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Kovářová J, Moos M, Barrett MP, Horn D, Zíková A. The bloodstream form of Trypanosoma brucei displays non-canonical gluconeogenesis. PLoS Negl Trop Dis 2024; 18:e0012007. [PMID: 38394337 PMCID: PMC10917290 DOI: 10.1371/journal.pntd.0012007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/06/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Trypanosoma brucei is a causative agent of the Human and Animal African Trypanosomiases. The mammalian stage parasites infect various tissues and organs including the bloodstream, central nervous system, skin, adipose tissue and lungs. They rely on ATP produced in glycolysis, consuming large amounts of glucose, which is readily available in the mammalian host. In addition to glucose, glycerol can also be used as a source of carbon and ATP and as a substrate for gluconeogenesis. However, the physiological relevance of glycerol-fed gluconeogenesis for the mammalian-infective life cycle forms remains elusive. To demonstrate its (in)dispensability, first we must identify the enzyme(s) of the pathway. Loss of the canonical gluconeogenic enzyme, fructose-1,6-bisphosphatase, does not abolish the process hence at least one other enzyme must participate in gluconeogenesis in trypanosomes. Using a combination of CRISPR/Cas9 gene editing and RNA interference, we generated mutants for four enzymes potentially capable of contributing to gluconeogenesis: fructose-1,6-bisphoshatase, sedoheptulose-1,7-bisphosphatase, phosphofructokinase and transaldolase, alone or in various combinations. Metabolomic analyses revealed that flux through gluconeogenesis was maintained irrespective of which of these genes were lost. Our data render unlikely a previously hypothesised role of a reverse phosphofructokinase reaction in gluconeogenesis and preclude the participation of a novel biochemical pathway involving transaldolase in the process. The sustained metabolic flux in gluconeogenesis in our mutants, including a triple-null strain, indicates the presence of a unique enzyme participating in gluconeogenesis. Additionally, the data provide new insights into gluconeogenesis and the pentose phosphate pathway, and improve the current understanding of carbon metabolism of the mammalian-infective stages of T. brucei.
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Affiliation(s)
- Julie Kovářová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Martin Moos
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - David Horn
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Alena Zíková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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Roster CP, LaVigne D, Milanes JE, Knight E, Anderson HD, Pizarro S, Harding EM, Morris MT, Yan VC, Pham CD, Muller F, Kwain S, Rees KC, Dominy B, Whitehead DC, Uddin MN, Millward SW, Morris JC. Enolase Inhibitors as Early Lead Therapeutics against Trypanosoma brucei. Pathogens 2023; 12:1290. [PMID: 38003754 PMCID: PMC10675445 DOI: 10.3390/pathogens12111290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Glucose metabolism is critical for the African trypanosome, Trypanosoma brucei, serving as the lone source of ATP production for the bloodstream form (BSF) parasite in the glucose-rich environment of the host blood. Recently, phosphonate inhibitors of human enolase (ENO), the enzyme responsible for the interconversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP) in glycolysis or PEP to 2-PG in gluconeogenesis, have been developed for the treatment of glioblastoma multiforme (GBM). Here, we have tested these agents against T. brucei ENO (TbENO) and found the compounds to be potent enzyme inhibitors and trypanocides. For example, (1-hydroxy-2-oxopyrrolidin-3-yl) phosphonic acid (deoxy-SF2312) was a potent enzyme inhibitor (IC50 value of 0.60 ± 0.23 µM), while a six-membered ring-bearing phosphonate, (1-hydroxy-2-oxopiperidin-3-yl) phosphonic acid (HEX), was less potent (IC50 value of 2.1 ± 1.1 µM). An analog with a larger seven-membered ring, (1-hydroxy-2-oxoazepan-3-yl) phosphonic acid (HEPTA), was not active. Molecular docking simulations revealed that deoxy-SF2312 and HEX had binding affinities of -6.8 and -7.5 kcal/mol, respectively, while the larger HEPTA did not bind as well, with a binding of affinity of -4.8 kcal/mol. None of these compounds were toxic to BSF parasites; however, modification of enzyme-active phosphonates through the addition of pivaloyloxymethyl (POM) groups improved activity against T. brucei, with POM-modified (1,5-dihydroxy-2-oxopyrrolidin-3-yl) phosphonic acid (POMSF) and POMHEX having EC50 values of 0.45 ± 0.10 and 0.61 ± 0.08 µM, respectively. These findings suggest that HEX is a promising lead against T. brucei and that further development of prodrug HEX analogs is warranted.
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Affiliation(s)
- Colm P. Roster
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Danielle LaVigne
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Jillian E. Milanes
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Emily Knight
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Heidi D. Anderson
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Sabrina Pizarro
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Elijah M. Harding
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Meredith T. Morris
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
| | - Victoria C. Yan
- Department of Cancer Systems Imaging, UT MD Anderson Cancer Center, Houston, TX 77030, USA; (V.C.Y.); (C.-D.P.); (M.N.U.); (S.W.M.)
| | - Cong-Dat Pham
- Department of Cancer Systems Imaging, UT MD Anderson Cancer Center, Houston, TX 77030, USA; (V.C.Y.); (C.-D.P.); (M.N.U.); (S.W.M.)
| | - Florian Muller
- Sporos Bioventures, 3000 Bissonnet, Belmont Suite 5303, Houston, TX 77005, USA;
| | - Samuel Kwain
- Eukaryotic Pathogens Innovation Center, Department of Chemistry, Clemson University, Clemson, SC 29634, USA; (S.K.); (K.C.R.); (D.C.W.)
| | - Kerrick C. Rees
- Eukaryotic Pathogens Innovation Center, Department of Chemistry, Clemson University, Clemson, SC 29634, USA; (S.K.); (K.C.R.); (D.C.W.)
| | - Brian Dominy
- Department of Chemistry, Clemson University, Clemson, SC 29634, USA;
| | - Daniel C. Whitehead
- Eukaryotic Pathogens Innovation Center, Department of Chemistry, Clemson University, Clemson, SC 29634, USA; (S.K.); (K.C.R.); (D.C.W.)
| | - Md Nasir Uddin
- Department of Cancer Systems Imaging, UT MD Anderson Cancer Center, Houston, TX 77030, USA; (V.C.Y.); (C.-D.P.); (M.N.U.); (S.W.M.)
| | - Steven W. Millward
- Department of Cancer Systems Imaging, UT MD Anderson Cancer Center, Houston, TX 77030, USA; (V.C.Y.); (C.-D.P.); (M.N.U.); (S.W.M.)
| | - James C. Morris
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; (C.P.R.); (D.L.); (J.E.M.); (E.K.); (H.D.A.); (S.P.); (E.M.H.); (M.T.M.)
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Mlozen MM, Van Marwijk J, Wilhelmi BS, Whiteley C. Comparative Analysis of the Interaction of Silver Nanoparticles with Hexokinase from Trypanosoma brucei and Humans. Int J Nanomedicine 2023; 18:1399-1411. [PMID: 36992823 PMCID: PMC10041994 DOI: 10.2147/ijn.s401319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Background Regardless of the efforts to ease cases of human African trypanosomiasis (HAT), an increased number of cases get reported annually. This is because of drug resistant Trypanosoma brucei (Tb), the causative agent of the illness. This has renewed the need for creative methods to find new anti-trypanosomal drugs. The blood stream form (BSF) of the parasite depends exclusively on the glycolytic pathway for energy production while it is in the human host. Interruptions in this pathway efficiently kills the parasite. Trypanosoma brucei hexokinase (TbHK) is the first enzyme in glycolysis, and any effectors or inhibitors of TbHK would have potential as anti-trypanosomal agents. Methods TbHK and human glucokinase (hGCK) were over-expressed with a 6 histidine-tag in E. coli BL21(DE3) cells having the pRARE2 plasmid. Results TbHK had thermal and pH stability between 30°C and 55°C and 7.5 and 8.5, respectively, while hGCK exhibited thermal and pH stability between 30°C and 40°C and 7.0 and 8.0, respectively. Kinetically, TbHK had a Km of 39.3 µM, Vmax of 0.066 µmol.min-1.mL-1, kcat of 2.05 min-1 and kcat/Km of 0.0526 min-1.µmol-1. hGCK exhibited a Km of 4.5 µM, Vmax of 0.032 µnmol.min-1.mL-1, kcat of 11.25 min-1, and kcat/Km of 2.5 min-1.µmol-1. Interaction kinetic studies of silver nanoparticles (AgNPs) (0.1 µM) of average size of 6 nm with TbHK and hGCK were conducted. AgNPs selectively inhibited TbHK over hGCK. TbHK showed a non-competitive inhibition with a 50% and 28% decrease in Vmax, and kcat/km, respectively. HsGCK showed a 33% increase in affinity, 9% decrease in Vmax, and a 50% increase in enzyme efficiency. Conclusion The observed pattern of hGCK and AgNPs falls under the uncompetitive inhibition. The observed highly selective inhibitory effects of AgNPs between TbHK and hGCK may be used in development of new anti-trypanosomal drugs.
