1
|
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.
Collapse
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
| |
Collapse
|
2
|
Wang C, Zhang L, Zhang Q, Zheng H, Yang X, Cai W, Zou Q, Lin J, Zhang L, Zhong L, Li X, Liao Y, Liu Q, Chen L, Li Y. Transketolase drives the development of aortic dissection by impairing mitochondrial bioenergetics. Acta Physiol (Oxf) 2024; 240:e14113. [PMID: 38380737 DOI: 10.1111/apha.14113] [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: 08/17/2023] [Revised: 01/12/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
AIM Aortic dissection (AD) is a disease with rapid onset but with no effective therapeutic drugs yet. Previous studies have suggested that glucose metabolism plays a critical role in the progression of AD. Transketolase (TKT) is an essential bridge between glycolysis and the pentose phosphate pathway. However, its role in the development of AD has not yet been elucidated. In this study, we aimed to explore the role of TKT in AD. METHODS We collected AD patients' aortic tissues and used high-throughput proteome sequencing to analyze the main factors influencing AD development. We generated an AD model using BAPN in combination with angiotensin II (Ang II) and pharmacological inhibitors to reduce TKT expression. The effects of TKT and its downstream mediators on AD were elucidated using human aortic vascular smooth muscle cells (HAVSMCs). RESULTS We found that glucose metabolism plays an important role in the development of AD and that TKT is upregulated in patients with AD. Western blot and immunohistochemistry confirmed that TKT expression was upregulated in mice with AD. Reduced TKT expression attenuated AD incidence and mortality, maintained the structural integrity of the aorta, aligned elastic fibers, and reduced collagen deposition. Mechanistically, TKT was positively associated with impaired mitochondrial bioenergetics by upregulating AKT/MDM2 expression, ultimately contributing to NDUFS1 downregulation. CONCLUSION Our results provide new insights into the role of TKT in mitochondrial bioenergetics and AD progression. These findings provide new intervention options for the treatment of AD.
Collapse
Affiliation(s)
- Chaoyun Wang
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Li Zhang
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Department of Physiology & Pathophysiology, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qinghua Zhang
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Hui Zheng
- Department of Cardiac Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xi Yang
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, China
| | - Weixing Cai
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Qiuying Zou
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Jingjing Lin
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Lin Zhang
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Lin Zhong
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Xinyao Li
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Yuqing Liao
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Qin Liu
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Liangwan Chen
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, China
| | - Yumei Li
- Fujian Center for Safety Evaluation of New Drug, The School of Pharmacy, Fujian Medical University, Fuzhou, China
- Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Aleshin VA, Kaehne T, Maslova MV, Graf AV, Bunik VI. Posttranslational Acylations of the Rat Brain Transketolase Discriminate the Enzyme Responses to Inhibitors of ThDP-Dependent Enzymes or Thiamine Transport. Int J Mol Sci 2024; 25:917. [PMID: 38255994 PMCID: PMC10815635 DOI: 10.3390/ijms25020917] [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: 10/24/2023] [Revised: 12/23/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Transketolase (TKT) is an essential thiamine diphosphate (ThDP)-dependent enzyme of the non-oxidative branch of the pentose phosphate pathway, with the glucose-6P flux through the pathway regulated in various medically important conditions. Here, we characterize the brain TKT regulation by acylation in rats with perturbed thiamine-dependent metabolism, known to occur in neurodegenerative diseases. The perturbations are modeled by the administration of oxythiamine inhibiting ThDP-dependent enzymes in vivo or by reduced thiamine availability in the presence of metformin and amprolium, inhibiting intracellular thiamine transporters. Compared to control rats, chronic administration of oxythiamine does not significantly change the modification level of the two detected TKT acetylation sites (K6 and K102) but doubles malonylation of TKT K499, concomitantly decreasing 1.7-fold the level of demalonylase sirtuin 5. The inhibitors of thiamine transporters do not change average levels of TKT acylation or sirtuin 5. TKT structures indicate that the acylated residues are distant from the active sites. The acylations-perturbed electrostatic interactions may be involved in conformational shifts and/or the formation of TKT complexes with other proteins or nucleic acids. Acetylation of K102 may affect the active site entrance/exit and subunit interactions. Correlation analysis reveals that the action of oxythiamine is characterized by significant negative correlations of K499 malonylation or K6 acetylation with TKT activity, not observed upon the action of the inhibitors of thiamine transport. However, the transport inhibitors induce significant negative correlations between the TKT activity and K102 acetylation or TKT expression, absent in the oxythiamine group. Thus, perturbations in the ThDP-dependent catalysis or thiamine transport manifest in the insult-specific patterns of the brain TKT malonylation and acetylations.
Collapse
Affiliation(s)
- Vasily A. Aleshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Thilo Kaehne
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39106 Magdeburg, Germany;
| | - Maria V. Maslova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Anastasia V. Graf
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Victoria I. Bunik
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| |
Collapse
|
5
|
Lv Z, Ji F, Song J, Li P, Chen M, Chang J. Predicting the spatial structure of membrane protein and B-cell epitopes of the MPXV_VEROE6 strain of monkeypox virus. Heliyon 2023; 9:e20386. [PMID: 37767496 PMCID: PMC10520823 DOI: 10.1016/j.heliyon.2023.e20386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
By targeting the membrane (M) proteins of monkeypox virus (MPXV) strain VEROE6, we analyzed its evolutionary hierarchy and predicted its dominant antigenic B-cell epitope to provide a theoretical basis for the development of MPXV epitope vaccines and related monoclonal antibodies. In this study, phylogenetic trees were constructed based on the nucleic acid sequences of MPXV and the amino acid sequences of M proteins. The 3D structure of the MPXV_VEROE6 M proteins was predicted with AlphaFold v2.0 and the dominant antigenic B-cell epitopes were comprehensively predicted by analyzing parameters such as flexible segments, the hydrophilic index, the antigenic index, and the protein surface probability. The results showed that the M protein of MPXV_VEROE6 contained 377 amino acids, and their spatial configuration was relatively regular with a turning and random coil structure. The results of a comprehensive multiparameter analysis indicated that possible B-cell epitopes were located in the 23-28, 57-63, 67-78, 80-93, 98-105, 125-131, 143-149, 201-206, 231-237, 261-270, 291-303, and 346-362 amino acid segments. This study elucidated the structural and evolutionary characteristics of MPXV membrane proteins with the aim of providing theoretical information for the development of epitope vaccines, rapid diagnostic reagents, and monoclonal antibodies for monkeypox virus.
Collapse
Affiliation(s)
- Zhiyuan Lv
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
| | - Feng Ji
- Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Jianzhong Song
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
- Department of Pharmacy, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011,China
| | - Panpan Li
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
| | - Ming Chen
- Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Junmin Chang
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
| |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Olga N Solovjeva
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia
| |
Collapse
|
7
|
Hao S, Meng Q, Sun H, Li Y, Li Y, Gu L, Liu B, Zhang Y, Zhou H, Xu Z, Wang Y. The role of transketolase in human cancer progression and therapy. Biomed Pharmacother 2022; 154:113607. [PMID: 36030587 DOI: 10.1016/j.biopha.2022.113607] [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: 07/10/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/02/2022] Open
Abstract
Transketolase (TKT) is an enzyme that is ubiquitously expressed in all living organisms and has been identified as an important regulator of cancer. Recent studies have shown that the TKT family includes the TKT gene and two TKT-like (TKTL) genes; TKTL1 and TKTL2. TKT and TKTL1 have been reported to be involved in the regulation of multiple cancer-related events, such as cancer cell proliferation, metastasis, invasion, epithelial-mesenchymal transition, chemoradiotherapy resistance, and patient survival and prognosis. Therefore, TKT may be an ideal target for cancer treatment. More importantly, the levels of TKTL1 were detected using EDIM technology for the early detection of some malignancies, and TKTL1 was more sensitive and specific than traditional tumor markers. Detecting TKTL1 levels before and after surgery could be used to evaluate the surgery's effect. While targeted TKT suppresses cancer in multiple ways, in some cases, it has detrimental effects on the organism. In this review, we discuss the role of TKT in different tumors and the detailed mechanisms while evaluating its value and limitations in clinical applications. Therefore, this review provides a basis for the clinical application of targeted therapy for TKT in the future, and a strategy for subsequent cancer-related research.
