1
|
Gao Y, Xie R, Chen Y, Yang B, Wang M, Hua L, Wang X, Wang W, Wang N, Ge H, Ma J. Structural basis for substrate recognition by a S-adenosylhomocysteine hydrolase Lpg2021 from Legionella pneumophila. Int J Biol Macromol 2024; 270:132289. [PMID: 38735607 DOI: 10.1016/j.ijbiomac.2024.132289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/24/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
S-Adenosyl-l-homocysteine hydrolase (SAHH) is a crucial enzyme that governs S-adenosyl methionine (SAM)-dependent methylation reactions within cells and regulates the intracellular concentration of SAH. Legionella pneumophila, the causative pathogen of Legionnaires' disease, encodes Lpg2021, which is the first identified dimeric SAHH in bacteria and is a promising target for drug development. Here, we report the structure of Lpg2021 in its ligand-free state and in complexes with adenine (ADE), adenosine (ADO), and 3-Deazaneplanocin A (DZNep). X-ray crystallography, isothermal titration calorimetry (ITC), and molecular docking were used to elucidate the binding mechanisms of Lpg2021 to its substrates and inhibitors. Virtual screening was performed to identify potential Lpg2021 inhibitors. This study contributes a novel perspective to the understanding of SAHH evolution and establishes a structural framework for designing specific inhibitors targeting pathogenic Legionella pneumophila SAHH.
Collapse
Affiliation(s)
- Yongshan Gao
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Rao Xie
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yanan Chen
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Beibei Yang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Min Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Lan Hua
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Xu Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Weiqiang Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Na Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China.
| | - Honghua Ge
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China.
| | - Jinming Ma
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China.
| |
Collapse
|
2
|
Koeppl LH, Popadić D, Saleem-Batcha R, Germer P, Andexer JN. Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases. Commun Biol 2024; 7:380. [PMID: 38548921 PMCID: PMC10978960 DOI: 10.1038/s42003-024-06078-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/20/2024] [Indexed: 04/01/2024] Open
Abstract
S-Adenosyl-L-homocysteine hydrolase (SAHH) reversibly cleaves S-adenosyl-L-homocysteine, the product of S-adenosyl-L-methionine-dependent methylation reactions. The conversion of S-adenosyl-L-homocysteine into adenosine and L-homocysteine plays an important role in the regulation of the methyl cycle. An alternative metabolic route for S-adenosyl-L-methionine regeneration in the extremophiles Methanocaldococcus jannaschii and Thermotoga maritima has been identified, featuring the deamination of S-adenosyl-L-homocysteine to S-inosyl-L-homocysteine. Herein, we report the structural characterisation of different archaeal SAHHs together with a biochemical analysis of various SAHHs from all three domains of life. Homologues deriving from the Euryarchaeota phylum show a higher conversion rate with S-inosyl-L-homocysteine compared to S-adenosyl-L-homocysteine. Crystal structures of SAHH originating from Pyrococcus furiosus in complex with SLH and inosine as ligands, show architectural flexibility in the active site and offer deeper insights into the binding mode of hypoxanthine-containing substrates. Altogether, the findings of our study support the understanding of an alternative metabolic route for S-adenosyl-L-methionine and offer insights into the evolutionary progression and diversification of SAHHs involved in methyl and purine salvage pathways.
Collapse
Affiliation(s)
- Lars-Hendrik Koeppl
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Désirée Popadić
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Philipp Germer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany.