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Affiliation(s)
- Madalitso M Mlozen
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
- Malawi Adventist University, Malamulo Campus, Department of Biomedical Sciences, Makwasa, Malawi
- Correspondence: Madalitso M Mlozen, Malawi Adventist University, Malamulo campus, Department of Biomedical Sciences, P.O.Box 55, Makwasa, Tel +265 884628334, Email
| | - Jacqueline Van Marwijk
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Brendan Shane Wilhelmi
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Chris Whiteley
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
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Zíková A. Mitochondrial adaptations throughout the Trypanosoma brucei life cycle. J Eukaryot Microbiol 2022; 69:e12911. [PMID: 35325490 DOI: 10.1111/jeu.12911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022]
Abstract
The unicellular parasite Trypanosoma brucei has a digenetic life cycle that alternates between a mammalian host and an insect vector. During programmed development, this extracellular parasite encounters strikingly different environments that determine its energy metabolism. Functioning as a bioenergetic, biosynthetic, and signaling center, the single mitochondrion of T. brucei is drastically remodeled to support the dynamic cellular demands of the parasite. This manuscript will provide an up-to-date overview of how the distinct T. brucei developmental stages differ in their mitochondrial metabolic and bioenergetic pathways, with a focus on the electron transport chain, proline oxidation, TCA cycle, acetate production, and ATP generation. Although mitochondrial metabolic rewiring has always been simply viewed as a consequence of the differentiation process, the possibility that certain mitochondrial activities reinforce parasite differentiation will be explored.
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Affiliation(s)
- Alena Zíková
- Biology Centre CAS, Institute of Parasitology, University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
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Bishola Tshitenge T, Reichert L, Liu B, Clayton C. Several different sequences are implicated in bloodstream-form-specific gene expression in Trypanosoma brucei. PLoS Negl Trop Dis 2022; 16:e0010030. [PMID: 35312693 PMCID: PMC8982893 DOI: 10.1371/journal.pntd.0010030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/05/2022] [Accepted: 03/03/2022] [Indexed: 12/30/2022] Open
Abstract
The parasite Trypanosoma brucei grows as bloodstream forms in mammalian hosts, and as procyclic forms in tsetse flies. In trypanosomes, gene expression regulation depends heavily on post-transcriptional mechanisms. Both the RNA-binding protein RBP10 and glycosomal phosphoglycerate kinase PGKC are expressed only in mammalian-infective forms. RBP10 targets procyclic-specific mRNAs for destruction, while PGKC is required for bloodstream-form glycolysis. Developmental regulation of both is essential: expression of either RBP10 or PGKC in procyclic forms inhibits their proliferation. We show that the 3’-untranslated region of the RBP10 mRNA is extraordinarily long—7.3kb—and were able to identify six different sequences, scattered across the untranslated region, which can independently cause bloodstream-form-specific expression. The 3’-untranslated region of the PGKC mRNA, although much shorter, still contains two different regions, of 125 and 153nt, that independently gave developmental regulation. No short consensus sequences were identified that were enriched either within these regulatory regions, or when compared with other mRNAs with similar regulation, suggesting that more than one regulatory RNA-binding protein is important for repression of mRNAs in procyclic forms. We also identified regions, including an AU repeat, that increased expression in bloodstream forms, or suppressed it in both forms. Trypanosome mRNAs that encode RNA-binding proteins often have extremely extended 3’-untranslated regions. We suggest that one function of this might be to act as a fail-safe mechanism to ensure correct regulation even if mRNA processing or expression of trans regulators is defective. The parasite Trypanosoma brucei causes sleeping sickness in humans, and nagana in cattle, and is transmitted by Tsetse flies. It grows in the bloodstream and tissue fluids of mammalian hosts, as "bloodstream forms", and as "procyclic forms" in the midgut of tsetse flies. Several hundred proteins are expressed in a stage-specific fashion, and this is essential for parasite survival in the different environments. RBP10 is an RNA-binding protein that is expressed only in bloodstream forms. It binds to procyclic-specific mRNAs, and causes their destruction. PGKC is an enzyme that is also specifically expressed in bloodstream forms. Developmental regulation of both is essential: expression of either RBP10 or PGKC in procyclic forms prevents their growth. The mRNAs encoding both proteins are very unstable in procyclic forms, and the sequences responsible are in an "untranslated region" of the mRNA—sequences that follow the part that codes for protein. We here show that the mRNA encoding PGKC has two regions that independently cause developmental regulation, and that the very long untranslated region of the RBP10 mRNA has no fewer than six regulatory regions, but there were no obvious similarities between them. We suggest that the presence of several different regulatory sequences in trypanosome mRNAs might be a fail-safe mechanism to ensure correct regulation.
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Affiliation(s)
| | - Lena Reichert
- Heidelberg University Center for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Bin Liu
- Heidelberg University Center for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Center for Molecular Biology (ZMBH), Heidelberg, Germany
- * E-mail:
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El-Hawary SS, Mohammed R, Lithy NM, AbouZid SF, Mansour MA, Almahmoud SA, Huwaimel B, Amin E. Digalloyl Glycoside: A Potential Inhibitor of Trypanosomal PFK from Euphorbia abyssinica J.F. Gmel. PLANTS (BASEL, SWITZERLAND) 2022; 11:173. [PMID: 35050063 PMCID: PMC8779944 DOI: 10.3390/plants11020173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Human African trypanosomiasis is an endemic infectious disease caused by Trypanosoma brucei via the bite of tsetse-fly. Most of the drugs used for the treatment, e.g., Suramin, have shown several problems, including the high level of toxicity. Accordingly, the discovery of anti-trypanosomal drugs from natural sources has become an urgent requirement. In our previous study on the anti-trypanosomal potential of Euphorbia species, Euphorbia abyssinica displayed significant anti-trypanosomal activity. Therefore, a phytochemical investigation of the methanolic extract of E. abyssinica was carried out. Twelve compounds, including two triterpenes (1, 2); one sterol-glucoside (4); three ellagic acid derivatives (3, 9, 11); three gallic acid derivatives (5, 6, 10); and three flavonoids (7, 8, 12), were isolated. The structures of isolated compounds were determined through different spectroscopic techniques. Compound (10) was obtained for the first time from genus Euphorbia while all other compounds except compound (4), were firstly reported in E. abyssinica. Consequently, an in silico study was used to estimate the anti-trypanosomal activity of the isolated compounds. Several compounds displayed interesting activity where 1,6-di-O-galloyl-d-glucose (10) appeared as the most potent inhibitor of trypanosomal phosphofructokinase (PFK). Moreover, molecular dynamics (MD) simulations and ADMET calculations were performed for 1,6-di-O-galloyl-d-glucose. In conclusion, 1,6-di-O-galloyl-d-glucose revealed high binding free energy as well as desirable molecular dynamics and pharmacokinetic properties; therefore, it could be suggested for further in vitro and in vivo studies for trypanosomiasis.
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Affiliation(s)
- Seham S. El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Giza 12613, Egypt;
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (R.M.); (S.F.A.)
| | - Nadia M. Lithy
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University Beni-Suef, Beni-Suef 62521, Egypt;
| | - Sameh Fekry AbouZid
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (R.M.); (S.F.A.)
- Department of Pharmacognosy, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Mostafa A. Mansour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University Beni-Suef, Beni-Suef 62521, Egypt;
| | - Suliman A. Almahmoud
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah 51452, Saudi Arabia;
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 34464, Saudi Arabia;
| | - Elham Amin
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (R.M.); (S.F.A.)
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah 51452, Saudi Arabia;
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Ramakrishnan S, Baptista RP, Asady B, Huang G, Docampo R. TbVps41 regulates trafficking of endocytic but not biosynthetic cargo to lysosomes of bloodstream forms of Trypanosoma brucei. FASEB J 2021; 35:e21641. [PMID: 34041791 DOI: 10.1096/fj.202100487r] [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: 03/21/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 11/11/2022]
Abstract
The bloodstream stage of Trypanosoma brucei, the causative agent of African trypanosomiasis, is characterized by its high rate of endocytosis, which is involved in remodeling of its surface coat. Here we present evidence that RNAi-mediated expression down-regulation of vacuolar protein sorting 41 (Vps41), a component of the homotypic fusion and vacuole protein sorting (HOPS) complex, leads to a strong inhibition of endocytosis, vesicle accumulation, enlargement of the flagellar pocket ("big eye" phenotype), and dramatic effect on cell growth. Unexpectedly, other functions described for Vps41 in mammalian cells and yeasts, such as delivery of proteins to lysosomes, and lysosome-related organelles (acidocalcisomes) were unaffected, indicating that in trypanosomes post-Golgi trafficking is distinct from that of mammalian cells and yeasts. The essentiality of TbVps41 suggests that it is a potential drug target.
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Affiliation(s)
| | | | - Beejan Asady
- Center for Tropical and Emerging Global Diseases, Athens, GA, USA
| | - Guozhong Huang
- Center for Tropical and Emerging Global Diseases, Athens, GA, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, Athens, GA, USA.,Department of Cellular Biology, University of Georgia, Athens, GA, USA
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Michels PAM, Villafraz O, Pineda E, Alencar MB, Cáceres AJ, Silber AM, Bringaud F. Carbohydrate metabolism in trypanosomatids: New insights revealing novel complexity, diversity and species-unique features. Exp Parasitol 2021; 224:108102. [PMID: 33775649 DOI: 10.1016/j.exppara.2021.108102] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
The human pathogenic trypanosomatid species collectively called the "TriTryp parasites" - Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. - have complex life cycles, with each of these parasitic protists residing in a different niche during their successive developmental stages where they encounter diverse nutrients. Consequently, they adapt their metabolic network accordingly. Yet, throughout the life cycles, carbohydrate metabolism - involving the glycolytic, gluconeogenic and pentose-phosphate pathways - always plays a central role in the biology of these parasites, whether the available carbon and free energy sources are saccharides, amino acids or lipids. In this paper, we provide an updated review of the carbohydrate metabolism of the TriTryps, highlighting new data about this metabolic network, the interconnection of its pathways and the compartmentalisation of its enzymes within glycosomes, cytosol and mitochondrion. Differences in the expression of the branches of the metabolic network between the successive life-cycle stages of each of these parasitic trypanosomatids are discussed, as well as differences between them. Recent structural and kinetic studies have revealed unique regulatory mechanisms for some of the network's key enzymes with important species-specific variations. Furthermore, reports of multiple post-translational modifications of trypanosomal glycolytic enzymes suggest that additional mechanisms for stage- and/or environmental cues that regulate activity are operational in the parasites. The detailed comparison of the carbohydrate metabolism of the TriTryps has thus revealed multiple differences and a greater complexity, including for the reduced metabolic network in bloodstream-form T. brucei, than previously appreciated. Although these parasites are related, share many cytological and metabolic features and are grouped within a single taxonomic family, the differences highlighted in this review reflect their separate evolutionary tracks from a common ancestor to the extant organisms. These differences are indicative of their adaptation to the different insect vectors and niches occupied in their mammalian hosts.