Collapse
Affiliation(s)
- Shiming Hao
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Qingfei Meng
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Huihui Sun
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Yunkuo Li
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China
| | - Yao Li
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Liting Gu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Bin Liu
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China
| | - Yanghe Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Honglan Zhou
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China.
| | - Zhixiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| |
Collapse
|
8
|
Lari E, Jeong TY, Labine LM, Simpson MJ. Metabolomic analysis predicted changes in growth rate in Daphnia magna exposed to acetaminophen. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 249:106233. [PMID: 35779485 DOI: 10.1016/j.aquatox.2022.106233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/08/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
As urbanization and the global population increases, pollutants associated with municipal wastewater such as pharmaceuticals are becoming more prevalent in aquatic environments. Acetaminophen (paracetamol) is a widely used drug worldwide and one of the most frequently detected pharmaceuticals in freshwater ecosystems. This study investigated the impact of acetaminophen on the metabolite profile of Daphnia magna at two life stages; and used these metabolomic findings to hypothesize a potential impact at a higher organismal level which was subsequently tested experimentally. Targeted polar metabolite analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to measure changes in the concentration of 51 metabolites in the neonate (> 24 h old) and adult (8 day-old) daphnids following a 48-h exposure to sub-lethal concentrations of acetaminophen. The impact of acetaminophen on the metabolic profile of neonates was widely different from adults. Also, acetaminophen exposure perturbed the abundance of nucleotides more extensively than other metabolites. The acute metabolomic experimental results led to the hypotheses that exposure to sub-lethal concentrations of acetaminophen upregulates protein synthesis in D. magna and subsequently increases growth during early life stages and has an opposite impact on adults. Accordingly, a 10 day growth rate experiment indicated that exposure to acetaminophen elevated biomass production in neonates but not in adults. These novel findings demonstrate that a targeted analysis and interpretation of the changes in the polar metabolic profile of organisms in response to environmental stressors could be used as a tool to predict changes at higher biological levels. As such, this study further emphasizes the incorporation of molecular-level platforms as critical and robust tools in environmental assessment frameworks and biomonitoring of aquatic ecosystems.
Collapse
Affiliation(s)
- Ebrahim Lari
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tae-Yong Jeong
- Department of Physical and Environmental Sciences and Environmental NMR Centre, University of Toronto Scarborough, Ontario, Canada; Department of Environmental Science, College of Natural Sciences, Hankuk University of Foreign Studies, 81, Oedae-ro, Mohyeon-eup, Cheoin-gu, Yongin-si, Gyeonggi-do 17035, Republic of Korea
| | - Lisa M Labine
- Department of Physical and Environmental Sciences and Environmental NMR Centre, University of Toronto Scarborough, Ontario, Canada
| | - Myrna J Simpson
- Department of Physical and Environmental Sciences and Environmental NMR Centre, University of Toronto Scarborough, Ontario, Canada.
| |
Collapse
|
9
|
Morris P, García-Arrazola R, Rios-Solis L, Dalby PA. Biophysical characterization of the inactivation of E. coli transketolase by aqueous co-solvents. Sci Rep 2021; 11:23584. [PMID: 34880340 PMCID: PMC8654844 DOI: 10.1038/s41598-021-03001-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.
Collapse
Affiliation(s)
- Phattaraporn Morris
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
- Chemical Metrology and Biometry Department, National Institute of Metrology, 3/4-5 Moo 3, Klong 5, Klong Luang, 12120, Pathumthani, Thailand
| | - Ribia García-Arrazola
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, UK
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, King's Buildings, Edinburgh, EH9 3JL, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
10
|
Fursultiamine Prevents Drug-Induced Ototoxicity by Reducing Accumulation of Reactive Oxygen Species in Mouse Cochlea. Antioxidants (Basel) 2021; 10:antiox10101526. [PMID: 34679662 PMCID: PMC8533091 DOI: 10.3390/antiox10101526] [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: 08/09/2021] [Revised: 09/04/2021] [Accepted: 09/23/2021] [Indexed: 01/19/2023] Open
Abstract
Drug-induced hearing loss is a major type of acquired sensorineural hearing loss. Cisplatin and aminoglycoside antibiotics have been known to cause ototoxicity, and excessive accumulation of intracellular reactive oxygen species (ROS) are suggested as the common major pathology of cisplatin- and aminoglycoside antibiotics-induced ototoxicity. Fursultiamine, also called thiamine tetrahydrofurfuryl disulfide, is a thiamine disulfide derivative that may have antioxidant effects. To evaluate whether fursultiamine can prevent cisplatin- and kanamycin-induced ototoxicity, we investigated their preventive potential using mouse cochlear explant culture system. Immunofluorescence staining of mouse cochlear hair cells showed that fursultiamine pretreatment reduced cisplatin- and kanamycin-induced damage to both inner and outer hair cells. Fursultiamine attenuated mitochondrial ROS accumulation as evidenced by MitoSOX Red staining and restored mitochondrial membrane potential in a JC-1 assay. In addition, fursultiamine pretreatment reduced active caspase-3 and TUNEL signals after cisplatin or kanamycin treatment, indicating that fursultiamine decreased apoptotic hair cell death. This study is the first to show a protective effect of fursultiamine against cisplatin- and aminoglycoside antibiotics-induced ototoxicity. Our results suggest that fursultiamine could act as an antioxidant and anti-apoptotic agent against mitochondrial oxidative stress.in cochlear hair cells.
Collapse
|
11
|
Nauton L, Hecquet L, Théry V. QM/MM Study of Human Transketolase: Thiamine Diphosphate Activation Mechanism and Complete Catalytic Cycle. J Chem Inf Model 2021; 61:3502-3515. [PMID: 34161071 DOI: 10.1021/acs.jcim.1c00190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A computational model for human transketolase was proposed, showing that thiamine diphosphate activation was based on His110 in place of His481 reported in yeast transketolase. In addition, a complete catalytic reaction pathway was investigated using d-xylulose-5-phosphate and d-ribose-5-phosphate as substrates, showing at every step a perfect superimposition of our model with high-resolution crystallographic structures 3MOS, 4KXV, and 4KXX. This study shows that H2N4' of the active thiamine diphosphate "V form" no longer has a self-activating role but allows self-stabilization of the cofactor and of the Breslow intermediate. These advances in our knowledge of the human transketolase mechanism offer interesting prospects for the design of new drugs, this enzyme being involved in several diseases, and for a better understanding of the reactions catalyzed by transketolases from other sources.
Collapse
Affiliation(s)
- Lionel Nauton
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Vincent Théry
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| |
Collapse
|
12
|
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: 33] [Impact Index Per Article: 11.0] [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.
Collapse
|
13
|
Nemeria NS, Zhang X, Leandro J, Zhou J, Yang L, Houten SM, Jordan F. Toward an Understanding of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxoacid Dehydrogenase Complexes. Life (Basel) 2021; 11:life11050407. [PMID: 33946784 PMCID: PMC8146983 DOI: 10.3390/life11050407] [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: 04/03/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/24/2022] Open
Abstract
The 2-oxoglutarate dehydrogenase complex (OGDHc) is a key enzyme in the tricarboxylic acid (TCA) cycle and represents one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. The OGDHc impacts cell metabolic and cell signaling pathways through the coupling of 2-oxoglutarate metabolism to gene transcription related to tumor cell proliferation and aging. DHTKD1 is a gene encoding 2-oxoadipate dehydrogenase (E1a), which functions in the L-lysine degradation pathway. The potentially damaging variants in DHTKD1 have been associated to the (neuro) pathogenesis of several diseases. Evidence was obtained for the formation of a hybrid complex between the OGDHc and E1a, suggesting a potential cross talk between the two metabolic pathways and raising fundamental questions about their assembly. Here we reviewed the recent findings and advances in understanding of protein-protein interactions in OGDHc and 2-oxoadipate dehydrogenase complex (OADHc), an understanding that will create a scaffold to help design approaches to mitigate the effects of diseases associated with dysfunction of the TCA cycle or lysine degradation. A combination of biochemical, biophysical and structural approaches such as chemical cross-linking MS and cryo-EM appears particularly promising to provide vital information for the assembly of 2-oxoacid dehydrogenase complexes, their function and regulation.
