand complexes showed key residues involved in binding. CONCLUSIONS This study highlights significant differences between plasmodial and human TKTs and may provide valuable information for the development of novel anti-malarial inhibitors. Identified compounds may provide a starting point in the rational design of PTKT inhibitors and analogues based on these scaffolds.
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Affiliation(s)
- Rita Afriyie Boateng
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa.
| | - Thommas Mutemi Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa.
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31
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Solovjeva ON. The mechanism of a one-substrate transketolase reaction. Part II. Anal Biochem 2020; 613:114022. [PMID: 33217405 DOI: 10.1016/j.ab.2020.114022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 11/15/2022]
Abstract
In a recent paper, we showed the difference between the first stage of the one-substrate and the two-substrate transketolase reactions - the possibility of transfer of glycolaldehyde formed as a result of cleavage of the donor substrate from the thiazole ring of thiamine diphosphate to its aminopyrimidine ring through the tricycle formation stage, which is necessary for binding and splitting the second molecule of donor substrate [O.N. Solovjeva et al., The mechanism of a one-substrate transketolase reaction, Biosci. Rep. 40 (8) (2020) BSR20180246]. Here we show that under the action of the reducing agent a tricycle accumulates in a significant amount. Therefore, a significant decrease in the reaction rate of the one-substrate transketolase reaction compared to the two-substrate reaction is due to the stage of transferring the first glycolaldehyde molecule from the thiazole ring to the aminopyrimidine ring of thiamine diphosphate. Fragmentation of the four-carbon thiamine diphosphate derivatives showed that two glycolaldehyde molecules are bound to both coenzyme rings and the erythrulose molecule is bound to a thiazole ring. It was concluded that in the one-substrate reaction erythrulose is formed on the thiazole ring of thiamine diphosphate from two glycol aldehyde molecules linked to both thiamine diphosphate rings. The kinetic characteristics were determined for the two substrates, fructose 6-phosphate and glycolaldehyde.
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Affiliation(s)
- Olga N Solovjeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russian Federation.
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James P, Isupov MN, De Rose SA, Sayer C, Cole IS, Littlechild JA. A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans: Structure and Biochemical Characterization. Front Microbiol 2020; 11:592353. [PMID: 33193259 PMCID: PMC7661550 DOI: 10.3389/fmicb.2020.592353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
A novel transketolase has been reconstituted from two separate polypeptide chains encoded by a ‘split-gene’ identified in the genome of the hyperthermophilic bacterium, Carboxydothermus hydrogenoformans. The reconstituted active α2β2 tetrameric enzyme has been biochemically characterized and its activity has been determined using a range of aldehydes including glycolaldehyde, phenylacetaldehyde and cyclohexanecarboxaldehyde as the ketol acceptor and hydroxypyruvate as the donor. This reaction proceeds to near 100% completion due to the release of the product carbon dioxide and can be used for the synthesis of a range of sugars of interest to the pharmaceutical industry. This novel reconstituted transketolase is thermally stable with no loss of activity after incubation for 1 h at 70°C and is stable after 1 h incubation with 50% of the organic solvents methanol, ethanol, isopropanol, DMSO, acetonitrile and acetone. The X-ray structure of the holo reconstituted α2β2 tetrameric transketolase has been determined to 1.4 Å resolution. In addition, the structure of an inactive tetrameric β4 protein has been determined to 1.9 Å resolution. The structure of the active reconstituted α2β2 enzyme has been compared to the structures of related enzymes; the E1 component of the pyruvate dehydrogenase complex and D-xylulose-5-phosphate synthase, in an attempt to rationalize differences in structure and substrate specificity between these enzymes. This is the first example of a reconstituted ‘split-gene’ transketolase to be biochemically and structurally characterized allowing its potential for industrial biocatalysis to be evaluated.