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Affiliation(s)
- Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
| | - Oriana Villafraz
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Erika Pineda
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Mayke B Alencar
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela.
| | - Ariel M Silber
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil.
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France.
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Sampaio Guther ML, Prescott AR, Kuettel S, Tinti M, Ferguson MAJ. Nucleotide sugar biosynthesis occurs in the glycosomes of procyclic and bloodstream form Trypanosoma brucei. PLoS Negl Trop Dis 2021; 15:e0009132. [PMID: 33592041 PMCID: PMC7909634 DOI: 10.1371/journal.pntd.0009132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 02/26/2021] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
In Trypanosoma brucei, there are fourteen enzymatic biotransformations that collectively convert glucose into five essential nucleotide sugars: UDP-Glc, UDP-Gal, UDP-GlcNAc, GDP-Man and GDP-Fuc. These biotransformations are catalyzed by thirteen discrete enzymes, five of which possess putative peroxisome targeting sequences. Published experimental analyses using immunofluorescence microscopy and/or digitonin latency and/or subcellular fractionation and/or organelle proteomics have localized eight and six of these enzymes to the glycosomes of bloodstream form and procyclic form T. brucei, respectively. Here we increase these glycosome localizations to eleven in both lifecycle stages while noting that one, phospho-N-acetylglucosamine mutase, also localizes to the cytoplasm. In the course of these studies, the heterogeneity of glycosome contents was also noted. These data suggest that, unlike other eukaryotes, all of nucleotide sugar biosynthesis in T. brucei is compartmentalized to the glycosomes in both lifecycle stages. The implications are discussed.
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Affiliation(s)
- Maria Lucia Sampaio Guther
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sabine Kuettel
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael A. J. Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail:
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10
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Hassan A, Huang Q, Xu H, Wu J, Mehmood N. Silencing of the phosphofructokinase gene impairs glycolysis and causes abnormal locomotion in the subterranean termite Reticulitermes chinensis Snyder. INSECT MOLECULAR BIOLOGY 2021; 30:57-70. [PMID: 33068440 DOI: 10.1111/imb.12672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
Phosphofructokinase (PFK) is a rate-limiting enzyme in glycolysis, but its linkage with locomotion in termites is not well understood, despite the demonstrated involvement of this gene in the locomotion of different animals. Here, we investigated the effect of the pfk gene on locomotion in the subterranean termite Reticulitermes chinensis Snyder through RNA interference and the use of an Ethovision XT tracking system. The knockdown of pfk resulted in significantly decreased expression of the pfk gene in different castes of termites. The pfk-silenced workers displayed higher levels of glucose but lower levels of nicotinamide adenine dinucleotide (NADH) and adenosine triphosphate (ATP) production and decreased activity of the PFK enzyme. Furthermore, abnormal locomotion (decreased distance travelled, velocity and acceleration but increased turn angle, angular velocity and meander) was observed in different castes of pfk-silenced termites. We found caste-specific locomotion among workers, soldiers and dealates. Additionally, soldiers and dealates showed higher velocity in the inner zone than in the wall zone, which is considered an effective behaviour to avoid predation. These findings reveal the close linkage between the pfk gene and locomotion in termites, which helps us to better understand the regulatory mechanism and caste specificity of social behaviours in social insects.
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Affiliation(s)
- A Hassan
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Q Huang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
| | - H Xu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
| | - J Wu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
| | - N Mehmood
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
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11
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Pinto Torres JE, Yuan M, Goossens J, Versées W, Caljon G, Michels PA, Walkinshaw MD, Magez S, Sterckx YGJ. Structural and kinetic characterization of Trypanosoma congolense pyruvate kinase. Mol Biochem Parasitol 2020; 236:111263. [PMID: 32084384 DOI: 10.1016/j.molbiopara.2020.111263] [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: 12/01/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 11/18/2022]
Abstract
Trypanosoma are blood-borne parasites and are the causative agents of neglected tropical diseases (NTDs) affecting both humans and animals. These parasites mainly rely on glycolysis for their energy production within the mammalian host, which is why trypanosomal glycolytic enzymes have been pursued as interesting targets for the development of trypanocidal drugs. The structure-function relationships of pyruvate kinases (PYKs) from trypanosomatids (Trypanosoma and Leishmania) have been well-studied within this context. In this paper, we describe the structural and enzymatic characterization of PYK from T. congolense (TcoPYK), the main causative agent of Animal African Trypanosomosis (AAT), by employing a combination of enzymatic assays, thermal unfolding studies and X-ray crystallography.
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Affiliation(s)
- Joar Esteban Pinto Torres
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Meng Yuan
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Julie Goossens
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Paul A Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Stefan Magez
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Ghent University Global Campus, Songdomunhwa-Ro 119, Yeonsu-Gu, 406-840 Incheon, South Korea
| | - Yann G-J Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium.
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12
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Fernandes PM, Kinkead J, McNae IW, Vásquez-Valdivieso M, Wear MA, Michels PAM, Walkinshaw MD. Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis. FEBS J 2020; 287:2847-2861. [PMID: 31838765 PMCID: PMC7383607 DOI: 10.1111/febs.15177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/13/2019] [Accepted: 12/12/2019] [Indexed: 11/30/2022]
Abstract
Trypanosomatids possess glycosome organelles that contain much of the glycolytic machinery, including phosphofructokinase (PFK). We present kinetic and structural data for PFK from three human pathogenic trypanosomatids, illustrating intriguing differences that may reflect evolutionary adaptations to differing ecological niches. The activity of Leishmania PFK – to a much larger extent than Trypanosoma PFK – is reliant on AMP for activity regulation, with 1 mm AMP increasing the L. infantum PFK (LiPFK) kcat/K0.5F6P value by 10‐fold, compared to only a 1.3‐ and 1.4‐fold increase for T. cruzi and T. brucei PFK, respectively. We also show that Leishmania PFK melts at a significantly lower (> 15 °C) temperature than Trypanosoma PFKs and that addition of either AMP or ATP results in a marked stabilization of the protein. Sequence comparisons of Trypanosoma spp. and Leishmania spp. show that divergence of the two genera involved amino acid substitutions that occur in the enzyme’s ‘reaching arms’ and ‘embracing arms’ that determine tetramer stability. The dramatic effects of AMP on Leishmania activity compared with the Trypanosoma PFKs may be explained by differences between the T‐to‐R equilibria for the two families, with the low‐melting Leishmania PFK favouring the flexible inactive T‐state in the absence of AMP. Sequence comparisons along with the enzymatic and structural data presented here also suggest there was a loss of AMP‐dependent regulation in Trypanosoma species rather than gain of this characteristic in Leishmania species and that AMP acts as a key regulator in Leishmania governing the balance between glycolysis and gluconeogenesis.
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Affiliation(s)
- Peter M Fernandes
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - James Kinkead
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Iain W McNae
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Monserrat Vásquez-Valdivieso
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Martin A Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Paul A M Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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13
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In silico prediction of a new lead compound targeting enolase of trypanosomatids through structure-based virtual screening and molecular dynamic studies. J Mol Model 2020; 26:23. [PMID: 31912304 DOI: 10.1007/s00894-019-4284-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 12/20/2019] [Indexed: 10/25/2022]
Abstract
Enolase is one of the key glycolytic metalloenzyme in many organisms, and it is a potential therapeutic target including trypanosomatids. Sequence and structural analysis of enolase of Trypanosoma bruzi (TbENO), Trypanosoma cruzi (TcENO) and Leishmania donovani (LdENO) revealed conserved sequence pattern and structural features. Hence identification of an inhibitor against enolase of one trypanosomatid organism may have similar effects on enolase of homologous organisms belonging to same family. In the process to identify potent inhibitor compounds against TbENO by in silico methods, compounds containing the substructures of substrate, i.e. phosphoenolpyruvate (PEP) and the well-known inhibitors, fluoro-2-phosphono-acetohydroxamate (FPAH) and phosphono-acetohydroxamate (PAH), were collected. Virtual screening and induced fit docking studies were carried out to explore compounds that have better binding affinity than PEP and FPAH. PPPi was found to be the top hit exhibiting significant binding affinity towards enolase. Glide energy values of two other compounds represented by PubChem ID: 511392 and 101803456 was in good agreement with PEP and PAH. TbENO-PPPi complex was subjected to molecular orbital analysis and molecular dynamic studies by considering its remarkable binding affinity as it could be a potent inhibitor of enolase. Despite being an endogenous compound, based on the results of this study, we highlight PPPi to be a lead compound, and its structure can be treated as a model for further chemical modifications to obtain more potent antagonists.