Collapse
Affiliation(s)
- Natalia S. Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
- Correspondence: (N.S.N.); (X.Z.); (F.J.)
| | - Xu Zhang
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
- Correspondence: (N.S.N.); (X.Z.); (F.J.)
| | - Joao Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.L.); (S.M.H.)
| | - Jieyu Zhou
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Luying Yang
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.L.); (S.M.H.)
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
- Correspondence: (N.S.N.); (X.Z.); (F.J.)
| |
Collapse
|
14
|
Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 707:108849. [PMID: 33832752 DOI: 10.1016/j.abb.2021.108849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4 kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9 kcal mol-1 at 27 °C.
Collapse
Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, UK; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
15
|
Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 701:108807. [PMID: 33587902 DOI: 10.1016/j.abb.2021.108807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9kcal mol-1 at 27 °C.
Collapse
Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, United Kingdom; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Olga N Solovjeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russian Federation.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Zhang M, Wang J, Niu C, Zheng F, Liu C, Li Q. Screening of thermosensitive autolytic mutant brewer’s yeast and transcriptomic analysis of heat stress response. Can J Microbiol 2020; 66:631-640. [DOI: 10.1139/cjm-2019-0456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Brewer’s yeast has been widely used in the food industry, and the autolysates thereof are increasingly being studied for their valuable nutritional compositions. Yeast autolysis is most affected by medium composition and temperature. In this study, a thermosensitive autolytic brewer’s yeast P-510 was obtained with atmospheric and room temperature plasma mutagenesis plus 5-bromo-chloro-3-indolyl phosphate screening. The mutant rapidly autolyzed at 37 °C and the autolysates contained more active components and showed higher antioxidant activities compared with that of the parental strain, which indicated that the mutant’s autolysates can potentially be used as functional food and nutritional ingredients. Transcriptomic analysis of the mutant and parental strains at 28 and 37 °C suggested that thermosensitive autolysis of P-510 was probably caused by mitochondrial disfunction, glycogen metabolic flux of glycolysis and pentose phosphate pathway disorder, as well as hexose transport inhibition. The results revealed the important role of mitochondrial metabolism and glycogen utilization regulation in heat stress response of yeast.
Collapse
Affiliation(s)
- Mingfang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| |
Collapse
|
20
|
Wilkinson HC, Dalby PA. Fine-tuning the activity and stability of an evolved enzyme active-site through noncanonical amino-acids. FEBS J 2020; 288:1935-1955. [PMID: 32897608 DOI: 10.1111/febs.15560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/14/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023]
Abstract
Site-specific saturation mutagenesis within enzyme active sites can radically alter reaction specificity, though often with a trade-off in stability. Extending saturation mutagenesis with a range of noncanonical amino acids (ncAA) potentially increases the ability to improve activity and stability simultaneously. Previously, an Escherichia coli transketolase variant (S385Y/D469T/R520Q) was evolved to accept aromatic aldehydes not converted by wild-type. The aromatic residue Y385 was critical to the new acceptor substrate binding, and so was explored here beyond the natural aromatic residues, to probe side chain structure and electronics effects on enzyme function and stability. A series of five variants introduced decreasing aromatic ring electron density at position 385 in the order para-aminophenylalanine (pAMF), tyrosine (Y), phenylalanine (F), para-cyanophenylalanine (pCNF) and para-nitrophenylalanine (pNTF), and simultaneously modified the hydrogen-bonding potential of the aromatic substituent from accepting to donating. The fine-tuning of residue 385 yielded variants with a 43-fold increase in specific activity for 50 mm 3-HBA and 100% increased kcat (pCNF), 290% improvement in Km (pNTF), 240% improvement in kcat /Km (pAMF) and decreased substrate inhibition relative to Y. Structural modelling suggested switching of the ring-substituted functional group, from donating to accepting, stabilised a helix-turn (D259-H261) through an intersubunit H-bond with G262, to give a 7.8 °C increase in the thermal transition mid-point, Tm , and improved packing of pAMF. This is one of the first examples in which both catalytic activity and stability are simultaneously improved via site-specific ncAA incorporation into an enzyme active site, and further demonstrates the benefits of expanding designer libraries to include ncAAs.
Collapse
Affiliation(s)
- Henry C Wilkinson
- Department of Biochemical Engineering, University College London, London, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, London, UK
| |
Collapse
|
21
|
Sharma S, Arora A. Tracking strategic developments for conferring xylose utilization/fermentation by Saccharomyces cerevisiae. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01590-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Purpose
Efficient ethanol production through lignocellulosic biomass hydrolysates could solve energy crisis as it is economically sustainable and ecofriendly. Saccharomyces cerevisiae is the work horse for lignocellulosic bioethanol production at industrial level. But its inability to ferment and utilize xylose limits the overall efficacy of the process.
Method
Data for the review was selected using different sources, such as Biofuels digest, Statista, International energy agency (IEA). Google scholar was used as a search engine to search literature for yeast metabolic engineering approaches. Keywords used were metabolic engineering of yeast for bioethanol production from lignocellulosic biomass.
Result
Through these approaches, interconnected pathways can be targeted randomly. Moreover, the improved strains genetic makeup can help us understand the mechanisms involved for this purpose.
Conclusion
This review discusses all possible approaches for metabolic engineering of yeast. These approaches may reveal unknown hidden mechanisms and construct ways for the researchers to produce novel and modified strains.
Collapse
|
22
|
Zhang R, Ye J, Huang H, Du X. Mining featured biomarkers associated with vascular invasion in HCC by bioinformatics analysis with TCGA RNA sequencing data. Biomed Pharmacother 2019; 118:109274. [DOI: 10.1016/j.biopha.2019.109274] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022] Open
|
23
|
Liu YD, Chu X, Liu RH, Sun Y, Kong QX, Li QB. Paroxysmal spasticity of lower extremities as the initial symptom in two siblings with maple syrup urine disease. Mol Med Rep 2019; 19:4872-4880. [PMID: 30957186 PMCID: PMC6522870 DOI: 10.3892/mmr.2019.10133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/01/2019] [Indexed: 12/28/2022] Open
Abstract
Maple syrup urine disease (MSUD) is a rare autosomal recessive metabolic disorder caused by mutations in genes that encode subunits of the branched‑chain α‑ketoacid dehydrogenase (BCKD) complex. Impairment of the BCKD complex results in an abnormal accumulation of branched‑chain amino acids and their corresponding branched‑chain keto acids in the blood and cerebrospinal fluid, which are neurovirulent and may become life‑threatening. An 11‑day‑old boy was admitted to the hospital with paroxysmal spasticity of lower extremities. Of note, his 10‑year‑old sister presented similar symptoms during the neonatal period, and her condition was diagnosed as MSUD when she was 1.5 years old. Genetic screening was performed, and the boy and his sister exhibited two novel compound heterozygous mutations in the branched chain keto acid dehydrogenase E1 subunit β (BCKDHB) gene: A substitution from guanine to adenine in the coding region at position 1,076 (c.1,076G>A) in exon 10 and a deletion of a thymine at position 705 (c.705delT) in exon 6. The missense mutation c.1076G>A results in an amino acid substitution from arginine to lysine at position 359 (p.Arg359Lys), whereas the mutation c.705delT results in the replacement of a cysteine at position 235 with a stop codon (p.Cys235Ter). Neither of the BCKDHB alleles in the compound heterozygote patients is able to generate normal E1β subunits, resulting in a possible impairment of the activity of the BCKD complex. In the present study, it was hypothesized that the two novel heterozygous mutations in the BCKDHB gene found in the Chinese family may be responsible for the phenotype of the two siblings with MSUD.