| |
Collapse
|
3
|
El-Sayed SAES, El-Alfy ES, Baghdadi HB, Sayed-Ahmed MZ, Alqahtani SS, Alam N, Ahmad S, Ali MS, Igarashi I, Rizk MA. Antiparasitic activity of FLLL-32 against four Babesia species, B. bovis, B. bigemina, B. divergens and B. caballi, and one Theileria species, Theileria equi in vitro, and Babesia microti in mice. Front Pharmacol 2023; 14:1278451. [PMID: 38027032 PMCID: PMC10651744 DOI: 10.3389/fphar.2023.1278451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: FLLL-32, a synthetic analog of curcumin, is a potent inhibitor of STAT3's constitutive activation in a variety of cancer cells, and its anticancer properties have been demonstrated both in vitro and in vivo. It is also suggested that it might have other pharmacological activities including activity against different parasites. Aim: This study therefore investigated the in vitro antiparasitic activity of FLLL-32 against four pathogenic Babesia species, B. bovis, B. bigemina, B. divergens, and B. caballi, and one Theileria species, Theileria equi. In vivo anti-Babesia microti activity of FLLL-32 was also evaluated in mice. Methods: The FLLL-32, in the growth inhibition assay with a concentration range (0.005-50 μM), was tested for it's activity against these pathogens. The reverse transcription PCR (RT-PCR) assay was used to evaluate the possible effects of FLLL-32 treatment on the mRNA transcription of the target B. bovis genes including S-adenosylhomocysteine hydrolase and histone deacetylase. Results: The in vitro growth of B. bovis, B. bigemina, B. divergens, B. caballi, and T. equi was significantly inhibited in a dose-dependent manner (in all cases, p < 0.05). FLLL-32 exhibits the highest inhibitory effects on B. bovis growth in vitro, and it's IC50 value against this species was 9.57 μM. The RT-PCR results showed that FLLL-32 inhibited the transcription of the B. bovis S-adenosylhomocysteine hydrolase gene. In vivo, the FLLL-32 showed significant inhibition (p < 0.05) of B. microti parasitemia in infected mice with results comparable to that of diminazene aceturate. Parasitemia level in B. microti-infected mice treated with FLLL-32 from day 12 post infection (pi) was reduced to reach zero level at day 16 pi when compared to the infected non-treated mice. Conclusion: The present study demonstrated the antibabesial properties of FLLL-32 and suggested it's usage in the treatment of babesiosis especially when utilized in combination therapy with other antibabesial drugs.
Collapse
Affiliation(s)
- Shimaa Abd El-Salam El-Sayed
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - El-Sayed El-Alfy
- Parasitology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Hanadi B. Baghdadi
- Biology Department, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mohamed Z. Sayed-Ahmed
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jizan, Saudi Arabia
| | - Saad S. Alqahtani
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Nawazish Alam
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jizan, Saudi Arabia
| | - Sarfaraz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jizan, Saudi Arabia
| | - Md. Sajid Ali
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jizan, Saudi Arabia
| | - Ikuo Igarashi
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Mohamed Abdo Rizk
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| |
Collapse
|
4
|
Harris CT, Tong X, Campelo R, Marreiros IM, Vanheer LN, Nahiyaan N, Zuzarte-Luís VA, Deitsch KW, Mota MM, Rhee KY, Kafsack BFC. Sexual differentiation in human malaria parasites is regulated by competition between phospholipid metabolism and histone methylation. Nat Microbiol 2023; 8:1280-1292. [PMID: 37277533 DOI: 10.1038/s41564-023-01396-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 04/25/2023] [Indexed: 06/07/2023]
Abstract
For Plasmodium falciparum, the most widespread and virulent malaria parasite that infects humans, persistence depends on continuous asexual replication in red blood cells, while transmission to their mosquito vector requires asexual blood-stage parasites to differentiate into non-replicating gametocytes. This decision is controlled by stochastic derepression of a heterochromatin-silenced locus encoding AP2-G, the master transcription factor of sexual differentiation. The frequency of ap2-g derepression was shown to be responsive to extracellular phospholipid precursors but the mechanism linking these metabolites to epigenetic regulation of ap2-g was unknown. Through a combination of molecular genetics, metabolomics and chromatin profiling, we show that this response is mediated by metabolic competition for the methyl donor S-adenosylmethionine between histone methyltransferases and phosphoethanolamine methyltransferase, a critical enzyme in the parasite's pathway for de novo phosphatidylcholine synthesis. When phosphatidylcholine precursors are scarce, increased consumption of SAM for de novo phosphatidylcholine synthesis impairs maintenance of the histone methylation responsible for silencing ap2-g, increasing the frequency of derepression and sexual differentiation. This provides a key mechanistic link that explains how LysoPC and choline availability can alter the chromatin status of the ap2-g locus controlling sexual differentiation.