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14
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Saavedra E, González-Chávez Z, Moreno-Sánchez R, Michels PA. Drug Target Selection for Trypanosoma cruzi Metabolism by Metabolic Control Analysis and Kinetic Modeling. Curr Med Chem 2019; 26:6652-6671. [DOI: 10.2174/0929867325666180917104242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 11/22/2022]
Abstract
In the search for therapeutic targets in the intermediary metabolism of trypanosomatids
the gene essentiality criterion as determined by using knock-out and knock-down genetic
strategies is commonly applied. As most of the evaluated enzymes/transporters have
turned out to be essential for parasite survival, additional criteria and approaches are clearly
required for suitable drug target prioritization. The fundamentals of Metabolic Control
Analysis (MCA; an approach in the study of control and regulation of metabolism) and kinetic
modeling of metabolic pathways (a bottom-up systems biology approach) allow quantification
of the degree of control that each enzyme exerts on the pathway flux (flux control coefficient)
and metabolic intermediate concentrations (concentration control coefficient). MCA
studies have demonstrated that metabolic pathways usually have two or three enzymes with
the highest control of flux; their inhibition has more negative effects on the pathway function
than inhibition of enzymes exerting low flux control. Therefore, the enzymes with the highest
pathway control are the most convenient targets for therapeutic intervention. In this review,
the fundamentals of MCA as well as experimental strategies to determine the flux control coefficients
and metabolic modeling are analyzed. MCA and kinetic modeling have been applied
to trypanothione metabolism in Trypanosoma cruzi and the model predictions subsequently
validated in vivo. The results showed that three out of ten enzyme reactions analyzed
in the T. cruzi anti-oxidant metabolism were the most controlling enzymes. Hence, MCA and
metabolic modeling allow a further step in target prioritization for drug development against
trypanosomatids and other parasites.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Zabdi González-Chávez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Paul A.M. Michels
- Centre for Immunity, Infection and Evolution (CIIE) and Centre for Translational and Chemical Biology (CTCB), School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
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15
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Valera-Vera EA, Sayé M, Reigada C, Miranda MR, Pereira CA. In silico repositioning of etidronate as a potential inhibitor of the Trypanosoma cruzi enolase. J Mol Graph Model 2019; 95:107506. [PMID: 31821935 DOI: 10.1016/j.jmgm.2019.107506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022]
Abstract
Enolase is a glycolytic enzyme that catalyzes the interconversion between 2-phosphoglycerate and phosphoenolpyruvate. In trypanosomatids, enolase was proposed as a key enzyme after in silico and in vivo analysis and it was validated as a protein essential for the survival of the parasite. Therefore, enolase constitutes an interesting enzyme target for the identification of drugs against Chagas disease. In this work, a combined virtual screening strategy was implemented, employing similarity virtual screening, molecular docking, and molecular dynamics. First, two known enolase inhibitors and the enzyme substrates were used as queries for the similarity screening on the Sweetlead database using five different algorithms. Compounds retrieved in the top 10 of at least three search algorithms were selected for further analysis, resulting in six compounds of medical use (etidronate, pamidronate, fosfomycin, acetohydroxamate, triclofos, and aminohydroxybutyrate). Molecular docking simulations and pose re-scoring predicted that binding with acetohydroxamate and triclofos would be weak, while fosfomycin and aminohydroxybutyrate predicted binding is experimentally implausible. Docking poses obtained for etidronate, pamidronate, and PEP were used for molecular dynamics calculations to describe their mode of binding. From the obtained results, we propose etidronate as a potential TcENO inhibitor and describe molecular motifs to be taken into account in the repurposing or design of drugs targeting this enzyme active site.
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Affiliation(s)
- Edward A Valera-Vera
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Melisa Sayé
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Chantal Reigada
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Mariana R Miranda
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Claudio A Pereira
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina.
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Design, synthesis and molecular docking studies of novel N-arylsulfonyl-benzimidazoles with anti Trypanosoma cruzi activity. Eur J Med Chem 2019; 165:1-10. [DOI: 10.1016/j.ejmech.2019.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/12/2018] [Accepted: 01/06/2019] [Indexed: 12/18/2022]
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17
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The kinetic characteristics of human and trypanosomatid phosphofructokinases for the reverse reaction. Biochem J 2019; 476:179-191. [PMID: 30404924 PMCID: PMC6340114 DOI: 10.1042/bcj20180635] [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: 08/14/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023]
Abstract
Eukaryotic ATP-dependent phosphofructokinases (PFKs) are often considered unidirectional enzymes catalysing the transfer of a phospho moiety from ATP to fructose 6-phosphate to produce ADP and fructose 1,6-bisphosphate. The reverse reaction is not generally considered to occur under normal conditions and has never been demonstrated for any eukaryotic ATP-dependent PFKs, though it does occur in inorganic pyrophosphate-dependent PFKs and has been experimentally shown for bacterial ATP-dependent PFKs. The evidence is provided via two orthogonal assays that all three human PFK isoforms can catalyse the reverse reaction in vitro, allowing determination of kinetic properties. Additionally, the reverse reaction was shown possible for PFKs from three clinically important trypanosomatids; these enzymes are contained within glycosomes in vivo. This compartmentalisation may facilitate reversal, given the potential for trypanosomatids to have an altered ATP/ADP ratio in glycosomes compared with the cytosol. The kinetic properties of each trypanosomatid PFK were determined, including the response to natural and artificial modulators of enzyme activity. The possible physiological relevance of the reverse reaction in trypanosomatid and human PFKs is discussed.
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18
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Osorio-Méndez JF, Cevallos AM. Discovery and Genetic Validation of Chemotherapeutic Targets for Chagas' Disease. Front Cell Infect Microbiol 2019; 8:439. [PMID: 30666299 PMCID: PMC6330712 DOI: 10.3389/fcimb.2018.00439] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 12/10/2018] [Indexed: 01/06/2023] Open
Abstract
There is an urgent need to develop new treatments for Chagas' disease. To identify drug targets, it is important to understand the basic biology of Trypanosoma cruzi, in particular with respect to the biological pathways or proteins that are essential for its survival within the host. This review provides a streamlined approach for identifying drug targets using freely available chemogenetic databases and outlines the relevant characteristics of an ideal chemotherapeutic target. Among those are their essentiality, druggability, availability of structural information, and selectivity. At the moment only 16 genes have been found as essential by gene disruption in T. cruzi. At the TDR Targets database, a chemogenomics resource for neglected diseases, information about published structures for these genes was only found for three of these genes, and annotation of validated inhibitors was found in two. These inhibitors have activity against the parasitic stages present in the host. We then analyzed three of the pathways that are considered promising in the search for new targets: (1) Ergosterol biosynthesis, (2) Resistance to oxidative stress, (3) Synthesis of surface glycoconjugates. We have annotated all the genes that participate in them, identified those that are considered as druggable, and incorporated evidence from either Trypanosoma brucei, and Leishmania spp. that supports the hypothesis that these pathways are essential for T. cruzi survival.
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Affiliation(s)
- Juan Felipe Osorio-Méndez
- Laboratorio de Microbiología y Biología Molecular, Programa de Medicina, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia, Colombia.,Grupo de Estudio en Parasitología Molecular, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Ramirez-Barrios R, Reyna-Bello A, Parra O, Valeris R, Tavares-Marques L, Brizard JP, Demettre E, Seveno M, Martinez-Moreno A, Holzmuller P. Trypanosoma vivax infection in sheep: Different patterns of virulence and pathogenicity associated with differentially expressed proteomes. Vet Parasitol 2019; 276S:100014. [PMID: 32904712 PMCID: PMC7458391 DOI: 10.1016/j.vpoa.2019.100014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 11/18/2022]
Abstract
Trypanosoma vivax strains exhibit different virulence and pathogenicity patterns. TvMT1 strain showed low virulence and high pathogenicity. TvLIEM176 strain showed high virulence and moderate pathogenicity. Protein expression varies in high virulence/moderate pathogenicity strain vs low virulence/high pathogenicity strain.
Cattle trypanosomosis caused by Trypanosoma vivax is a widely distributed disease in Africa and Latin America. It causes significant losses in the livestock industry and is characterized by fluctuating parasitemia, anemia, fever, lethargy, and weight loss. In this study we evaluated the virulence (capacity to multiply inside the host and to modulate the host response) and pathogenicity (ability to produce disease and/or mortality) patterns of two T. vivax strains (TvMT1 and TvLIEM176) in experimentally-infected sheep and determined the proteins differentially expressed in the proteomes of these two strains. Hematological and clinical parameters were monitored in experimentally-infected versus non-infected sheep for 60 days. All the infected animals developed discernable parasitemia at 3 days post-infection (dpi), and the first parasitemia peak was observed at 6 dpi. The maximum average value of parasitemia was 1.3 × 107 (95% CI, 7.9 × 105–2 × 108) parasites/ml in TvLIEM176-infected animals, and 2.5 × 106 (95% CI, 1.6 × 105–4 × 107) parasites/ml in TvMT1-infected ones. Anemia and clinical manifestations were more severe in the animals infected by TvMT1 strain than in those infected by TvLIEM176. In the proteomic analysis, a total of 29 proteins were identified, of which 14 exhibited significant differences in their expression levels between strains. Proteins with higher expression in TvLIEM176 were: alpha tubulin, beta tubulin, arginine kinase, glucose-regulated protein 78, paraflagellar protein 3, and T-complex protein 1 subunit theta. Proteins with higher expression in TvMT1 were: chaperonin HSP60, T-complex protein 1 subunit alpha, heat shock protein 70, pyruvate kinase, glycerol kinase, inosine-5'-monophosphate dehydrogenase, 73 kDa paraflagellar rod protein, and vacuolar ATP synthase. There was a difference in the virulence and pathogenicity between the T. vivax strains: TvLIEM176 showed high virulence and moderate pathogenicity, whereas TvMT1 showed low virulence and high pathogenicity. The proteins identified in this study are discussed for their potential involvement in strains’ virulence and pathogenicity, to be further defined as biomarkers of severity in T. vivax infections.