Collapse
Affiliation(s)
- Yi-Dan Liu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Xu Chu
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Rui-Hua Liu
- Department of Pediatrics, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Ying Sun
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Qing-Xia Kong
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Qiu-Bo Li
- Department of Pediatrics, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| |
Collapse
|
24
|
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]
|
25
|
Planas F, McLeish MJ, Himo F. Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis. Beilstein J Org Chem 2019; 15:145-159. [PMID: 30745990 PMCID: PMC6350894 DOI: 10.3762/bjoc.15.15] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/10/2018] [Indexed: 12/05/2022] Open
Abstract
Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon–carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate. Given that the cofactor can adopt up to seven states on an enzyme, identifying the factors affecting the stability of the pre-reactant states is important for the overall understanding of the kinetics and mechanism of the individual reactions. In this paper we use density functional theory calculations to systematically study the different cofactor states in terms of energies and geometries. Benzoylformate decarboxylase (BFDC), which is a well characterized chiral catalyst, serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as inhibitor). Overall, the calculations reveal that the relative stabilities of the cofactor states are greatly affected by the presence and identity of the bound ligands. A surprising finding is that benzoylformate binding, while favoring ylide formation, provided even greater stabilization to a catalytically inactive tricyclic state. Conversely, the inhibitor binding greatly destabilized the ylide formation. Together, these observations have significant implications for the reaction kinetics of the ThDP-dependent enzymes, and, potentially, for the use of unnatural substrates in such reactions.
Collapse
Affiliation(s)
- Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis IN 46202, USA
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| |
Collapse
|
26
|
Deshpande GP, Patterton HG, Faadiel Essop M. The human transketolase-like proteins TKTL1 and TKTL2 are bona fide transketolases. BMC STRUCTURAL BIOLOGY 2019; 19:2. [PMID: 30646877 PMCID: PMC6334435 DOI: 10.1186/s12900-018-0099-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 12/13/2018] [Indexed: 12/22/2022]
Abstract
Background Three transketolase genes have been identified in the human genome to date: transketolase (TKT), transketolase-like 1 (TKTL1) and transketolase-like 2 (TKTL2). Altered TKT functionality is strongly implicated in the development of diabetes and various cancers, thus offering possible therapeutic utility. It will be of great value to know whether TKTL1 and TKTL2 are, similarly, potential therapeutic targets. However, it remains unclear whether TKTL1 and TKTL2 are functional transketolases. Results Homology modelling of TKTL1 and TKTL2 using TKT as template, revealed that both TKTL1 and TKTL2 could assume a folded structure like TKT. TKTL1/2 presented a cleft of suitable dimensions between the homodimer surfaces that could accommodate the co-factor-substrate. An appropriate cavity and a hydrophobic nodule were also present in TKTL1/2, into which the diphosphate group fitted, and that was implicated in aminopyrimidine and thiazole ring binding in TKT, respectively. The presence of several identical residues at structurally equivalent positions in TKTL1/2 and TKT identified a network of interactions between the protein and co-factor-substrate, suggesting the functional fidelity of TKTL1/2 as transketolases. Conclusions Our data support the hypothesis that TKTL1 and TKTL2 are functional transketolases and represent novel therapeutic targets for diabetes and cancer. Electronic supplementary material The online version of this article (10.1186/s12900-018-0099-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gaurang P Deshpande
- Cardio-Metabolic Research Group (CMRG), Department of Physiological Sciences, Stellenbosch University, Room 2005, Mike De Vries Building, Merriman Avenue, Stellenbosch, 7600, South Africa
| | - Hugh-George Patterton
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - M Faadiel Essop
- Cardio-Metabolic Research Group (CMRG), Department of Physiological Sciences, Stellenbosch University, Room 2005, Mike De Vries Building, Merriman Avenue, Stellenbosch, 7600, South Africa.
| |
Collapse
|
27
|
Yu Y, Tang J, Su J, Cui J, Xie X, Chen F. Integrative Analysis of MicroRNAome, Transcriptome, and Proteome during the Limb Regeneration of Cynops orientalis. J Proteome Res 2019; 18:1088-1098. [DOI: 10.1021/acs.jproteome.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yuan Yu
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| | - Jie Tang
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Shaanxi Institute of Zoology, 88 Xingqing Road, Xi’an 710032, PR China
| | - Jiaojiao Su
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
| | - Jihong Cui
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| | - Xin Xie
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| | - Fulin Chen
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| |
Collapse
|
28
|
Magnusson AO, Szekrenyi A, Joosten HJ, Finnigan J, Charnock S, Fessner WD. nanoDSF as screening tool for enzyme libraries and biotechnology development. FEBS J 2018; 286:184-204. [PMID: 30414312 PMCID: PMC7379660 DOI: 10.1111/febs.14696] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/24/2018] [Accepted: 11/07/2018] [Indexed: 12/24/2022]
Abstract
Enzymes are attractive tools for synthetic applications. To be viable for industrial use, enzymes need sufficient stability towards the desired reaction conditions such as high substrate and cosolvent concentration, non-neutral pH and elevated temperatures. Thermal stability is an attractive feature not only because it allows for protein purification by thermal treatment and higher process temperatures but also due to the associated higher stability against other destabilising factors. Therefore, high-throughput screening (HTS) methods are desirable for the identification of thermostable biocatalysts by discovery from nature or by protein engineering but current methods have low throughput and require time-demanding purification of protein samples. We found that nanoscale differential scanning fluorimetry (nanoDSF) is a valuable tool to rapidly and reliably determine melting points of native proteins. To avoid intrinsic problems posed by crude protein extracts, hypotonic extraction of overexpressed protein from bacterial host cells resulted in higher sample quality and accurate manual determination of several hundred melting temperatures per day. We have probed the use of nanoDSF for HTS of a phylogenetically diverse aldolase library to identify novel thermostable enzymes from metagenomic sources and for the rapid measurements of variants from saturation mutagenesis. The feasibility of nanoDSF for the screening of synthetic reaction conditions was proved by studies of cosolvent tolerance, which showed protein melting temperature to decrease linearly with increasing cosolvent concentration for all combinations of six enzymes and eight water-miscible cosolvents investigated, and of substrate affinity, which showed stabilisation of hexokinase by sugars in the absence of ATP cofactor. ENZYMES: Alcohol dehydrogenase (NADP+ ) (EC 1.1.1.2), transketolase (EC 2.2.1.1), hexokinase (EC 2.7.1.1), 2-deoxyribose-5-phosphate aldolase (EC 4.1.2.4), fructose-6-phosphate aldolase (EC 4.1.2.n).
Collapse
Affiliation(s)
- Anders O Magnusson
- Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Germany
| | - Anna Szekrenyi
- Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Germany
| | | | | | | | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Germany
| |
Collapse
|
29
|
Aymard CMG, Halma M, Comte A, Mousty C, Prévot V, Hecquet L, Charmantray F, Blum LJ, Doumèche B. Innovative Electrochemical Screening Allows Transketolase Inhibitors to Be Identified. Anal Chem 2018; 90:9241-9248. [PMID: 29950093 DOI: 10.1021/acs.analchem.8b01752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Transketolases (TKs) are ubiquitous thiamine pyrophosphate (TPP)-dependent enzymes of the nonoxidative branch of the pentose phosphate pathway. They are considered as interesting therapeutic targets in numerous diseases and infections (e.g., cancer, tuberculosis, malaria), for which it is important to find specific and efficient inhibitors. Current TK assays require important amounts of enzyme, are time-consuming, and are not specific. Here, we report a new high throughput electrochemical assay based on the oxidative trapping of the TK-TPP intermediate. After electrode characterization, the enzyme loading, electrochemical protocol, and substrate concentration were optimized. Finally, 96 electrochemical assays could be performed in parallel in only 7 min, which allows a rapid screening of TK inhibitors. Then, 1360 molecules of an in-house chemical library were screened and one early lead compound was identified to inhibit TK from E. coli with an IC50 of 63 μM and an inhibition constant ( KI) of 3.4 μM. The electrochemical assay was also used to propose an inhibition mechanism.