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Affiliation(s)
- Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Isobel S Cole
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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da Silva JSV, Seres DS, Sabino K, Adams SC, Berdahl GJ, Citty SW, Cober MP, Evans DC, Greaves JR, Gura KM, Michalski A, Plogsted S, Sacks GS, Tucker AM, Worthington P, Walker RN, Ayers P. ASPEN Consensus Recommendations for Refeeding Syndrome. Nutr Clin Pract 2020; 35:178-195. [DOI: 10.1002/ncp.10474] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
| | - David S. Seres
- Columbia University Irving Medical Center New York New York USA
| | - Kim Sabino
- Saint Francis Hospital and Medical Center Hartford Connecticut USA
| | | | - Gideon J. Berdahl
- School of Pharmacy, University of Mississippi Jackson Mississippi USA
| | | | - M. Petrea Cober
- Akron Children's Hospital Akron Ohio USA
- Northeast Ohio Medical University Rootstown Ohio USA
| | - David C. Evans
- Ohio Health Trauma and Surgical Services Columbus Ohio USA
| | - June R. Greaves
- Coram CVS Speciality Infusion Services Northbrook Illinois USA
| | | | - Austin Michalski
- Patient Food and Nutrition ServicesMichigan Medicine Ann Arbor Michigan USA
| | - Stephen Plogsted
- Nutrition Support ServiceNationwide Children's Hospital Columbus Ohio USA
| | - Gordon S. Sacks
- Medical AffairsFresenius Kabi USA LLC Lake Zurich Illinois USA
| | - Anne M. Tucker
- Critical Care and Nutrition SupportUniversity of Texas M D Anderson Cancer Center Houston Texas USA
| | | | - Renee N. Walker
- Michael E. DeBakey Veterans Affairs Medical Center Houston Texas USA
| | - Phil Ayers
- Clinical Pharmacy ServicesMississippi Baptist Medical Center Jackson Mississippi USA
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Understanding and Eliminating the Detrimental Effect of Thiamine Deficiency on the Oleaginous Yeast Yarrowia lipolytica. Appl Environ Microbiol 2020; 86:AEM.02299-19. [PMID: 31704686 DOI: 10.1128/aem.02299-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/05/2019] [Indexed: 01/19/2023] Open
Abstract
Thiamine is a vitamin that functions as a cofactor for key enzymes in carbon and energy metabolism in all living cells. While most plants, fungi, and bacteria can synthesize thiamine de novo, the oleaginous yeast Yarrowia lipolytica cannot. In this study, we used proteomics together with physiological characterization to elucidate key metabolic processes influenced and regulated by thiamine availability and to identify the genetic basis of thiamine auxotrophy in Y. lipolytica Specifically, we found that thiamine depletion results in decreased protein abundance for the lipid biosynthesis pathway and energy metabolism (i.e., ATP synthase), leading to the negligible growth and poor sugar assimilation observed in our study. Using comparative genomics, we identified the missing 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase (THI13) gene for the de novo thiamine biosynthesis in Y. lipolytica and discovered an exceptional promoter, P3, that exhibits strong activation and tight repression by low and high thiamine concentrations, respectively. Capitalizing on the strength of our thiamine-regulated promoter (P3) to express the missing gene from Saccharomyces cerevisiae (scTHI13), we engineered a thiamine-prototrophic Y. lipolytica strain. By comparing this engineered strain to the wild-type strain, we revealed the tight relationship between thiamine availability and lipid biosynthesis and demonstrated enhanced lipid production with thiamine supplementation in the engineered thiamine-prototrophic Y. lipolytica strain.IMPORTANCE Thiamine plays a crucial role as an essential cofactor for enzymes involved in carbon and energy metabolism in all living cells. Thiamine deficiency has detrimental consequences for cellular health. Yarrowia lipolytica, a nonconventional oleaginous yeast with broad biotechnological applications, is a native thiamine auxotroph whose affected cellular metabolism is not well understood. Therefore, Y. lipolytica is an ideal eukaryotic host for the study of thiamine metabolism, especially because mammalian cells are also thiamine auxotrophic and thiamine deficiency is implicated in several human diseases. This study elucidates the fundamental effects of thiamine deficiency on cellular metabolism in Y. lipolytica and identifies genes and novel thiamine-regulated elements that eliminate thiamine auxotrophy in Y. lipolytica Furthermore, the discovery of thiamine-regulated elements enables the development of thiamine biosensors with useful applications in synthetic biology and metabolic engineering.
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Bi H, Li F, Wang H, Ai X. Overexpression of transketolase gene promotes chilling tolerance by increasing the activities of photosynthetic enzymes, alleviating oxidative damage and stabilizing cell structure in Cucumis sativus L. PHYSIOLOGIA PLANTARUM 2019; 167:502-515. [PMID: 30548278 DOI: 10.1111/ppl.12903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/29/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Despite being a key enzyme of Cavin cycle, transketolase (TK) is believed to be related to abiotic resistance in higher plants. However, how TK affects chilling tolerance still remains largely unknown. Here, we describe the effect of overexpression of the Cucumis sativa TK gene (CsTK) on growth, photosynthesis, ROS metabolism and cell ultrastructure under chilling stress. Low temperature led to a decrease of the photosynthetic rate (Pn), the stomatal conductance (Gs), the actual photochemical efficiency (ΦPSII) and the sucrose content, whereas there was an increase of the intercellular CO2 concentration (Ci) and MDA content. These changes were alleviated in the CsTK plants after 5 days of chilling stress, however, inhibition of CsTK showed the opposite results. Furthermore, transgenic plants with overexpression of CsTK showed higher increase in leaf area and dry matter, higher activity of the enzymes and higher increase in the contents of metabolism substance involved in Calvin cycle and reactive oxygen scavenging system as well as lower • OH and H2 O2 content, superoxide anion production rate compared with the control cucumber plants under chilling stress. At the end of the chilling stress, compared to wild-type (WT) which exhibited dramatically destroyed cell ultrastructure, expanded chloroplast, broken cell and chloroplast membranes as well as the disappeared grana lamella, the CsTK sense plants showed a more complete cell ultrastructure, whereas, the damage of the cell ultrastructure was aggravated in CsTK antisense plants. Taken together, these results imply that CsTK promoted chilling tolerance in cucumber plants mainly through increasing the capacity to assimilate carbon, alleviating oxidative damage and stabilizing cell structure.