Collapse
Affiliation(s)
- Chantal T Harris
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Xinran Tong
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- BCMB Allied Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Riward Campelo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Inês M Marreiros
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Leen N Vanheer
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Navid Nahiyaan
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Vanessa A Zuzarte-Luís
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Maria M Mota
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Björn F C Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
5
|
Silva FSR, Santos SPO, Meyer R, Silva ES, Pinheiro CS, Alcantara-Neves NM, Pacheco LGC. In vivo cleavage of solubility tags as a tool to enhance the levels of soluble recombinant proteins in Escherichia coli. Biotechnol Bioeng 2021; 118:4159-4167. [PMID: 34370304 DOI: 10.1002/bit.27912] [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: 02/03/2021] [Revised: 07/02/2021] [Accepted: 08/06/2021] [Indexed: 11/09/2022]
Abstract
Recombinant proteins are generally fused with solubility enhancer tags to improve the folding and solubility of the target protein of interest. However, the fusion protein strategy usually requires expensive proteases to perform in vitro proteolysis and additional chromatographic steps to obtain tag-free recombinant proteins. Expression systems based on intracellular processing of solubility tags in Escherichia coli, through co-expression of a site-specific protease, simplify the recombinant protein purification process, and promote the screening of molecules that fail to remain soluble after tag removal. High yields of soluble target proteins have already been achieved using these protease co-expression systems. Herein, we review approaches for controlled intracellular processing systems tailored to produce soluble untagged proteins in E. coli. We discuss the different genetic systems available for intracellular processing of recombinant proteins regarding system design features, advantages, and limitations of the various strategies.
Collapse
Affiliation(s)
- Filipe S R Silva
- Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Sara P O Santos
- Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Roberto Meyer
- Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil.,Post-Graduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Eduardo S Silva
- Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil.,Post-Graduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Carina S Pinheiro
- Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil.,Post-Graduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Neuza M Alcantara-Neves
- Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil.,Post-Graduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Luis G C Pacheco
- Post-Graduate Program in Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil.,Department of Biotechnology, Federal University of Bahia, Salvador, Bahia, Brazil
| |
Collapse
|
6
|
Vizán P, Di Croce L, Aranda S. Functional and Pathological Roles of AHCY. Front Cell Dev Biol 2021; 9:654344. [PMID: 33869213 PMCID: PMC8044520 DOI: 10.3389/fcell.2021.654344] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/24/2021] [Indexed: 11/25/2022] Open
Abstract
Adenosylhomocysteinase (AHCY) is a unique enzyme and one of the most conserved proteins in living organisms. AHCY catalyzes the reversible break of S-adenosylhomocysteine (SAH), the by-product and a potent inhibitor of methyltransferases activity. In mammals, AHCY is the only enzyme capable of performing this reaction. Controlled subcellular localization of AHCY is believed to facilitate local transmethylation reactions, by removing excess of SAH. Accordingly, AHCY is recruited to chromatin during replication and active transcription, correlating with increasing demands for DNA, RNA, and histone methylation. AHCY deletion is embryonic lethal in many organisms (from plants to mammals). In humans, AHCY deficiency is associated with an incurable rare recessive disorder in methionine metabolism. In this review, we focus on the AHCY protein from an evolutionary, biochemical, and functional point of view, and we discuss the most recent, relevant, and controversial contributions to the study of this enzyme.
Collapse
Affiliation(s)
- Pedro Vizán
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| |
Collapse
|
7
|
Abstract
Over the past few years, nucleosides have maintained a prominent role as one of the cornerstones of antiviral and anticancer therapeutics, and many approaches to nucleoside drug design have been pursued. One such approach involves flexibility in the sugar moiety of nucleosides, for example, in the highly successful anti-HIV and HBV drug tenofovir. In contrast, introduction of flexibility to the nucleobase scaffold has only more recently gained significance with the invention of our fleximers. The history, development, and some biological relevance for this innovative class of nucleosides are detailed herein.