Collapse
Affiliation(s)
- Chloé M G Aymard
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS UMR 5246 CNRS, Université de Lyon, Université Lyon 1, CNRS, INSA Lyon, CPE Lyon, 43 bd du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France
| | - Matilte Halma
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, ICCF UMR 6296 CNRS-UCA-Sigma, F-63000 Clermont-Ferrand , France
| | - Arnaud Comte
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS UMR 5246 CNRS, Université de Lyon, Université Lyon 1, CNRS, INSA Lyon, CPE Lyon, 43 bd du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France
| | - Christine Mousty
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, ICCF UMR 6296 CNRS-UCA-Sigma, F-63000 Clermont-Ferrand , France
| | - Vanessa Prévot
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, ICCF UMR 6296 CNRS-UCA-Sigma, F-63000 Clermont-Ferrand , France
| | - Laurence Hecquet
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, ICCF UMR 6296 CNRS-UCA-Sigma, F-63000 Clermont-Ferrand , France
| | - Franck Charmantray
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, ICCF UMR 6296 CNRS-UCA-Sigma, F-63000 Clermont-Ferrand , France
| | - Loïc J Blum
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS UMR 5246 CNRS, Université de Lyon, Université Lyon 1, CNRS, INSA Lyon, CPE Lyon, 43 bd du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France
| | - Bastien Doumèche
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS UMR 5246 CNRS, Université de Lyon, Université Lyon 1, CNRS, INSA Lyon, CPE Lyon, 43 bd du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France
| |
Collapse
|
30
|
Baierl A, Theorell A, Mackfeld U, Marquardt P, Hoffmann F, Moers S, Nöh K, Buchholz PCF, Pleiss J, Pohl M. Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase. ChemCatChem 2018. [DOI: 10.1002/cctc.201800299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anna Baierl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Axel Theorell
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Ursula Mackfeld
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Philipp Marquardt
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | | | - Stephanie Moers
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Katharina Nöh
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry; University of Stuttgart; 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry; University of Stuttgart; 70569 Stuttgart Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| |
Collapse
|
31
|
Qi F, Lei C, Li F, Zhang X, Wang J, Zhang W, Fan Z, Li W, Tang GL, Xiao Y, Zhao G, Li S. Deciphering the late steps of rifamycin biosynthesis. Nat Commun 2018; 9:2342. [PMID: 29904078 PMCID: PMC6002545 DOI: 10.1038/s41467-018-04772-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/12/2018] [Indexed: 12/12/2022] Open
Abstract
Rifamycin-derived drugs, including rifampin, rifabutin, rifapentine, and rifaximin, have long been used as first-line therapies for the treatment of tuberculosis and other deadly infections. However, the late steps leading to the biosynthesis of the industrially important rifamycin SV and B remain largely unknown. Here, we characterize a network of reactions underlying the biosynthesis of rifamycin SV, S, L, O, and B. The two-subunit transketolase Rif15 and the cytochrome P450 enzyme Rif16 are found to mediate, respectively, a unique C–O bond formation in rifamycin L and an atypical P450 ester-to-ether transformation from rifamycin L to B. Both reactions showcase interesting chemistries for these two widespread and well-studied enzyme families. The enzymes Rif15 and Rif16 are involved in the late steps of the biosynthesis of rifamycins, a group of antibiotics. Here, the authors characterized these two proteins and found that they catalyse unusual biochemical reactions.
Collapse
Affiliation(s)
- Feifei Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Chao Lei
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Fengwei Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Zhen Fan
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| |
Collapse
|
32
|
Shaw JA, Henard CA, Liu L, Dieckman LM, Vázquez-Torres A, Bourret TJ. Salmonella enterica serovar Typhimurium has three transketolase enzymes contributing to the pentose phosphate pathway. J Biol Chem 2018; 293:11271-11282. [PMID: 29848552 DOI: 10.1074/jbc.ra118.003661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 11/06/2022] Open
Abstract
The genus Salmonella is responsible for many illnesses in humans and other vertebrate animals. We report here that Salmonella enterica serovar Typhimurium harbors three transketolases that support the non-oxidative branch of the pentose phosphate pathway. BLAST analysis identified two genes, STM14_2885 and STM14_2886, that together encode a putative transketolase (TktC) with 46-47% similarity to the known TktA and TktB isoforms. Assessing the mRNA and protein expression for each of the three transketolases, we determined that all are expressed in WT cells and regulated to varying extents by the alternative sigma factor RpoS. Enzyme assays with lysates from WT and transketolase-knockout strains established that TktA is responsible for >88% of the transketolase activity in WT cells. We purified recombinant forms of each isoenzyme to assess the kinetics for canonical transketolase reactions. TktA and TktB had comparable values for Vmax (539-1362 μm NADH consumed/s), Km (80-739 μm), and catalytic efficiency (1.02 × 108-1.06 × 109 m-1/s) for each substrate tested. The recombinant form of TktC had lower Km values (23-120 μm), whereas the Vmax (7.8-16 μm NADH consumed/s) and catalytic efficiency (5.58 × 106 to 6.07 × 108 m-1/s) were 10-100-fold lower. Using a murine model of Salmonella infection, we showed that a strain lacking all three transketolases is avirulent in C57BL/6 mice. These data provide evidence that S Typhimurium possesses three transketolases that contribute to pathogenesis.
Collapse
Affiliation(s)
- Jeff A Shaw
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Calvin A Henard
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lynne M Dieckman
- Department of Chemistry, Creighton University, Omaha, Nebraska 68178
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011; Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado 80220
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178.
| |
Collapse
|
33
|
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.
Collapse
|
34
|
Structural basis for the magnesium-dependent activation of transketolase from Chlamydomonas reinhardtii. Biochim Biophys Acta Gen Subj 2017; 1861:2132-2145. [DOI: 10.1016/j.bbagen.2017.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/20/2017] [Accepted: 05/23/2017] [Indexed: 01/18/2023]
|
35
|
Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production. ACTA ACUST UNITED AC 2017; 44:879-891. [DOI: 10.1007/s10295-017-1912-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/29/2017] [Indexed: 11/26/2022]
Abstract
Abstract
The pentose phosphate pathway (PPP) plays an important role in the efficiency of xylose fermentation during cellulosic ethanol production. In simultaneous saccharification and co-fermentation (SSCF), the optimal temperature for cellulase hydrolysis of lignocellulose is much higher than that of fermentation. Successful use of SSCF requires optimization of the expression of PPP genes at elevated temperatures. This study examined the combinatorial expression of PPP genes at high temperature. The results revealed that over-expression of TAL1 and TKL1 in Saccharomyces cerevisiae (S. cerevisiae) at 30 °C and over-expression of all PPP genes at 36 °C resulted in the highest ethanol productivities. Furthermore, combinatorial over-expression of PPP genes derived from S. cerevisiae and a thermostable yeast Kluyveromyces marxianus allowed the strain to ferment xylose with ethanol productivity of 0.51 g/L/h, even at 38 °C. These results clearly demonstrate that xylose metabolism can be improved by the utilization of appropriate combinations of thermostable PPP genes in high-temperature production of ethanol.