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Affiliation(s)
- Huangai Bi
- StateKey Laboratory of Crop Biology/Key Laboratory of Crop Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Fude Li
- StateKey Laboratory of Crop Biology/Key Laboratory of Crop Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Haiguang Wang
- StateKey Laboratory of Crop Biology/Key Laboratory of Crop Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xizhen Ai
- StateKey Laboratory of Crop Biology/Key Laboratory of Crop Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region/College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Yu H, Hernández López RI, Steadman D, Méndez‐Sánchez D, Higson S, Cázares‐Körner A, Sheppard TD, Ward JM, Hailes HC, Dalby PA. Engineering transketolase to accept both unnatural donor and acceptor substrates and produce α‐hydroxyketones. FEBS J 2019; 287:1758-1776. [DOI: 10.1111/febs.15108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/26/2019] [Accepted: 10/23/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering University College London UK
| | | | | | | | - Sally Higson
- Department of Chemistry University College London UK
| | | | | | - John M. Ward
- Department of Biochemical Engineering University College London UK
| | | | - Paul A. Dalby
- Department of Biochemical Engineering University College London UK
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Akram M, Ali Shah SM, Munir N, Daniyal M, Tahir IM, Mahmood Z, Irshad M, Akhlaq M, Sultana S, Zainab R. Hexose monophosphate shunt, the role of its metabolites and associated disorders: A review. J Cell Physiol 2019; 234:14473-14482. [PMID: 30697723 DOI: 10.1002/jcp.28228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 01/24/2023]
Abstract
The hexose monophosphate (HMP) shunt acts as an essential component of cellular metabolism in maintaining carbon homeostasis. The HMP shunt comprises two phases viz. oxidative and nonoxidative, which provide different intermediates for the synthesis of biomolecules like nucleotides, DNA, RNA, amino acids, and so forth; reducing molecules for anabolism and detoxifying the reactive oxygen species during oxidative stress. The HMP shunt is significantly important in the liver, adipose tissue, erythrocytes, adrenal glands, lactating mammary glands and testes. We have researched the articles related to the HMP pathway, its metabolites and disorders related to its metabolic abnormalities. The literature for this paper was taken typically from a personal database, the Cochrane database of systemic reviews, PubMed publications, biochemistry textbooks, and electronic journals uptil date on the hexose monophosphate shunt. The HMP shunt is a tightly controlled metabolic pathway, which is also interconnected with other metabolic pathways in the body like glycolysis, gluconeogenesis, and glucuronic acid depending upon the metabolic needs of the body and depending upon the biochemical demand. The HMP shunt plays a significant role in NADPH2 formation and in pentose sugars that are biosynthetic precursors of nucleic acids and amino acids. Cells can be protected from highly reactive oxygen species by NADPH 2 . Deficiency in the hexose monophosphate pathway is linked to numerous disorders. Furthermore, it was also reported that this metabolic pathway could act as a therapeutic target to treat different types of cancers, so treatments at the molecular level could be planned by limiting the synthesis of biomolecules required for proliferating cells provided by the HMP shunt, hence, more experiments still could be carried out to find additional discoveries.