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20
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Wang G, Wang JJ, Yin PH, Xu K, Wang YZ, Shi F, Gao J, Fu XL. New strategies for targeting glucose metabolism-mediated acidosis for colorectal cancer therapy. J Cell Physiol 2018; 234:348-368. [PMID: 30069931 DOI: 10.1002/jcp.26917] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
Abstract
Colorectal cancer (CRC) is a heterogeneous group of diseases that are the result of abnormal glucose metabolism alterations with high lactate production by pyruvate to lactate conversion, which remodels acidosis and offers an evolutional advantage for tumor cells, even enhancing their aggressive phenotype. This review summarizes recent findings that involve multiple genes, molecules, and downstream signaling in the dysregulated glycolytic pathway, which can allow a tumor to initiate acid byproducts and to progress, thereby resulting in acidosis commonly found in the tumor microenvironment of CRC. Moreover, the relationship between CRC cells and the tumor acidic microenvironment, especially for regulating lactate production and lactate dehydrogenase A levels, is also discussed, as well as comprehensively defining different aspects of glycolytic pathways that affect cancer cell proliferation, invasion, and migration. Furthermore, this review concentrates on glucose metabolism-mediated transduction factors in CRC, which include acid-sensing ion channels, triosephosphate isomerase and key glycolysis-related enzymes that regulate glycolytic metabolites, coupled with the effect on tumor cell glycolysis as well as signaling pathways. In conclusion, glucose metabolism mediated by glycolytic pathways that are integral to tumor acidosis in CRC is demonstrated. Therefore, selective metabolic inhibitors or agents against these targets in glucose metabolism through glycolytic pathways may be clinically useful to regulate the tumor's acidic microenvironment for CRC treatment and to identify specific targets that regulate tumor acidosis through a cancer patient-personalized approach. Furthermore, strategies for modifying the metabolic processes that effectively inhibit cancer cell growth and tumor progression and activate potent anticancer effects may provide more effective antitumor prospects for CRC therapy.
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Affiliation(s)
- Gang Wang
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Jun-Jie Wang
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Pei-Hao Yin
- Department of Cancer, Institute of Chinese Integrative Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ke Xu
- Department of Cancer, Institute of Chinese Integrative Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu-Zhu Wang
- Department of Medicine, Jiangsu University, Zhenjiang, China
| | - Feng Shi
- Department of Medicine, Jiangsu University, Zhenjiang, China
| | - Jing Gao
- Department of Medicine, Jiangsu University, Zhenjiang, China
| | - Xing-Li Fu
- Department of Medicine, Jiangsu University, Zhenjiang, China
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Voyton CM, Morris MT, Ackroyd PC, Morris JC, Christensen KA. FRET Flow Cytometry-Based High Throughput Screening Assay To Identify Disrupters of Glucose Levels in Trypanosoma brucei. ACS Infect Dis 2018; 4:1058-1066. [PMID: 29741365 DOI: 10.1021/acsinfecdis.8b00058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trypanosoma brucei, which causes human African typanosomiasis (HAT), derives cellular ATP from glucose metabolism while in the mammalian host. Targeting glucose uptake or regulation in the parasite has been proposed as a potential therapeutic strategy. However, few methods have been described to identify and characterize potential inhibitors of glucose uptake and regulation. Here, we report development of a screening assay that identifies small molecule disrupters of glucose levels in the cytosol and glycosomes. Using an endogenously expressed fluorescent protein glucose sensor expressed in cytosol or glycosomes, we monitored intracellular glucose depletion in the different cellular compartments. Two glucose level disrupters were identified, one of which only exhibited inhibition of glycosomal glucose and did not affect cytosolic levels. In addition to inhibiting glucose uptake with relatively high potency (EC50 = 700 nM), the compound also showed modest bloodstream form parasite killing activity. Expanding this assay will allow for identification of candidate compounds that disrupt parasite glucose metabolism.
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Affiliation(s)
- Charles M. Voyton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84601, United States
| | | | - P. Christine Ackroyd
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84601, United States
| | | | - Kenneth A. Christensen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84601, United States
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22
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Vázquez-Raygoza A, Cano-González L, Velázquez-Martínez I, Trejo-Soto PJ, Castillo R, Hernández-Campos A, Hernández-Luis F, Oria-Hernández J, Castillo-Villanueva A, Avitia-Domínguez C, Sierra-Campos E, Valdez-Solana M, Téllez-Valencia A. Species-Specific Inactivation of Triosephosphate Isomerase from Trypanosoma brucei: Kinetic and Molecular Dynamics Studies. Molecules 2017; 22:molecules22122055. [PMID: 29186784 PMCID: PMC6149853 DOI: 10.3390/molecules22122055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023] Open
Abstract
Human African Trypanosomiasis (HAT), a disease that provokes 2184 new cases a year in Sub-Saharan Africa, is caused by Trypanosoma brucei. Current treatments are limited, highly toxic, and parasite strains resistant to them are emerging. Therefore, there is an urgency to find new drugs against HAT. In this context, T. brucei depends on glycolysis as the unique source for ATP supply; therefore, the enzyme triosephosphate isomerase (TIM) is an attractive target for drug design. In the present work, three new benzimidazole derivatives were found as TbTIM inactivators (compounds 1, 2 and 3) with an I50 value of 84, 82 and 73 µM, respectively. Kinetic analyses indicated that the three molecules were selective when tested against human TIM (HsTIM) activity. Additionally, to study their binding mode in TbTIM, we performed a 100 ns molecular dynamics simulation of TbTIM-inactivator complexes. Simulations showed that the binding of compounds disturbs the structure of the protein, affecting the conformations of important domains such as loop 6 and loop 8. In addition, the physicochemical and drug-like parameters showed by the three compounds suggest a good oral absorption. In conclusion, these molecules will serve as a guide to design more potent inactivators that could be used to obtain new drugs against HAT.
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Affiliation(s)
- Alejandra Vázquez-Raygoza
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Lucia Cano-González
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Israel Velázquez-Martínez
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Pedro Josué Trejo-Soto
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Rafael Castillo
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Alicia Hernández-Campos
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Francisco Hernández-Luis
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Jesús Oria-Hernández
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Adriana Castillo-Villanueva
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Claudia Avitia-Domínguez
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Erick Sierra-Campos
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Mónica Valdez-Solana
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Alfredo Téllez-Valencia
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
- Correspondence: ; Tel./Fax: +52-618-812-1687
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23
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Novel Therapeutic Targets for Human African Trypanosomiasis. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2017. [DOI: 10.1007/s40506-017-0120-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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24
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Targeting pathogen metabolism without collateral damage to the host. Sci Rep 2017; 7:40406. [PMID: 28084422 PMCID: PMC5234033 DOI: 10.1038/srep40406] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/06/2016] [Indexed: 12/14/2022] Open
Abstract
The development of drugs that can inactivate disease-causing cells (e.g. cancer cells or parasites) without causing collateral damage to healthy or to host cells is complicated by the fact that many proteins are very similar between organisms. Nevertheless, due to subtle, quantitative differences between the biochemical reaction networks of target cell and host, a drug can limit the flux of the same essential process in one organism more than in another. We identified precise criteria for this ‘network-based’ drug selectivity, which can serve as an alternative or additive to structural differences. We combined computational and experimental approaches to compare energy metabolism in the causative agent of sleeping sickness, Trypanosoma brucei, with that of human erythrocytes, and identified glucose transport and glyceraldehyde-3-phosphate dehydrogenase as the most selective antiparasitic targets. Computational predictions were validated experimentally in a novel parasite-erythrocytes co-culture system. Glucose-transport inhibitors killed trypanosomes without killing erythrocytes, neurons or liver cells.
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25
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Ghafari M, Mashaghi A. On the role of topology in regulating transcriptional cascades. Phys Chem Chem Phys 2017; 19:25168-25179. [DOI: 10.1039/c7cp02671d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Topology of interactions in a transcriptional cascade determines the behavior of its signal-response profile and the activation states of genes.
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Affiliation(s)
- Mahan Ghafari
- Leiden Academic Centre for Drug Research
- Faculty of Mathematics and Natural Sciences
- Leiden University
- Leiden
- The Netherlands
| | - Alireza Mashaghi
- Leiden Academic Centre for Drug Research
- Faculty of Mathematics and Natural Sciences
- Leiden University
- Leiden
- The Netherlands
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26
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Orlenko A, Hermansen RA, Liberles DA. Flux Control in Glycolysis Varies Across the Tree of Life. J Mol Evol 2016; 82:146-61. [PMID: 26920685 DOI: 10.1007/s00239-016-9731-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 11/29/2022]
Abstract
Biochemical thought posits that rate-limiting steps (defined here as points of flux control) are strongly selected as points of pathway regulation and control and are thus expected to be evolutionarily conserved. Conversely, population genetic thought based upon the concepts of mutation-selection-drift balance at the pathway level might suggest variation in flux controlling steps over evolutionary time. Glycolysis, as one of the most conserved and best characterized pathways, was studied to evaluate its evolutionary conservation. The flux controlling step in glycolysis was found to vary over the tree of life. Further, phylogenetic analysis suggested at least 60 events of gene duplication and additional events of putative positive selection that might alter pathway kinetic properties. Together, these results suggest that even with presumed largely negative selection on pathway output on glycolysis, the co-evolutionary process under the hood is dynamic.