Collapse
|
36
|
White JK, Handa S, Vankayala SL, Merkler DJ, Woodcock HL. Thiamin Diphosphate Activation in 1-Deoxy-d-xylulose 5-Phosphate Synthase: Insights into the Mechanism and Underlying Intermolecular Interactions. J Phys Chem B 2016; 120:9922-34. [PMID: 27537621 PMCID: PMC5379999 DOI: 10.1021/acs.jpcb.6b07248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
1-Deoxy-d-xylulose 5-phosphate synthase (DXS) is a thiamin diphosphate (TDP) dependent enzyme that marks the beginning of the methylerythritol 4-phosphate isoprenoid biosynthesis pathway. The mechanism of action for DXS is still poorly understood and begins with the formation of a thiazolium ylide. This TDP activation step is thought to proceed through an intramolecular deprotonation by the 4'-aminopyrimidine ring of TDP; however, this step would occur only after an initial deprotonation of its own 4'-amino group. The mechanism of the initial deprotonation has been hypothesized, by analogy to transketolases, to occur via a histidine or an active site water molecule. Results from hybrid quantum mechanical/molecular mechanical (QM/MM) reaction path calculations reveal an ∼10 kcal/mol difference in transition state energies, favoring a water mediated mechanism over direct deprotonation by histidine. This difference was determined to be largely governed by electrostatic changes induced by conformational variations in the active site. Additionally, mutagenesis studies reveal DXS to be an evolutionarily resilient enzyme. Particularly, we hypothesize that residues H82 and H304 may act in a compensatory fashion if the other is lost due to mutation. Further, nucleus-independent chemical shifts (NICSs) and aromatic stabilization energy (ASE) calculations suggest that reduction in TDP aromaticity also serves as a factor for regulating ylide formation and controlling reactivity.
Collapse
Affiliation(s)
- Justin K. White
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Sumit Handa
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0332, United States
| | - Sai Lakshmana Vankayala
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - David J. Merkler
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| |
Collapse
|
37
|
Brereton NJB, Gonzalez E, Marleau J, Nissim WG, Labrecque M, Joly S, Pitre FE. Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants. PLANT PHYSIOLOGY 2016; 171:3-24. [PMID: 27002060 PMCID: PMC4854704 DOI: 10.1104/pp.16.00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/20/2016] [Indexed: 05/09/2023]
Abstract
Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.
Collapse
Affiliation(s)
- Nicholas J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Emmanuel Gonzalez
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Julie Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Werther Guidi Nissim
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Michel Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Simon Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| |
Collapse
|
38
|
Abstract
Decarboxylation reactions occur rapidly in enzymes but usually are many orders of magnitude slower in solution, if the reaction occurs at all. Where the reaction produces a carbanion and CO2, we would expect that the high energy of the carbanion causes the transition state for C-C bond cleavage also to be high in energy. Since the energy of the carbanion is a thermodynamic property, an enzyme obviously cannot change that property. Yet, enzymes overcome the barrier to forming the carbanion. In thinking about decarboxylation, we had assumed that CO2 is well behaved and forms without its own barriers. However, we analyzed reactions in solution of compounds that resemble intermediates in enzymic reaction and found some of them to be subject to unexpected forms of catalysis. Those results caused us to discard the usual assumptions about CO2 and carbanions. We learned that CO2 can be a very reactive electrophile. In decarboxylation reactions, where CO2 forms in the same step as a carbanion, separation of the products might be the main problem preventing the forward reaction because the carbanion can add readily to CO2 in competition with their separation and solvation. The basicity of the carbanion also might be overestimated because when we see that the decarboxylation is slow, we assume that it is because the carbanion is high in energy. We found reactions where the carbanion is protonated internally; CO2 appears to be able to depart without reversion more rapidly. We tested these ideas using kinetic analysis of catalytic reactions, carbon kinetic isotope effects, and synthesis of predecarboxylation intermediates. In another case, we observed that the decarboxylation is subject to general base catalysis while producing a significant carbon kinetic isotope effect. This requires both a proton transfer from an intermediate and C-C bond-breaking in the rate-determining step. This would occur if the route involves the surprising initial addition of water to the carboxyl, with the cleavage step producing bicarbonate. Interestingly, some enzyme-catalyzed reactions also appear to produce intermediates formed by the initial addition of water or a nucleophile to the carboxyl or to nascent CO2. We conclude that decarboxylation is not necessarily a problem that results from the energy of the carbanionic products alone but from their formation in the presence of CO2. Catalysts that facilitate the separation of the species on either side of the C-C bond that cleaves could solve the problem using catalytic principles that we find in many enzymes that promote hydrolytic processes, suggesting linkages in catalysis through evolution of activity.
Collapse
Affiliation(s)
- Ronald Kluger
- Davenport Laboratories, Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| |
Collapse
|
39
|
Lukacik P, Lobley CMC, Bumann M, Arena de Souza V, Owens RJ, O’Toole PW, Walsh MA. High-resolution structures of Lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate. Acta Crystallogr F Struct Biol Commun 2015; 71:1327-34. [PMID: 26457526 PMCID: PMC4601599 DOI: 10.1107/s2053230x1501657x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/04/2015] [Indexed: 11/12/2023] Open
Abstract
Probiotic bacterial strains have been shown to enhance the health of the host through a range of mechanisms including colonization, resistance against pathogens, secretion of antimicrobial compounds and modulation of the activity of the innate immune system. Lactobacillus salivarius UCC118 is a well characterized probiotic strain which survives intestinal transit and has many desirable host-interaction properties. Probiotic bacteria display a wide range of catabolic activities, which determine their competitiveness in vivo. Some lactobacilli are heterofermentative and can metabolize pentoses, using a pathway in which transketolase and transaldolase are key enzymes. L. salivarius UCC118 is capable of pentose utilization because it encodes the key enzymes on a megaplasmid. The crystal structures of the megaplasmid-encoded transketolase with and without the enzyme cofactor thiamine pyrophosphate have been determined. Comparisons with other known transketolase structures reveal a high degree of structural conservation in both the catalytic site and the overall conformation. This work extends structural knowledge of the transketolases to the industrially and commercially important Lactobacillus genus.
Collapse
Affiliation(s)
- Petra Lukacik
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell OX11 0FA, England
| | - Carina M. C. Lobley
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Mario Bumann
- MRC France, BM14, c/o ESRF, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, France
| | - Victoria Arena de Souza
- Oxford Protein Production Facility UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell OX11 0FA, England
| | - Raymond J. Owens
- Oxford Protein Production Facility UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell OX11 0FA, England
| | - Paul W. O’Toole
- MRC France, BM14, c/o ESRF, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, France
- Department of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Martin A. Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell OX11 0FA, England
- MRC France, BM14, c/o ESRF, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, France
| |
Collapse
|
40
|
Chen X, Pu H, Fang Y, Wang X, Zhao S, Lin Y, Zhang M, Dai HE, Gong W, Liu L. Crystal structure of the catalytic subunit of magnesium chelatase. NATURE PLANTS 2015; 1:15125. [PMID: 27250678 DOI: 10.1038/nplants.2015.125] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/30/2015] [Indexed: 05/20/2023]
Abstract
Tetrapyrroles, including haem and chlorophyll, play vital roles for various biological processes, such as respiration and photosynthesis, and their biosynthesis is critical for virtually all organisms. In photosynthetic organisms, magnesium chelatase (MgCh) catalyses insertion of magnesium into the centre of protoporphyrin IX, the branch-point precursor for both haem and chlorophyll, leading tetrapyrrole biosynthesis into the magnesium branch(1,2). This reaction needs a cooperated action of the three subunits of MgCh: the catalytic subunit ChlH and two AAA(+) subunits, ChlI and ChlD (refs 3-5). To date, the mechanism of MgCh awaits further elucidation due to a lack of high-resolution structures, especially for the ∼150 kDa catalytic subunit. Here we report the crystal structure of ChlH from the photosynthetic cyanobacterium Synechocystis PCC 6803, solved at 2.5 Å resolution. The active site is buried deeply inside the protein interior, and the surrounding residues are conserved throughout evolution. This structure helps to explain the loss of function reported for the cch and gun5 mutations of the ChlH subunit, and to provide the molecular basis of substrate channelling during the magnesium-chelating process. The structure advances our understanding of the holoenzyme of MgCh, a metal chelating enzyme other than ferrochelatase.