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Affiliation(s)
- Muhammad Akram
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Syed Muhammad Ali Shah
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Naveed Munir
- College of Allied Health Professional, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan.,Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Muhammad Daniyal
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Imtiaz Mahmood Tahir
- College of Allied Health Professional, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Zahed Mahmood
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Muhammad Irshad
- Department of Chemistry, University of Kotli, Azad Jammu & Kashmir (UoKAJK), Pakistan
| | - Muhammad Akhlaq
- Department of Pharmaceutics, Faculty of Pharmacy, Gomal University, DIK, KP, Pakistan
| | - Sabira Sultana
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
| | - Rida Zainab
- Department of Eastern Medicine, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
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Washburn LA, Foley B, Martinez F, Lee RP, Pryor K, Rimes E, Watanabe CMH. Transketolase Activity in the Formation of the Azinomycin Azabicycle Moiety. Biochemistry 2019; 58:5255-5258. [DOI: 10.1021/acs.biochem.9b00477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Lauren A. Washburn
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Brendan Foley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Flor Martinez
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rachel P. Lee
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kendall Pryor
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Emily Rimes
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Coran M. H. Watanabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Transketolase and vitamin B1 influence on ROS-dependent neutrophil extracellular traps (NETs) formation. PLoS One 2019; 14:e0221016. [PMID: 31415630 PMCID: PMC6695114 DOI: 10.1371/journal.pone.0221016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Neutrophil extracellular traps (NETs) are a recently identified, web-like, extracellular structure composed of decondensed nuclear DNA and associated antimicrobial granules. NETs are extruded into the extracellular environment via the reactive oxygen species (ROS)-dependent cell death pathway participating in inflammation and autoimmune diseases. Transketolase (TKT) is a thiamine pyrophosphate (vitamin B1)-dependent enzyme that links the pentose phosphate pathway with the glycolytic pathway by feeding excess sugar phosphates into the main carbohydrate metabolic pathways to generate biosynthetic reducing capacity in the form of NADPH as a substrate for ROS generation. In this work, TKT was selected as a lead candidate from 24 NET-associated proteins obtained by literature screening and knowledge gap assessment. Consequently, we determined whether TKT influenced NET formation in vitro. We firstly established that the release of ROS-dependent NETs was significantly decreased after purified human PMNs were pretreated with oxythiamine, a TKT inhibitor, and in a concentration dependent manner. As a cofactor for TKT reaction, we evaluated the release of NET formation either in vitamin B1 treatment or in combined use of oxythiamine and vitamin B1, and found that those treatments also exerted a significant suppressive effect on the amount of NET-DNA and ROS production. The regulation of TKT by oxythiamine and/or vitamin B1 may therefore be associated with response to the modulation of NET formation by preventing generation of excessive NETs in inflammatory diseases.
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Ning M, Xiu Y, Yuan M, Bi J, Hou L, Gu W, Wang W, Meng Q. Spiroplasma eriocheiris Invasion Into Macrobrachium rosenbergii Hemocytes Is Mediated by Pathogen Enolase and Host Lipopolysaccharide and β-1, 3-Glucan Binding Protein. Front Immunol 2019; 10:1852. [PMID: 31440244 PMCID: PMC6694788 DOI: 10.3389/fimmu.2019.01852] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 07/23/2019] [Indexed: 01/01/2023] Open
Abstract
Spiroplasma eriocheiris is a crustacean pathogen, without a cell wall, that causes enormous economic loss. Macrobrachium rosenbergii hemocytes are the major targets during S. eriocheiris infection. As wall-less bacteria, S. eriocheiris, its membrane protein should interact with host membrane protein directly and firstly when invaded in host cell. In this investigation, six potential hemocyte receptor proteins were identified firstly that mediate interaction between S. eriocheiris and M. rosenbergii. Among these proteins, lipopolysaccharide and β-1, 3-glucan binding protein (MrLGBP) demonstrated to bind to S. eriocheiris using bacterial binding assays and confocal microscopy. Four spiroplasma ligand proteins for MrLGBP were isolated and identified. But, competitive assessment demonstrated that only enolase of S. eriocheiris (SeEnolase) could be a candidate ligand for MrLGBP. Subsequently, the interaction between MrLGBP and SeEnolase was confirmed by co-immunoprecipitation and co-localization in vitro. After the interaction between MrLGBP and SeEnolase was inhibited by antibody neutralization test, the virulence ability of S. eriocheiris was effectively reduced. The quantity of S. eriocheiris decreased in Drosophila S2 cells after overexpression of MrLGBP, compared with the controls. In addition, RNA interference (RNAi) knockdown of MrLGBP made M. rosenbergii more sensitive to S. eriocheiris infection. Further studies found that the immune genes, including MrLGBP and prophenoloxidase (MrproPO), MrRab7A, and Mrintegrin α1 were significantly up-regulated by SeEnolase stimulation. After SeEnolase pre-stimulation, the ability of M. rosenbergii resistance to S. eriocheiris was significantly improved. Collectively, this investigation demonstrated that MrLGBP and pathogen SeEnolase involved in mediating S. eriocheiris invasion into M. rosenbergii hemocytes.