Collapse
|
8
|
Singh DB, Dwivedi S. Structural insight into binding mode of inhibitor with SAHH of Plasmodium and human: interaction of curcumin with anti-malarial drug targets. J Chem Biol 2016; 9:107-120. [PMID: 27698948 DOI: 10.1007/s12154-016-0155-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/04/2016] [Indexed: 10/21/2022] Open
Abstract
S-adenosyl-L-homocysteine hydrolase of Plasmodium falciparum (PfSAHH) is a potential drug target against malaria, and selective inhibition of PfSAHH is the excellent strategy to prevent the growth of parasite inside the host. Therefore, a comparative analysis of human S-adenosyl-L-homocysteine hydrolase (HsSAHH) and PfSAHH has been performed to explore the structural differences. Structural superimposition of PfSAHH and HsSAHH has generated the RMSD of 0.749 Å over 394 alpha carbon pairs. Residues of PfSAHH from position Tyr152 to Lys193 aligned with insertion/deletion region in HsSAHH, and these extra residues results in an extent of variation in cavity region of PfSAHH. Nicotinamide adenine dinucleotide (NAD) was observed to form hydrogen bonding with Thr201, Thr202, Thr203, Asn235, Val268, Glu287, Asn322, Ile343, Asn391, Lys473, and Tyr477 and also forms hydrophobic interactions with Val268, Ile288, and Thr320 of PfSAHH. In comparison to HsSAHH, Asn322, Lys473, and Tyr477 residues of PfSAHH are unique in interaction with NAD. 2-Fluoroaristeromycin and other analogues of aristeromycin have shown the good binding affinity for both enzymes. Structural differences between PfSAHH and HsSAHH might be employed to design the potential inhibitor of PfSAHH. To find the target enzyme responsible for an anti-malarial effect, molecular docking and interaction analysis of curcumin were performed with 34 drug targets of P. falciparum. Curcumin shows high affinity for binding with HGPRT of PfHGPRT, and an anti-malarial effect of curcumin might be due to binding with PfHGPRT.
Collapse
Affiliation(s)
- Dev Bukhsh Singh
- Department of Biotechnology, Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208024 India ; School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, 201308 India
| | - Seema Dwivedi
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, 201308 India
| |
Collapse
|
9
|
Chakraborty A. Emerging drug resistance in Plasmodium falciparum: A review of well-characterized drug targets for novel antimalarial chemotherapy. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2016. [DOI: 10.1016/s2222-1808(16)61090-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
10
|
Xia L, Ma S, Zhang Y, Wang T, Zhou M, Wang Z, Zhang J. Daily variation in global and local DNA methylation in mouse livers. PLoS One 2015; 10:e0118101. [PMID: 25689298 PMCID: PMC4331433 DOI: 10.1371/journal.pone.0118101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/05/2015] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is one of the best-characterized epigenetic modifications and has an important biological relevance. Here we showed that global DNA methylation level in mouse livers displayed a daily variation where the peak phases occurred during the end of the day and the lowest level at the beginning of the day in the light-dark or dark-dark cycles. Typical repeat sequence long interspersed nucleotide element-1 (LINE-1) had a similar methylation rhythm to global DNA. DNA methyltransferase 3A (DNMT3A) and ratio of S-adenosylmethionine (SAM) to S-adenosylhomocysteine (SAH) brought a relative forward daily variation to global DNA methylation, and the temporary change in ratio of SAM to SAH had no influence on the DNA methylation level. The rhythm of global DNA methylation was lost and DNA methylation level was increased in Per1-/-Per2-/- double knockout mice, which were in accordance with changes of Dnmt3a mRNA levels and its rhythm. Our results suggest that the daily variation in global DNA methylation was associated with the change of Dnmt3a expression rather than ratio of SAM to SAH.