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Affiliation(s)
- Alena Orlenko
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Russell A Hermansen
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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27
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D'Antonio EL, Deinema MS, Kearns SP, Frey TA, Tanghe S, Perry K, Roy TA, Gracz HS, Rodriguez A, D'Antonio J. Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase. Mol Biochem Parasitol 2016; 204:64-76. [PMID: 26778112 DOI: 10.1016/j.molbiopara.2015.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 12/10/2015] [Accepted: 12/16/2015] [Indexed: 01/29/2023]
Abstract
Glucokinase and hexokinase from pathogenic protozoa Trypanosoma cruzi are potential drug targets for antiparasitic chemotherapy of Chagas' disease. These glucose kinases phosphorylate d-glucose with co-substrate ATP and yield glucose 6-phosphate and are involved in essential metabolic pathways, such as glycolysis and the pentose phosphate pathway. An inhibitor class was conceived that is selective for T. cruzi glucokinase (TcGlcK) using structure-based drug design involving glucosamine having a linker from the C2 amino that terminates with a hydrophobic group either being phenyl, p-hydroxyphenyl, or dioxobenzo[b]thiophenyl groups. The synthesis and characterization for two of the four compounds are presented while the other two compounds were commercially available. Four high-resolution X-ray crystal structures of TcGlcK inhibitor complexes are reported along with enzyme inhibition constants (Ki) for TcGlcK and Homo sapiens hexokinase IV (HsHxKIV). These glucosamine analogue inhibitors include three strongly selective TcGlcK inhibitors and a fourth inhibitor, benzoyl glucosamine (BENZ-GlcN), which is a similar variant exhibiting a shorter linker. Carboxybenzyl glucosamine (CBZ-GlcN) was found to be the strongest glucokinase inhibitor known to date, having a Ki of 0.71±0.05μM. Also reported are two biologically active inhibitors against in vitro T. cruzi culture that were BENZ-GlcN and CBZ-GlcN, with intracellular amastigote growth inhibition IC50 values of 16.08±0.16μM and 48.73±0.69μM, respectively. These compounds revealed little to no toxicity against mammalian NIH-3T3 fibroblasts and provide a key starting point for further drug development with this class of compound.
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Affiliation(s)
- Edward L D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA.
| | - Mason S Deinema
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Sean P Kearns
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Tyler A Frey
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Scott Tanghe
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA
| | - Kay Perry
- NE-CAT, Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Timothy A Roy
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Hanna S Gracz
- Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, North Carolina 27695, USA
| | - Ana Rodriguez
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA
| | - Jennifer D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
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28
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Haanstra JR, González-Marcano EB, Gualdrón-López M, Michels PAM. Biogenesis, maintenance and dynamics of glycosomes in trypanosomatid parasites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1038-48. [PMID: 26384872 DOI: 10.1016/j.bbamcr.2015.09.015] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 12/31/2022]
Abstract
Peroxisomes of organisms belonging to the protist group Kinetoplastea, which include trypanosomatid parasites of the genera Trypanosoma and Leishmania, are unique in playing a crucial role in glycolysis and other parts of intermediary metabolism. They sequester the majority of the glycolytic enzymes and hence are called glycosomes. Their glycosomal enzyme content can vary strongly, particularly quantitatively, between different trypanosomatid species, and within each species during its life cycle. Turnover of glycosomes by autophagy of redundant ones and biogenesis of a new population of organelles play a pivotal role in the efficient adaptation of the glycosomal metabolic repertoire to the sudden, major nutritional changes encountered during the transitions in their life cycle. The overall mechanism of glycosome biogenesis is similar to that of peroxisomes in other organisms, but the homologous peroxins involved display low sequence conservation as well as variations in motifs mediating crucial protein-protein interactions in the process. The correct compartmentalisation of enzymes is essential for the regulation of the trypanosomatids' metabolism and consequently for their viability. For Trypanosoma brucei it was shown that glycosomes also play a crucial role in its life-cycle regulation: a crucial developmental control switch involves the translocation of a protein phosphatase from the cytosol into the organelles. Many glycosomal proteins are differentially phosphorylated in different life-cycle stages, possibly indicative of regulation of enzyme activities as an additional means to adapt the metabolic network to the different environmental conditions encountered.
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Affiliation(s)
- Jurgen R Haanstra
- Systems Bioinformatics, Vrije Universiteit Amsterdam, The Netherlands
| | - Eglys B González-Marcano
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Melisa Gualdrón-López
- Federal University of Minas Gerais, Laboratory of Immunoregulation of Infectious Diseases, Department of Biochemistry and Immunology, Institute for Biological Sciences, Belo Horizonte, Brazil
| | - Paul A M Michels
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela; Centre for Translational and Chemical Biology, Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, United Kingdom.
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29
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Haanstra JR, Bakker BM. Drug target identification through systems biology. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 15:17-22. [PMID: 26464086 DOI: 10.1016/j.ddtec.2015.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 05/18/2015] [Accepted: 06/12/2015] [Indexed: 06/05/2023]
Abstract
To rationalise drug target selection, we should understand the role of putative targets in biological pathways quantitatively. We review here how experimental and computational network-based approaches can aid more rational drug target selection and illustrate this with results obtained for microbes and for cancer. Comparison of the drug response of biochemical networks in target cells and (healthy) host cells can reveal network-selective targets.
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Affiliation(s)
- Jurgen R Haanstra
- Department of Pediatrics and Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, The Netherlands; Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands.
| | - Barbara M Bakker
- Department of Pediatrics and Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, The Netherlands; Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands
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30
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Moreno SA, Nava M. Trypanosoma evansi is alike to Trypanosoma brucei brucei in the subcellular localisation of glycolytic enzymes. Mem Inst Oswaldo Cruz 2015; 110:468-75. [PMID: 26061149 PMCID: PMC4501409 DOI: 10.1590/0074-02760150024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/01/2015] [Indexed: 01/17/2023] Open
Abstract
Trypanosoma evansi, which causes surra, is descended from Trypanosoma brucei brucei, which causes nagana. Although both parasites are presumed to be metabolically similar, insufficient knowledge of T. evansi precludes a full comparison. Herein, we provide the first report on the subcellular localisation of the glycolytic enzymes in T. evansi, which is a alike to that of the bloodstream form (BSF) of T. b. brucei: (i) fructose-bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hexokinase, phosphofructokinase, glucose-6-phosphate isomerase, phosphoglycerate kinase, triosephosphate isomerase (glycolytic enzymes) and glycerol-3-phosphate dehydrogenase (a glycolysis-auxiliary enzyme) in glycosomes, (ii) enolase, phosphoglycerate mutase, pyruvate kinase (glycolytic enzymes) and a GAPDH isoenzyme in the cytosol, (iii) malate dehydrogenase in cytosol and (iv) glucose-6-phosphate dehydrogenase in both glycosomes and the cytosol. Specific enzymatic activities also suggest that T. evansi is alike to the BSF of T. b. brucei in glycolytic flux, which is much faster than the pentose phosphate pathway flux, and in the involvement of cytosolic GAPDH in the NAD+/NADH balance. These similarities were expected based on the close phylogenetic relationship of both parasites.
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Affiliation(s)
- S Andrea Moreno
- Departamento de Biología, Facultad de Ciencias, Universidad de Los
Andes, Mérida, Mérida, Venezuela
| | - Mayerly Nava
- Departamento de Biología, Facultad Experimental de Ciencias, Universidad
del Zulia, Maracaibo, Zulia, Venezuela
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31
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Wu Z, Pang W, Coghill GM. An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems. Soft comput 2015; 19:1595-1610. [PMID: 25999782 PMCID: PMC4433352 DOI: 10.1007/s00500-014-1467-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Computational modelling of biochemical systems based on top-down and bottom-up approaches has been well studied over the last decade. In this research, after illustrating how to generate atomic components by a set of given reactants and two user pre-defined component patterns, we propose an integrative top-down and bottom-up modelling approach for stepwise qualitative exploration of interactions among reactants in biochemical systems. Evolution strategy is applied to the top-down modelling approach to compose models, and simulated annealing is employed in the bottom-up modelling approach to explore potential interactions based on models constructed from the top-down modelling process. Both the top-down and bottom-up approaches support stepwise modular addition or subtraction for the model evolution. Experimental results indicate that our modelling approach is feasible to learn the relationships among biochemical reactants qualitatively. In addition, hidden reactants of the target biochemical system can be obtained by generating complex reactants in corresponding composed models. Moreover, qualitatively learned models with inferred reactants and alternative topologies can be used for further web-lab experimental investigations by biologists of interest, which may result in a better understanding of the system.