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Affiliation(s)
- Mingxiao Ning
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yunji Xiu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China.,Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, China
| | - Meijun Yuan
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingxiu Bi
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Libo Hou
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Gu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China.,Co-innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, China
| | - Wen Wang
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China.,College of Life Sciences, Nanjing Normal University, Nanjing, China.,Co-innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, China
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Yatoo MI, Parray OR, Bhat RA, Nazir QU, Haq AU, Malik HU, Fazilli MUR, Gopalakrishnan A, Bashir ST, Tiwari R, Khurana SK, Chaicumpa W, Dhama K. Novel Candidates for Vaccine Development Against Mycoplasma Capricolum Subspecies Capripneumoniae (Mccp)-Current Knowledge and Future Prospects. Vaccines (Basel) 2019; 7:E71. [PMID: 31340571 PMCID: PMC6789616 DOI: 10.3390/vaccines7030071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Exploration of novel candidates for vaccine development against Mycoplasma capricolum subspecies capripneumoniae (Mccp), the causative agent of contagious caprine pleuropneumonia (CCPP), has recently gained immense importance due to both the increased number of outbreaks and the alarming risk of transboundary spread of disease. Treatment by antibiotics as the only therapeutic strategy is not a viable option due to pathogen persistence, economic issues, and concerns of antibiotic resistance. Therefore, prophylactics or vaccines are becoming important under the current scenario. For quite some time inactivated, killed, or attenuated vaccines proved to be beneficial and provided good immunity up to a year. However, their adverse effects and requirement for larger doses led to the need for production of large quantities of Mccp. This is challenging because the required culture medium is costly and Mycoplasma growth is fastidious and slow. Furthermore, quality control is always an issue with such vaccines. Currently, novel candidate antigens including capsular polysaccharides (CPS), proteins, enzymes, and genes are being evaluated for potential use as vaccines. These have shown potential immunogenicity with promising results in eliciting protective immune responses. Being easy to produce, specific, effective and free from side effects, these novel vaccine candidates can revolutionize vaccination against CCPP. Use of novel proteomic approaches, including sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis, immunoblotting, matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry, tandem mass spectroscopy, fast protein liquid chromatography (FPLC), bioinformatics, computerized simulation and genomic approaches, including multilocus sequence analysis, next-generation sequencing, basic local alignment search tool (BLAST), gene expression, and recombinant expression, will further enable recognition of ideal antigenic proteins and virulence genes with vaccination potential.
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Affiliation(s)
- Mohd Iqbal Yatoo
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India.
| | - Oveas Raffiq Parray
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Riyaz Ahmed Bhat
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Qurat Un Nazir
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Abrar Ul Haq
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Hamid Ullah Malik
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Mujeeb Ur Rehman Fazilli
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Arumugam Gopalakrishnan
- Department of Veterinary Clinical Medicine, Madras Veterinary College, Tamilnadu Veterinary and Animal Sciences University, Vepery 600007, India
| | - Shah Tauseef Bashir
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura 281001, India
| | - Sandip Kumar Khurana
- ICAR-Central Institute for Research on Buffaloes, Sirsa Road, Hisar 125001, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
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Babele PK, Kumar J, Chaturvedi V. Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses. Front Microbiol 2019; 10:1315. [PMID: 31263458 PMCID: PMC6584798 DOI: 10.3389/fmicb.2019.01315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs, exhibiting a cosmopolitan distribution in almost all possible environments and are significantly responsible for half of the global net primary productivity. They are well adapted to the diverse environments including harsh conditions by evolving a range of fascinating repertoires of unique biomolecules and secondary metabolites to support their growth and survival. These phototrophs are proved as excellent models for unraveling the mysteries of basic biochemical and physiological processes taking place in higher plants. Several known species of cyanobacteria have tremendous biotechnological applications in diverse fields such as biofuels, biopolymers, secondary metabolites and much more. Due to their potential biotechnological and commercial applications in various fields, there is an imperative need to engineer robust cyanobacteria in such a way that they can tolerate and acclimatize to ever-changing environmental conditions. Adaptations to stress are mainly governed by a precise gene regulation pathways resulting in the expression of novel protein/enzymes and metabolites. Despite the demand, till date few proteins/enzymes have been identified which play a potential role in improving tolerance against abiotic stresses. Therefore, it is utmost important to study environmental stress responses related to post-genomic investigations, including proteomic changes employing advanced proteomics, synthetic and structural biology workflows. In this respect, the study of stress proteomics offers exclusive advantages to scientists working on these aspects. Advancements on these fields could be helpful in dissecting, characterization and manipulation of physiological and metabolic systems of cyanobacteria to understand the stress induced proteomic responses. Till date, it remains ambiguous how cyanobacteria perceive changes in the ambient environment that lead to the stress-induced proteins thus metabolic deregulation. This review briefly describes the current major findings in the fields of proteome research on the cyanobacteria under various abiotic stresses. These findings may improve and advance the information on the role of different class of proteins associated with the mechanism(s) of stress mitigation in cyanobacteria under harsh environmental conditions.