Collapse
Affiliation(s)
- Xuemin Chen
- Photosynthesis Research Centre, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Pu
- Photosynthesis Research Centre, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Fang
- Photosynthesis Research Centre, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Wang
- Photosynthesis Research Centre, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shun Zhao
- Photosynthesis Research Centre, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yajing Lin
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Huai-En Dai
- Photosynthesis Research Centre, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Weimin Gong
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Lin Liu
- Photosynthesis Research Centre, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| |
Collapse
|
41
|
Ricciardelli C, Lokman NA, Cheruvu S, Tan IA, Ween MP, Pyragius CE, Ruszkiewicz A, Hoffmann P, Oehler MK. Transketolase is upregulated in metastatic peritoneal implants and promotes ovarian cancer cell proliferation. Clin Exp Metastasis 2015; 32:441-55. [PMID: 25895698 DOI: 10.1007/s10585-015-9718-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
Abstract
Ovarian cancer, the most lethal gynaecological cancer, is characterised by the shedding of epithelial cells from the ovarian surface, followed by metastasis and implantation onto the peritoneal surfaces of abdominal organs. Our proteomic studies investigating the interactions between peritoneal (LP-9) and ovarian cancer (OVCAR-5) cells found transketolase (TKT) to be regulated in the co-culture system. This study characterized TKT expression in advanced stage (III/IV) serous ovarian cancers (n = 125 primary and n = 54 peritoneal metastases), normal ovaries (n = 6) and benign serous cystadenomas (n = 10) by immunohistochemistry. In addition, we also evaluated the function of TKT in ovarian cancer cells in vitro. Nuclear TKT was present in all primary serous ovarian cancer tissues examined (median 82.0 %, range 16.5-100 %) and was significantly increased in peritoneal metastases compared with matching primary cancers (P = 0.01, Wilcoxon Rank test). Kaplan-Meier survival and Cox regression analyses showed that high nuclear TKT positivity in peritoneal metastases (>94 %) was significantly associated with reduced overall survival (P = 0.006) and a 2.8 fold increased risk of ovarian cancer death (95 % CI 1.29-5.90, P = 0.009). Knockdown of TKT by siRNAs significantly reduced SKOV-3 cell proliferation but had no effect on their motility or invasion. Oxythiamine, an inhibitor of TKT activity, significantly inhibited the proliferation of four ovarian cancer cell lines (OV-90, SKOV-3, OVCAR-3 and OVCAR-5) and primary serous ovarian cancer cells isolated from patient ascites. In conclusion, these findings indicate that TKT plays an important role in the proliferation of metastatic ovarian cancer cells and could be used as novel therapeutic target for advanced disease.
Collapse
Affiliation(s)
- Carmela Ricciardelli
- Discipline of Obstetrics and Gynaecology, School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia,
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Sommer B, von Moeller H, Haack M, Qoura F, Langner C, Bourenkov G, Garbe D, Loll B, Brück T. Detailed structure-function correlations of Bacillus subtilis acetolactate synthase. Chembiochem 2014; 16:110-8. [PMID: 25393087 DOI: 10.1002/cbic.201402541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 02/04/2023]
Abstract
Isobutanol is deemed to be a next-generation biofuel and a renewable platform chemical.1 Non-natural biosynthetic pathways for isobutanol production have been implemented in cell-based and in vitro systems with Bacillus subtilis acetolactate synthase (AlsS) as key biocatalyst.2-6 AlsS catalyzes the condensation of two pyruvate molecules to acetolactate with thiamine diphosphate and Mg(2+) as cofactors. AlsS also catalyzes the conversion of 2-ketoisovalerate into isobutyraldehyde, the immediate precursor of isobutanol. Our phylogenetic analysis suggests that the ALS enzyme family forms a distinct subgroup of ThDP-dependent enzymes. To unravel catalytically relevant structure-function relationships, we solved the AlsS crystal structure at 2.3 Å in the presence of ThDP, Mg(2+) and in a transition state with a 2-lactyl moiety bound to ThDP. We supplemented our structural data by point mutations in the active site to identify catalytically important residues.
Collapse
Affiliation(s)
- Bettina Sommer
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching (Germany)
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Stincone A, Prigione A, Cramer T, Wamelink MMC, Campbell K, Cheung E, Olin-Sandoval V, Grüning NM, Krüger A, Tauqeer Alam M, Keller MA, Breitenbach M, Brindle KM, Rabinowitz JD, Ralser M. The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. Biol Rev Camb Philos Soc 2014; 90:927-63. [PMID: 25243985 PMCID: PMC4470864 DOI: 10.1111/brv.12140] [Citation(s) in RCA: 779] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/07/2014] [Accepted: 07/16/2014] [Indexed: 12/13/2022]
Abstract
The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism. The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide and amino acid biosynthesis, to provide reducing molecules for anabolism, and to defeat oxidative stress. The PPP shares reactions with the Entner–Doudoroff pathway and Calvin cycle and divides into an oxidative and non-oxidative branch. The oxidative branch is highly active in most eukaryotes and converts glucose 6-phosphate into carbon dioxide, ribulose 5-phosphate and NADPH. The latter function is critical to maintain redox balance under stress situations, when cells proliferate rapidly, in ageing, and for the ‘Warburg effect’ of cancer cells. The non-oxidative branch instead is virtually ubiquitous, and metabolizes the glycolytic intermediates fructose 6-phosphate and glyceraldehyde 3-phosphate as well as sedoheptulose sugars, yielding ribose 5-phosphate for the synthesis of nucleic acids and sugar phosphate precursors for the synthesis of amino acids. Whereas the oxidative PPP is considered unidirectional, the non-oxidative branch can supply glycolysis with intermediates derived from ribose 5-phosphate and vice versa, depending on the biochemical demand. These functions require dynamic regulation of the PPP pathway that is achieved through hierarchical interactions between transcriptome, proteome and metabolome. Consequently, the biochemistry and regulation of this pathway, while still unresolved in many cases, are archetypal for the dynamics of the metabolic network of the cell. In this comprehensive article we review seminal work that led to the discovery and description of the pathway that date back now for 80 years, and address recent results about genetic and metabolic mechanisms that regulate its activity. These biochemical principles are discussed in the context of PPP deficiencies causing metabolic disease and the role of this pathway in biotechnology, bacterial and parasite infections, neurons, stem cell potency and cancer metabolism.
Collapse
Affiliation(s)
- Anna Stincone
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Alessandro Prigione
- Max Delbrueck Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Thorsten Cramer
- Department of Gastroenterology and Hepatology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, De Boelelaaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Eric Cheung
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow G61 1BD, U.K
| | - Viridiana Olin-Sandoval
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Nana-Maria Grüning
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Antje Krüger
- Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
| | - Mohammad Tauqeer Alam
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Markus A Keller
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Michael Breitenbach
- Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria
| | - Kevin M Brindle
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cancer Research UK Cambridge Research Institute (CRI), Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, U.K
| | - Joshua D Rabinowitz
- Department of Chemistry, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, 08544 NJ, U.S.A
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Division of Physiology and Metabolism, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7, U.K
| |
Collapse
|
44
|
Tittmann K. Sweet siblings with different faces: the mechanisms of FBP and F6P aldolase, transaldolase, transketolase and phosphoketolase revisited in light of recent structural data. Bioorg Chem 2014; 57:263-280. [PMID: 25267444 DOI: 10.1016/j.bioorg.2014.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/25/2014] [Accepted: 09/01/2014] [Indexed: 10/24/2022]
Abstract
Nature has evolved different strategies for the reversible cleavage of ketose phosphosugars as essential metabolic reactions in all domains of life. Prominent examples are the Schiff-base forming class I FBP and F6P aldolase as well as transaldolase, which all exploit an active center lysine to reversibly cleave the C3-C4 bond of fructose-1,6-bisphosphate or fructose-6-phosphate to give two 3-carbon products (aldolase), or to shuttle 3-carbon units between various phosphosugars (transaldolase). In contrast, transketolase and phosphoketolase make use of the bioorganic cofactor thiamin diphosphate to cleave the preceding C2-C3 bond of ketose phosphates. While transketolase catalyzes the reversible transfer of 2-carbon ketol fragments in a reaction analogous to that of transaldolase, phosphoketolase forms acetyl phosphate as final product in a reaction that comprises ketol cleavage, dehydration and phosphorolysis. In this review, common and divergent catalytic principles of these enzymes will be discussed, mostly, but not exclusively, on the basis of crystallographic snapshots of catalysis. These studies in combination with mutagenesis and kinetic analysis not only delineated the stereochemical course of substrate binding and processing, but also identified key catalytic players acting at the various stages of the reaction. The structural basis for the different chemical fates and lifetimes of the central enamine intermediates in all five enzymes will be particularly discussed, in addition to the mechanisms of substrate cleavage, dehydration and ring-opening reactions of cyclic substrates. The observation of covalent enzymatic intermediates in hyperreactive conformations such as Schiff-bases with twisted double-bond linkages in transaldolase and physically distorted substrate-thiamin conjugates with elongated substrate bonds to be cleaved in transketolase, which probably epitomize a canonical feature of enzyme catalysis, will be also highlighted.