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Affiliation(s)
- Zujian Wu
- College of Information Science and Technology, Jinan University, Guangzhou, 510632 People’s Republic of China
- School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK
| | - Wei Pang
- School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK
| | - George M. Coghill
- School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE Scotland, UK
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32
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Loureiro I, Faria J, Clayton C, Macedo-Ribeiro S, Santarém N, Roy N, Cordeiro-da-Siva A, Tavares J. Ribose 5-phosphate isomerase B knockdown compromises Trypanosoma brucei bloodstream form infectivity. PLoS Negl Trop Dis 2015; 9:e3430. [PMID: 25568941 PMCID: PMC4287489 DOI: 10.1371/journal.pntd.0003430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/21/2014] [Indexed: 12/13/2022] Open
Abstract
Ribose 5-phosphate isomerase is an enzyme involved in the non-oxidative branch of the pentose phosphate pathway, and catalyzes the inter-conversion of D-ribose 5-phosphate and D-ribulose 5-phosphate. Trypanosomatids, including the agent of African sleeping sickness namely Trypanosoma brucei, have a type B ribose-5-phosphate isomerase. This enzyme is absent from humans, which have a structurally unrelated ribose 5-phosphate isomerase type A, and therefore has been proposed as an attractive drug target waiting further characterization. In this study, Trypanosoma brucei ribose 5-phosphate isomerase B showed in vitro isomerase activity. RNAi against this enzyme reduced parasites' in vitro growth, and more importantly, bloodstream forms infectivity. Mice infected with induced RNAi clones exhibited lower parasitaemia and a prolonged survival compared to control mice. Phenotypic reversion was achieved by complementing induced RNAi clones with an ectopic copy of Trypanosoma cruzi gene. Our results present the first functional characterization of Trypanosoma brucei ribose 5-phosphate isomerase B, and show the relevance of an enzyme belonging to the non-oxidative branch of the pentose phosphate pathway in the context of Trypanosoma brucei infection. Within the non-oxidative branch of the pentose phosphate pathway, ribose 5-phosphate isomerase catalyzes the inter-conversion of ribose 5-phosphate and ribulose 5-phosphate. There are two types of ribose 5-phosphate isomerase, namely A and B. The presence of type B in Trypanosoma brucei, and its absence in humans, make this protein a promising drug target. African sleeping sickness is a serious parasitic disease that relies on limited chemotherapeutic options for control. In our study, a functional characterization of Trypanosoma brucei ribose 5-phosphate isomerase B is reported. Biochemical studies confirmed enzyme isomerase activity and its downregulation by RNAi affected mainly parasites infectivity in vivo. Overall this study shows that ribose 5-phosphate isomerase depletion is detrimental for parasites infectivity under host pressure.
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Affiliation(s)
- Inês Loureiro
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Joana Faria
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH cv Alliance, Heidelberg, Germany
| | - Sandra Macedo-Ribeiro
- Protein Crystallography Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Nuno Santarém
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Nilanjan Roy
- Ashok & Rita Patel Institute of Integrated Study & Research in Biotechnology & Allied Sciences, New Vallabh Vidyanagar, Dist-Anand, Gujarat, India
| | - Anabela Cordeiro-da-Siva
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Departamento de Ciências Biológicas, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal
- * E-mail: (ACdS); (JT)
| | - Joana Tavares
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- * E-mail: (ACdS); (JT)
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33
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Kim DH, Achcar F, Breitling R, Burgess KE, Barrett MP. LC-MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes. Metabolomics 2015; 11:1721-1732. [PMID: 26491423 PMCID: PMC4605981 DOI: 10.1007/s11306-015-0827-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/25/2015] [Indexed: 01/15/2023]
Abstract
Human African trypanosomiasis is a neglected tropical disease caused by the protozoan parasite, Trypanosoma brucei. In the mammalian bloodstream, the trypanosome's metabolism differs significantly from that of its host. For example, the parasite relies exclusively on glycolysis for energy source. Recently, computational and mathematical models of trypanosome metabolism have been generated to assist in understanding the parasite metabolism with the aim of facilitating drug development. Optimisation of these models requires quantitative information, including metabolite concentrations and/or metabolic fluxes that have been hitherto unavailable on a large scale. Here, we have implemented an LC-MS-based method that allows large scale quantification of metabolite levels by using U-13C-labelled E.coli extracts as internal standards. Known amounts of labelled E. coli extract were added into the parasite samples, as well as calibration standards, and used to obtain calibration curves enabling us to convert intensities into concentrations. This method allowed us to reliably quantify the changes of 43 intracellular metabolites and 32 extracellular metabolites in the medium over time. Based on the absolute quantification, we were able to compute consumption and production fluxes. These quantitative data can now be used to optimise computational models of parasite metabolism.
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Affiliation(s)
- Dong-Hyun Kim
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Fiona Achcar
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
| | - Rainer Breitling
- Manchester Centre of Synthetic Biology for Fine and Speciality Chemicals, Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, M1 7DN UK
| | - Karl E. Burgess
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G61 1QH UK
| | - Michael P. Barrett
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G61 1QH UK
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From Bench to Bedside: Natural Products and Analogs for the Treatment of Neglected Tropical Diseases (NTDs). STUDIES IN NATURAL PRODUCTS CHEMISTRY 2015. [DOI: 10.1016/b978-0-444-63460-3.00002-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Achcar F, Fadda A, Haanstra JR, Kerkhoven EJ, Kim DH, Leroux AE, Papamarkou T, Rojas F, Bakker BM, Barrett MP, Clayton C, Girolami M, Krauth-Siegel RL, Matthews KR, Breitling R. The silicon trypanosome: a test case of iterative model extension in systems biology. Adv Microb Physiol 2014; 64:115-43. [PMID: 24797926 DOI: 10.1016/b978-0-12-800143-1.00003-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology.
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Affiliation(s)
- Fiona Achcar
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jurgen R Haanstra
- Department of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Eduard J Kerkhoven
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Dong-Hyun Kim
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Theodore Papamarkou
- The Department of Statistical Science and The Centre for Computational Statistics and Machine Learning University College London, London, United Kingdom
| | - Federico Rojas
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Barbara M Bakker
- Department of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael P Barrett
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mark Girolami
- The Department of Statistical Science and The Centre for Computational Statistics and Machine Learning University College London, London, United Kingdom
| | | | - Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
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Szöör B, Haanstra JR, Gualdrón-López M, Michels PAM. Evolution, dynamics and specialized functions of glycosomes in metabolism and development of trypanosomatids. Curr Opin Microbiol 2014; 22:79-87. [DOI: 10.1016/j.mib.2014.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 01/24/2023]
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Nagle A, Khare S, Kumar AB, Supek F, Buchynskyy A, Mathison CJN, Chennamaneni N, Pendem N, Buckner FS, Gelb M, Molteni V. Recent developments in drug discovery for leishmaniasis and human African trypanosomiasis. Chem Rev 2014; 114:11305-47. [PMID: 25365529 PMCID: PMC4633805 DOI: 10.1021/cr500365f] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Indexed: 02/08/2023]
Affiliation(s)
- Advait
S. Nagle
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Shilpi Khare
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Arun Babu Kumar
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Frantisek Supek
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Andriy Buchynskyy
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Casey J. N. Mathison
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Naveen
Kumar Chennamaneni
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Nagendar Pendem
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Frederick S. Buckner
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Michael
H. Gelb
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Valentina Molteni
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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Merritt C, Silva L, Tanner AL, Stuart K, Pollastri MP. Kinases as druggable targets in trypanosomatid protozoan parasites. Chem Rev 2014; 114:11280-304. [PMID: 26443079 PMCID: PMC4254031 DOI: 10.1021/cr500197d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Christopher Merritt
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Lisseth
E. Silva
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Angela L. Tanner
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Kenneth Stuart
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Michael P. Pollastri
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Haanstra JR, Bakker BM, Michels PA. In or out? On the tightness of glycosomal compartmentalization of metabolites and enzymes in Trypanosoma brucei. Mol Biochem Parasitol 2014; 198:18-28. [DOI: 10.1016/j.molbiopara.2014.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/10/2014] [Accepted: 11/20/2014] [Indexed: 11/16/2022]
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40
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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: 801] [Impact Index Per Article: 80.1] [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.
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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
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41
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Morgan HP, Zhong W, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Structures of pyruvate kinases display evolutionarily divergent allosteric strategies. ROYAL SOCIETY OPEN SCIENCE 2014; 1:140120. [PMID: 26064527 PMCID: PMC4448766 DOI: 10.1098/rsos.140120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/11/2014] [Indexed: 05/13/2023]
Abstract
The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (k cat/S 0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (k cat/S 0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors.
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42
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Brown RWB, Collingridge PW, Gull K, Rigden DJ, Ginger ML. Evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution. PLoS One 2014; 9:e103026. [PMID: 25050549 PMCID: PMC4106842 DOI: 10.1371/journal.pone.0103026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/27/2014] [Indexed: 11/18/2022] Open
Abstract
Classically viewed as a cytosolic pathway, glycolysis is increasingly recognized as a metabolic pathway exhibiting surprisingly wide-ranging variations in compartmentalization within eukaryotic cells. Trypanosomatid parasites provide an extreme view of glycolytic enzyme compartmentalization as several glycolytic enzymes are found exclusively in peroxisomes. Here, we characterize Trypanosoma brucei flagellar proteins resembling glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoglycerate kinase (PGK): we show the latter associates with the axoneme and the former is a novel paraflagellar rod component. The paraflagellar rod is an essential extra-axonemal structure in trypanosomes and related protists, providing a platform into which metabolic activities can be built. Yet, bioinformatics interrogation and structural modelling indicate neither the trypanosome PGK-like nor the GAPDH-like protein is catalytically active. Orthologs are present in a free-living ancestor of the trypanosomatids, Bodo saltans: the PGK-like protein from B. saltans also lacks key catalytic residues, but its GAPDH-like protein is predicted to be catalytically competent. We discuss the likelihood that the trypanosome GAPDH-like and PGK-like proteins constitute molecular evidence for evolutionary loss of a flagellar glycolytic pathway, either as a consequence of niche adaptation or the re-localization of glycolytic enzymes to peroxisomes and the extensive changes to glycolytic flux regulation that accompanied this re-localization. Evidence indicating loss of localized ATP provision via glycolytic enzymes therefore provides a novel contribution to an emerging theme of hidden diversity with respect to compartmentalization of the ubiquitous glycolytic pathway in eukaryotes. A possibility that trypanosome GAPDH-like protein additionally represents a degenerate example of a moonlighting protein is also discussed.