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Qin Z, Xiang C, Zhong F, Liu Y, Dong Q, Li K, Shi W, Ding C, Qin L, He F. Transketolase (TKT) activity and nuclear localization promote hepatocellular carcinoma in a metabolic and a non-metabolic manner. J Exp Clin Cancer Res 2019; 38:154. [PMID: 30971297 PMCID: PMC6458711 DOI: 10.1186/s13046-019-1131-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/08/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Metabolic reprogramming is one of the hallmarks of cancer cells. The pentose phosphate pathway (PPP), a branch of glycolysis, is an important metabolic pathway for the survival and biosynthesis of cancer cells. Transketolase (TKT) is a key enzyme in the non-oxidative phase of PPP. The mechanistic details of TKT in hepatocellular carcinoma (HCC) development remain unclear. METHODS TKT level and subcellular location were examined in HCC cell lines and tissue samples. We established the TKT overexpression and knocking-down stable cells in HCC cell lines. Proliferation, migration, viability and enzyme activity assays in vitro, tumor growth and metastasis assays in vivo were employed to test the effects of TKT on HCC development. GFP-tagged TKT truncations and mutants were used to locate the nuclear localization sequence (NLSs) of TKT. Cross-linking co-IP/MS was applied to identify the interaction proteins of nuclear TKT. RESULTS We showed that TKT increased the proliferation and migration of HCC cells, as well as the viability under oxidative stress in vitro and accelerated the growth and metastasis of HCC cells in vivo. We found as a key enzyme of PPP, TKT could promote the proliferation, cell cycle, migration and viability by regulating the metabolic flux. Moreover, it was firstly reported that unlike other key enzymes in PPP, TKT showed a strong nuclear localization in HCC cells. We found not only high TKT expression, but also its nuclear localization was a prediction for poor prognosis of HCC patients. We further identified the nuclear localization sequences (NLS) for TKT and demonstrated the NLS mutations decreased the pro-tumor function of TKT independent of the enzyme activity. Cross-linking Co-IP/MS showed that nuclear TKT interacted with kinases and transcriptional coregulators such as EGFR and MAPK3, which are associated with cell activation or stress response processes. EGF treatment significantly increased the viability and proliferation of HCC cells in the enzyme-inactivating mutation TKT-D155A overexpression cells but not in the NLS-D155A double mutant group, which could be blocked by EGFR inhibitor erlotinib treatment. CONCLUSIONS Our research suggests that in addition to the metabolic manner, TKT can promote the development of HCC in a non-metabolic manner via its nuclear localization and EGFR pathway.
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Affiliation(s)
- Zhaoyu Qin
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Fan Zhong
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Yang Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Qiongzhu Dong
- Department of Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai, 200040 China
| | - Kai Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China
| | - Wenhao Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China
| | - Chen Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Lunxiu Qin
- Department of Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai, 200040 China
| | - Fuchu He
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China
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Solovjeva ON, Selivanov VA, Orlov VN, Kochetov GA. Stages of the formation of nonequivalence of active centers of transketolase from baker’s yeast. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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45
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Zheng Y, Ming P, Zhu C, Si Y, Xu S, Chen A, Wang J, Zhang B. Hepatitis B virus X protein-induced SH2 domain-containing 5 (SH2D5) expression promotes hepatoma cell growth via an SH2D5-transketolase interaction. J Biol Chem 2019; 294:4815-4827. [PMID: 30659097 DOI: 10.1074/jbc.ra118.005739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/09/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus X protein (HBx) critically contributes to the development of hepatocellular carcinoma (HCC). However, the mechanisms by which HBx promotes HCC remain unclear. In the present study, using a combination of gene expression profiling and immunohistochemistry, we found higher levels of SH2 domain-containing 5 (SH2D5) in liver tissue from HBV-associated HCC (HBV-HCC) patients than in adjacent nontumor tissues. Moreover, HBV infection elevated SH2D5 levels, and we observed that HBx plays an important role in SH2D5 induction. We also found that HBx triggers SH2D5 expression through the NF-κB and c-Jun kinase pathways. Employing SH2D5 overexpression or knockdown, we further demonstrate that SH2D5 promotes HCC cell proliferation both in vitro and in vivo While investigating the mechanism of SH2D5-mediated stimulation of HCC cell proliferation, we noted that HBV induces SH2D5 binding to transketolase (TKT), a pentose phosphate pathway enzyme, thereby promoting an interaction between and signal transducer and activator of transcription 3 (STAT3). Furthermore, HBx stimulated STAT3 phosphorylation at Tyr-705 and promoted the activity and downstream signaling pathway of STAT3 via the SH2D5-TKT interaction. Taken together, our results suggest that SH2D5 is an HBV-induced protein capable of binding to TKT, leading to induction of HCC cell proliferation.
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Affiliation(s)
| | | | | | - Yu Si
- the Department of Otolaryngology-Head and Neck Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120
| | - Shilei Xu
- the Department of General Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510530
| | - Aidong Chen
- the Department of Physiology, Nanjing Medical University, Nanjing 211166, and
| | - Jun Wang
- the Center of Clinical Laboratory, Fifth People's Hospital of Wuxi, affiliated with Jiangnan University, Wuxi, Jiangsu 214005, China
| | - Binghong Zhang
- Neonatology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060,
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Wang Z, Cui J, Song J, Wang H, Gao K, Qiu X, Gou M, Li X, Hu Z, Wang X, Chang Y. Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:193-205. [PMID: 29492749 DOI: 10.1007/s10126-018-9796-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/24/2018] [Indexed: 06/08/2023]
Abstract
Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.