Collapse
Affiliation(s)
- Kai Tittmann
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| |
Collapse
|
45
|
Jordan F, Nemeria NS. Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations. Bioorg Chem 2014; 57:251-262. [PMID: 25228115 DOI: 10.1016/j.bioorg.2014.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/11/2014] [Indexed: 11/26/2022]
Abstract
Thiamin diphosphate (ThDP), the vitamin B1 coenzyme is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/carbene/C2-carbanion of the thiazolium ring and the C2α-carbanion/enamine, once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of several intermediates which are stable under acidic conditions, solid-state NMR and circular dichroism detection of the states of ionization and tautomerization of the 4'-aminopyrimidine moiety of ThDP in some of the intermediates. These methods also enabled in some cases determination of the rate-limiting step in the complex series of steps. This review is an update of a review with the same title published by the authors in 2005 in this Journal. Much progress has been made in the intervening decade in the identification of the intermediates and their application to gain additional mechanistic insight.
Collapse
Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | |
Collapse
|
46
|
Moreno-García J, García-Martínez T, Moreno J, Mauricio JC. Proteins involved in flor yeast carbon metabolism under biofilm formation conditions. Food Microbiol 2014; 46:25-33. [PMID: 25475262 DOI: 10.1016/j.fm.2014.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
Abstract
A lack of sugars during the production of biologically aged wines after fermentation of grape must causes flor yeasts to metabolize other carbon molecules formed during fermentation (ethanol and glycerol, mainly). In this work, a proteome analysis involving OFFGEL fractionation prior to LC/MS detection was used to elucidate the carbon metabolism of a flor yeast strain under biofilm formation conditions (BFC). The results were compared with those obtained under non-biofilm formation conditions (NBFC). Proteins associated to processes such as non-fermentable carbon uptake, the glyoxylate and TCA cycles, cellular respiration and inositol metabolism were detected at higher concentrations under BFC than under the reference conditions (NBFC). This study constitutes the first attempt at identifying the flor yeast proteins responsible for the peculiar sensory profile of biologically aged wines. A better metabolic knowledge of flor yeasts might facilitate the development of effective strategies for improved production of these special wines.
Collapse
Affiliation(s)
- Jaime Moreno-García
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Teresa García-Martínez
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Juan Moreno
- Department of Agricultural Chemistry, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Marie Curie Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Juan Carlos Mauricio
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain.
| |
Collapse
|
47
|
Patra KC, Hay N. The pentose phosphate pathway and cancer. Trends Biochem Sci 2014; 39:347-54. [PMID: 25037503 DOI: 10.1016/j.tibs.2014.06.005] [Citation(s) in RCA: 885] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 12/19/2022]
Abstract
The pentose phosphate pathway (PPP), which branches from glycolysis at the first committed step of glucose metabolism, is required for the synthesis of ribonucleotides and is a major source of NADPH. NADPH is required for and consumed during fatty acid synthesis and the scavenging of reactive oxygen species (ROS). Therefore, the PPP plays a pivotal role in helping glycolytic cancer cells to meet their anabolic demands and combat oxidative stress. Recently, several neoplastic lesions were shown to have evolved to facilitate the flux of glucose into the PPP. This review summarizes the fundamental functions of the PPP, its regulation in cancer cells, and its importance in cancer cell metabolism and survival.
Collapse
Affiliation(s)
- Krushna C Patra
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Nissim Hay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA; Research and Development Section, Jesse Brown VA Medical Center, Chicago, IL 60612, USA.
| |
Collapse
|
48
|
Gutiérrez Acosta OB, Schleheck D, Schink B. Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins. BMC Genomics 2014; 15:584. [PMID: 25012398 PMCID: PMC4103992 DOI: 10.1186/1471-2164-15-584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions. Results In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B12- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone. Conclusions We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-584) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | - Bernhard Schink
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany.
| |
Collapse
|
49
|
Structure and functioning mechanism of transketolase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1608-18. [PMID: 24929114 DOI: 10.1016/j.bbapap.2014.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 11/22/2022]
Abstract
Studies of thiamine diphosphate-dependent enzymes appear to have commenced in 1937, with the isolation of the coenzyme of yeast pyruvate decarboxylase, which was demonstrated to be a diphosphoric ester of thiamine. For quite a long time, these studies were largely focused on enzymes decarboxylating α-keto acids, such as pyruvate decarboxylase and pyruvate dehydrogenase complexes. Transketolase, discovered independently by Racker and Horecker in 1953 (and named by Racker) [1], did not receive much attention until 1992, when crystal X-ray structure analysis of the enzyme from Saccharomyces cerevisiae was performed [2]. These data, together with the results of site-directed mutagenesis, made it possible to understand in detail the mechanism of thiamine diphosphate-dependent catalysis. Some progress was also made in studies of the functional properties of transketolase. The last review on transketolase, which was fairly complete, appeared in 1998 [3]. Therefore, the publication of this paper should not seem premature.
Collapse
|
50
|
Patel H, Nemeria NS, Andrews FH, McLeish MJ, Jordan F. Identification of charge transfer transitions related to thiamin-bound intermediates on enzymes provides a plethora of signatures useful in mechanistic studies. Biochemistry 2014; 53:2145-52. [PMID: 24628377 PMCID: PMC3985856 DOI: 10.1021/bi4015743] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Identification
of enzyme-bound intermediates via their spectroscopic
signatures, which then allows direct monitoring of the kinetic fate
of these intermediates, poses a continuing challenge. As an electrophilic
covalent catalyst, the thiamin diphosphate (ThDP) coenzyme forms a
number of noncovalent and covalent intermediates along its reaction
pathways, and multiple UV–vis and circular dichroism (CD) bands
have been identified at Rutgers pertinent to several among them. These
electronic transitions fall into two classes: those for which the
conjugated system provides a reasonable guide to the observed λmax and others in which there is no corresponding conjugated
system and the observed CD bands are best ascribed to charge transfer
(CT) transitions. Herein is reported the reaction of four ThDP enzymes
with alternate substrates: (a) acetyl pyruvate, its methyl ester,
and fluoropyruvate, these providing the shortest side chains attached
at the thiazolium C2 atom and leading to CT bands with λmax values of >390 nm, not pertinent to any on-pathway conjugated
systems (estimated λmax values of <330 nm), and
(b) (E)-4-(4-chlorophenyl)-2-oxo-3-butenoic acid
displaying both a conjugated enamine (430 nm) and a CT transition
(480 nm). We suggest that the CT transitions result from an interaction
of the π bond on the ThDP C2 side chain as a donor, and the
positively charged thiazolium ring as an acceptor, and correspond
to covalent ThDP-bound intermediates. Time resolution of these bands
allows the rate constants for individual steps to be determined. These
CD methods can be applied to the entire ThDP superfamily of enzymes
and should find applications with other enzymes.
Collapse
Affiliation(s)
- Hetalben Patel
- Department of Chemistry, Rutgers, the State University of New Jersey , Newark, New Jersey 07102, United States
| | | | | | | | | |
Collapse
|