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Affiliation(s)
- Robert W. B. Brown
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | | | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael L. Ginger
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- * E-mail:
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43
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Trypanosomatid phosphoglycerate mutases have multiple conformational and oligomeric states. Biochem Biophys Res Commun 2014; 450:936-41. [DOI: 10.1016/j.bbrc.2014.06.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 06/15/2014] [Indexed: 12/31/2022]
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44
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Cayir E, Erdemir A, Ozkan E, Topuzogullari M, Bolat ZB, Akat A, Turgut-Balik D. Cloning of Intron-Removed Enolase Gene and Expression, Purification, Kinetic Characterization of the Enzyme from Theileria annulata. Mol Biotechnol 2014; 56:689-96. [DOI: 10.1007/s12033-014-9747-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Brimacombe KR, Walsh MJ, Liu L, Vásquez-Valdivieso MG, Morgan HP, McNae I, Fothergill-Gilmore LA, Michels PAM, Auld DS, Simeonov A, Walkinshaw MD, Shen M, Boxer MB. Identification of ML251, a Potent Inhibitor of T. brucei and T. cruzi Phosphofructokinase. ACS Med Chem Lett 2014; 5:12-7. [PMID: 24900769 DOI: 10.1021/ml400259d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022] Open
Abstract
Human African Trypanosomiasis (HAT) is a severe, often fatal disease caused by the parasitic protist Trypanosoma brucei. The glycolytic pathway has been identified as the sole mechanism for ATP generation in the infective stage of these organisms, and several glycolytic enzymes, phosphofructokinase (PFK) in particular, have shown promise as potential drug targets. Herein, we describe the discovery of ML251, a novel nanomolar inhibitor of T. brucei PFK, and the structure-activity relationships within the series.
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Affiliation(s)
- Kyle R. Brimacombe
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Martin J. Walsh
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Li Liu
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Montserrat G. Vásquez-Valdivieso
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Hugh P. Morgan
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Iain McNae
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Linda A. Fothergill-Gilmore
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Paul A. M. Michels
- Research
Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Douglas S. Auld
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Malcolm D. Walkinshaw
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew B. Boxer
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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46
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Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei. PLoS Comput Biol 2013; 9:e1003371. [PMID: 24339766 PMCID: PMC3854711 DOI: 10.1371/journal.pcbi.1003371] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 10/16/2013] [Indexed: 01/12/2023] Open
Abstract
Dynamic models of metabolism can be useful in identifying potential drug targets, especially in unicellular organisms. A model of glycolysis in the causative agent of human African trypanosomiasis, Trypanosoma brucei, has already shown the utility of this approach. Here we add the pentose phosphate pathway (PPP) of T. brucei to the glycolytic model. The PPP is localized to both the cytosol and the glycosome and adding it to the glycolytic model without further adjustments leads to a draining of the essential bound-phosphate moiety within the glycosome. This phosphate “leak” must be resolved for the model to be a reasonable representation of parasite physiology. Two main types of theoretical solution to the problem could be identified: (i) including additional enzymatic reactions in the glycosome, or (ii) adding a mechanism to transfer bound phosphates between cytosol and glycosome. One example of the first type of solution would be the presence of a glycosomal ribokinase to regenerate ATP from ribose 5-phosphate and ADP. Experimental characterization of ribokinase in T. brucei showed that very low enzyme levels are sufficient for parasite survival, indicating that other mechanisms are required in controlling the phosphate leak. Examples of the second type would involve the presence of an ATP:ADP exchanger or recently described permeability pores in the glycosomal membrane, although the current absence of identified genes encoding such molecules impedes experimental testing by genetic manipulation. Confronted with this uncertainty, we present a modeling strategy that identifies robust predictions in the context of incomplete system characterization. We illustrate this strategy by exploring the mechanism underlying the essential function of one of the PPP enzymes, and validate it by confirming the model predictions experimentally. Mathematical models have been valuable tools for investigating the complex behaviors of metabolism. Due to incomplete knowledge of biological systems, these models contain inevitable uncertainty. This uncertainty is present in the measured or estimated parameter values, but also in the structure of the metabolic network. In this paper we increase the coverage of a particularly well studied model of glucose metabolism in Trypanosoma brucei, a tropical parasite that causes African sleeping sickness, by extending it with an additional pathway in two compartments. During this modeling process we highlighted uncertainties in parameter values and network structure and used these to formulate new hypotheses which were subsequently tested experimentally. The models were improved with the experimentally derived data, but uncertainty remained concerning the exact topology of the system. These models allowed us to investigate the effects of the loss of one enzyme, 6-phosphogluconate dehydrogenase. By taking uncertainty into account, the models demonstrated that the loss of this enzyme is lethal to the parasite by a mechanism different than that in other organisms. Our methodology shows how formally introducing uncertainty into model building provides robust model behavior that is independent of the network structure or parameter values.
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47
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What can we learn from global sensitivity analysis of biochemical systems? PLoS One 2013; 8:e79244. [PMID: 24244458 PMCID: PMC3828278 DOI: 10.1371/journal.pone.0079244] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/20/2013] [Indexed: 01/21/2023] Open
Abstract
Most biological models of intermediate size, and probably all large models, need to cope with the fact that many of their parameter values are unknown. In addition, it may not be possible to identify these values unambiguously on the basis of experimental data. This poses the question how reliable predictions made using such models are. Sensitivity analysis is commonly used to measure the impact of each model parameter on its variables. However, the results of such analyses can be dependent on an exact set of parameter values due to nonlinearity. To mitigate this problem, global sensitivity analysis techniques are used to calculate parameter sensitivities in a wider parameter space. We applied global sensitivity analysis to a selection of five signalling and metabolic models, several of which incorporate experimentally well-determined parameters. Assuming these models represent physiological reality, we explored how the results could change under increasing amounts of parameter uncertainty. Our results show that parameter sensitivities calculated with the physiological parameter values are not necessarily the most frequently observed under random sampling, even in a small interval around the physiological values. Often multimodal distributions were observed. Unsurprisingly, the range of possible sensitivity coefficient values increased with the level of parameter uncertainty, though the amount of parameter uncertainty at which the pattern of control was able to change differed among the models analysed. We suggest that this level of uncertainty can be used as a global measure of model robustness. Finally a comparison of different global sensitivity analysis techniques shows that, if high-throughput computing resources are available, then random sampling may actually be the most suitable technique.
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Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G. An online model composition tool for system biology models. BMC SYSTEMS BIOLOGY 2013; 7:88. [PMID: 24006914 PMCID: PMC3846440 DOI: 10.1186/1752-0509-7-88] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 08/21/2013] [Indexed: 11/21/2022]
Abstract
Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.
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Affiliation(s)
- Sarp A Coskun
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA.
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Zhong W, Morgan HP, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. `In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1768-79. [PMID: 23999300 DOI: 10.1107/s0907444913013875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/20/2013] [Indexed: 11/10/2022]
Abstract
The active site of pyruvate kinase (PYK) is located between the AC core of the enzyme and a mobile lid corresponding to domain B. Many PYK structures have already been determined, but the first `effector-only' structure and the first with PEP (the true natural substrate) are now reported for the enzyme from Trypanosoma brucei. PEP soaked into crystals of the enzyme with bound allosteric activator fructose 2,6-bisphosphate (F26BP) and Mg(2+) triggers a substantial 23° rotation of the B domain `in crystallo', resulting in a partially closed active site. The interplay of side chains with Mg(2+) and PEP may explain the mechanism of the domain movement. Furthermore, it is apparent that when F26BP is present but PEP is absent Mg(2+) occupies a position that is distinct from the two canonical Mg(2+)-binding sites at the active site. This third site is adjacent to the active site and involves the same amino-acid side chains as in canonical site 1 but in altered orientations. Site 3 acts to sequester Mg(2+) in a `priming' position such that the enzyme is maintained in its R-state conformation. In this way, Mg(2+) cooperates with F26BP to ensure that the enzyme is in a conformation that has a high affinity for the substrate.
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Affiliation(s)
- Wenhe Zhong
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, Scotland
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Achcar F, Barrett MP, Breitling R. Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis. FEBS J 2013; 280:4640-51. [PMID: 23865459 DOI: 10.1111/febs.12436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/20/2013] [Accepted: 07/03/2013] [Indexed: 01/10/2023]
Abstract
Previous models of glycolysis in the sleeping sickness parasite Trypanosoma brucei assumed that the core part of glycolysis in this unicellular parasite is tightly compartimentalized within an organelle, the glycosome, which had previously been shown to contain most of the glycolytic enzymes. The glycosomes were assumed to be largely impermeable, and exchange of metabolites between the cytosol and the glycosome was assumed to be regulated by specific transporters in the glycosomal membrane. This tight compartmentalization was considered to be essential for parasite viability. Recently, size-specific metabolite pores were discovered in the membrane of glycosomes. These channels are proposed to allow smaller metabolites to diffuse across the membrane but not larger ones. In light of this new finding, we re-analyzed the model taking into account uncertainty about the topology of the metabolic system in T. brucei, as well as uncertainty about the values of all parameters of individual enzymatic reactions. Our analysis shows that these newly-discovered nonspecific pores are not necessarily incompatible with our current knowledge of the glycosomal metabolic system, provided that the known cytosolic activities of the glycosomal enzymes play an important role in the regulation of glycolytic fluxes and the concentration of metabolic intermediates of the pathway.
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Affiliation(s)
- Fiona Achcar
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
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