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Affiliation(s)
- Zhicheng Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jun Cui
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
| | - Haoze Wang
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Kailun Gao
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xuemei Qiu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Meng Gou
- School of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Xin Li
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Ziwen Hu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xiuli Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
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Papapetridis I, Goudriaan M, Vázquez Vitali M, de Keijzer NA, van den Broek M, van Maris AJA, Pronk JT. Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:17. [PMID: 29416562 PMCID: PMC5784725 DOI: 10.1186/s13068-017-1001-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/18/2017] [Indexed: 05/27/2023]
Abstract
BACKGROUND Reduction or elimination of by-product formation is of immediate economic relevance in fermentation processes for industrial bioethanol production with the yeast Saccharomyces cerevisiae. Anaerobic cultures of wild-type S. cerevisiae require formation of glycerol to maintain the intracellular NADH/NAD+ balance. Previously, functional expression of the Calvin-cycle enzymes ribulose-1,5-bisphosphate carboxylase (RuBisCO) and phosphoribulokinase (PRK) in S. cerevisiae was shown to enable reoxidation of NADH with CO2 as electron acceptor. In slow-growing cultures, this engineering strategy strongly decreased the glycerol yield, while increasing the ethanol yield on sugar. The present study explores engineering strategies to improve rates of growth and alcoholic fermentation in yeast strains that functionally express RuBisCO and PRK, while maximizing the positive impact on the ethanol yield. RESULTS Multi-copy integration of a bacterial-RuBisCO expression cassette was combined with expression of the Escherichia coli GroEL/GroES chaperones and expression of PRK from the anaerobically inducible DAN1 promoter. In anaerobic, glucose-grown bioreactor batch cultures, the resulting S. cerevisiae strain showed a 31% lower glycerol yield and a 31% lower specific growth rate than a non-engineered reference strain. Growth of the engineered strain in anaerobic, glucose-limited chemostat cultures revealed a negative correlation between its specific growth rate and the contribution of the Calvin-cycle enzymes to redox homeostasis. Additional deletion of GPD2, which encodes an isoenzyme of NAD+-dependent glycerol-3-phosphate dehydrogenase, combined with overexpression of the structural genes for enzymes of the non-oxidative pentose-phosphate pathway, yielded a CO2-reducing strain that grew at the same rate as a non-engineered reference strain in anaerobic bioreactor batch cultures, while exhibiting a 86% lower glycerol yield and a 15% higher ethanol yield. CONCLUSIONS The metabolic engineering strategy presented here enables an almost complete elimination of glycerol production in anaerobic, glucose-grown batch cultures of S. cerevisiae, with an associated increase in ethanol yield, while retaining near wild-type growth rates and a capacity for glycerol formation under osmotic stress. Using current genome-editing techniques, the required genetic modifications can be introduced in one or a few transformations. Evaluation of this concept in industrial strains and conditions is therefore a realistic next step towards its implementation for improving the efficiency of first- and second-generation bioethanol production.
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Affiliation(s)
- Ioannis Papapetridis
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maaike Goudriaan
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - María Vázquez Vitali
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Nikita A. de Keijzer
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Present Address: School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 10691 Stockholm, Sweden
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Hawkins JP, Ordonez PA, Oresnik IJ. Characterization of Mutations That Affect the Nonoxidative Pentose Phosphate Pathway in Sinorhizobium meliloti. J Bacteriol 2018; 200:e00436-17. [PMID: 29084855 PMCID: PMC5738737 DOI: 10.1128/jb.00436-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/21/2017] [Indexed: 12/12/2022] Open
Abstract
Sinorhizobium meliloti is a Gram-negative alphaproteobacterium that can enter into a symbiotic relationship with Medicago sativa and Medicago truncatula Previous work determined that a mutation in the tkt2 gene, which encodes a putative transketolase, could prevent medium acidification associated with a mutant strain unable to metabolize galactose. Since the pentose phosphate pathway in S. meliloti is not well studied, strains carrying mutations in either tkt2 and tal, which encodes a putative transaldolase, were characterized. Carbon metabolism phenotypes revealed that both mutants were impaired in growth on erythritol and ribose. This phenotype was more pronounced for the tkt2 mutant strain, which also displayed auxotrophy for aromatic amino acids. Changes in pentose phosphate pathway metabolite concentrations were also consistent with a mutation in either tkt2 or tal The concentrations of metabolites in central carbon metabolism were also found to shift dramatically in strains carrying a tkt2 mutation. While the concentrations of proteins involved in central carbon metabolism did not change significantly under any conditions, the levels of those associated with iron acquisition increased in the wild-type strain with erythritol induction. These proteins were not detected in either mutant, resulting in less observable rhizobactin production in the tkt2 mutant. While both mutants were impaired in succinoglycan synthesis, only the tkt2 mutant strain was unable to establish symbiosis with alfalfa. These results suggest that tkt2 and tal play central roles in regulating the carbon flow necessary for carbon metabolism and the establishment of symbiosis.IMPORTANCESinorhizobium meliloti is a model organism for the study of plant-microbe interactions and metabolism, especially because it effects nitrogen fixation. The ability to derive the energy necessary for nitrogen fixation is dependent on an organism's ability to metabolize carbon efficiently. The pentose phosphate pathway is central in the interconversion of hexoses and pentoses. This study characterizes the key enzymes of the nonoxidative branch of the pentose phosphate pathway by using defined genetic mutations and shows the effects the mutations have on the metabolite profile and on physiological processes such as the biosynthesis of exopolysaccharide, as well as the ability to regulate iron acquisition.
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Affiliation(s)
- Justin P Hawkins
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Patricia A Ordonez
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ivan J Oresnik
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Zhang J, Li Z, Liu L, Wang Q, Li S, Chen D, Hu Z, Yu T, Ding J, Li J, Yao M, Huang S, Zhao Y, He X. Long noncoding RNA TSLNC8 is a tumor suppressor that inactivates the interleukin-6/STAT3 signaling pathway. Hepatology 2018; 67:171-187. [PMID: 28746790 DOI: 10.1002/hep.29405] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/26/2017] [Accepted: 07/23/2017] [Indexed: 02/06/2023]
Abstract
UNLABELLED Long noncoding RNAs can serve as oncogenes or tumor suppressors in human cancer; however, their biological functions and underlying mechanism in hepatocarcinogenesis are largely unknown. Here, we report a novel tumor suppressor long noncoding RNA on chromosome 8p12 (termed TSLNC8) that is frequently deleted and down-regulated in hepatocellular carcinoma (HCC) tissues. The loss of TSLNC8 is highly associated with the malignant features of HCC and serves as a prognostic indicator for HCC patients. TSLNC8 significantly suppresses the proliferation and metastasis of HCC cells in vitro and in vivo. TSLNC8 exerts its tumor suppressive activity by competitively interacting with transketolase and signal transducer and activator of transcription 3 (STAT3) and modulating the STAT3-Tyr705 and STAT3-Ser727 phosphorylation levels and STAT3 transcriptional activity, thus resulting in inactivation of the interleukin-6-STAT3 signaling pathway in HCC cells. CONCLUSION TSLNC8 is a promising prognostic predictor for patients with HCC, and the TSLNC8-transketolase-STAT3 axis is a potential therapeutic target for HCC treatment. (Hepatology 2018;67:171-187).
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Affiliation(s)
- Jiwei Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhe Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Longzi Liu
- Liver Cancer Institute, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qifeng Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shengli Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Di Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tao Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Ding
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jinjun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yingjun Zhao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Iwata H, Kobayashi Y, Mizushima D, Watanabe T, Ogihara J, Kasumi T. Complementary function of two transketolase isoforms from Moniliella megachiliensis in relation to stress response. AMB Express 2017; 7:45. [PMID: 28224439 PMCID: PMC5319944 DOI: 10.1186/s13568-017-0342-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 01/22/2023] Open
Abstract
Two transketolase isogenes, MmTKL1 and MmTKL2, isolated from Moniliella megachiliensis were investigated for their roles in stress response and erythritol biosynthesis. The encoded proteins were highly homologous in amino acid sequence and domain structure. Two stress response elements (STREs) were found upstream of MmTKL1, while no STRE was found upstream of MmTKL2. In contrast, two Ap-1 elements were present upstream of MmTKL2, but none were detected upstream of MmTKL1. MmTKL2 partially complemented the aromatic amino acid auxotrophy of a Saccharomyces cerevisiae tkl1 deletion mutant, suggesting that at least one of the MmTKLs functioned as a transketolase in vivo. In response to short-term osmotic stress (20% glucose or 1.2 M NaCl) in Moniliella cells, MmTKL1 expression increased rapidly through the first 40 min before subsequently decreasing gradually, while MmTKL2 expression showed no significant change. In contrast, short-term oxidative stress (0.15 mM menadione) induced considerable increases in MmTKL2, while MmTKL1 expression remained low under the same conditions. Long-term osmotic stress (20% glucose) yielded increased expression of both genes starting at 12 h and continuing through 72 h. During either osmotic or oxidative stress, intracellular erythritol accumulation could clearly be correlated with the pattern of expression of either MmTKL1 or MmTKL2. These results strongly suggested that MmTKL1 is responsible primarily for the response to osmotic stress, while MmTKL2 is responsible primarily for the response to oxidative stress. Thus, we postulate that the two transketolase isoforms of M. megachiliensis play distinct and complementary roles in coordinating erythritol production in response to distinct environmental stresses.
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