Collapse
Affiliation(s)
- Lin Xia
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Shihong Ma
- Nanjing Institute for the Comprehensive Utilization of Wild Plant, Nanjing, 210042, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, 212013, China
| | - Tao Wang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Mengyi Zhou
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Zhongqiu Wang
- Department of Radiology, Nanjing University of Chinese Medicine, Nanjing, 210000, China
- * E-mail: (JZ); (ZW)
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
- * E-mail: (JZ); (ZW)
| |
Collapse
|
11
|
Design and synthesis of a series of truncated neplanocin fleximers. Molecules 2014; 19:21200-14. [PMID: 25521119 PMCID: PMC6270936 DOI: 10.3390/molecules191221200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 01/15/2023] Open
Abstract
In an effort to study the effects of flexibility on enzyme recognition and activity, we have developed several different series of flexible nucleoside analogues in which the purine base is split into its respective imidazole and pyrimidine components. The focus of this particular study was to synthesize the truncated neplanocin A fleximers to investigate their potential anti-protozoan activities by inhibition of S-adenosylhomocysteine hydrolase (SAHase). The three fleximers tested displayed poor anti-trypanocidal activities, with EC50 values around 200 μM. Further studies of the corresponding ribose fleximers, most closely related to the natural nucleoside substrates, revealed low affinity for the known T. brucei nucleoside transporters P1 and P2, which may be the reason for the lack of trypanocidal activity observed.
Collapse
|
12
|
He M, Zheng Y, Huang CH, Qian G, Xiao X, Ko TP, Shao W, Guo RT. Crystallization and preliminary X-ray diffraction analysis of the S-adenosylhomocysteine hydrolase (SAHH) from Thermotoga maritima. Acta Crystallogr F Struct Biol Commun 2014; 70:1563-5. [PMID: 25372832 PMCID: PMC4231867 DOI: 10.1107/s2053230x14013478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/10/2014] [Indexed: 11/10/2022] Open
Abstract
S-Adenosylhomocysteine hydrolase (SAHH) catalyzes the reversible conversion of S-adenosylhomocysteine into adenosine and homocysteine. The SAHH from Thermotoga maritima (TmSAHH) was expressed in Escherichia coli and the recombinant protein was purified and crystallized. TmSAHH crystals belonging to space group C2, with unit-cell parameters a=106.3, b=112.0, c=164.9 Å, β=103.5°, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.85 Å resolution. Initial phase determination by molecular replacement clearly indicated that the crystal contains one homotetramer per asymmetric unit. Further refinement of the crystal structure is in progress.
Collapse
Affiliation(s)
- Miao He
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People’s Republic of China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Guojun Qian
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang 212013, People’s Republic of China
| | - Xiansha Xiao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Weilan Shao
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang 212013, People’s Republic of China
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| |
Collapse
|
13
|
Nieh CC, Tseng WL. Thymine-based molecular beacon for sensing adenosine based on the inhibition of S-adenosylhomocysteine hydrolase activity. Biosens Bioelectron 2014; 61:404-9. [DOI: 10.1016/j.bios.2014.05.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 01/23/2023]
|
14
|
Ando H, Kawaai K, Mikoshiba K. IRBIT: a regulator of ion channels and ion transporters. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2195-204. [PMID: 24518248 DOI: 10.1016/j.bbamcr.2014.01.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 12/20/2022]
Abstract
IRBIT (also called AHCYL1) was originally identified as a binding protein of the intracellular Ca(2+) channel inositol 1,4,5-trisphosphate (IP3) receptor and functions as an inhibitory regulator of this receptor. Unexpectedly, many functions have subsequently been identified for IRBIT including the activation of multiple ion channels and ion transporters, such as the Na(+)/HCO3(-) co-transporter NBCe1-B, the Na(+)/H(+) exchanger NHE3, the Cl(-) channel cystic fibrosis transmembrane conductance regulator (CFTR), and the Cl(-)/HCO3(-) exchanger Slc26a6. The characteristic serine-rich region in IRBIT plays a critical role in the functions of this protein. In this review, we describe the evolution, domain structure, expression pattern, and physiological roles of IRBIT and discuss the potential molecular mechanisms underlying the coordinated regulation of these diverse ion channels/transporters through IRBIT. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.
Collapse
Affiliation(s)
- Hideaki Ando
- Laboratories for Developmental Neurobiology, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Katsuhiro Kawaai
- Laboratories for Developmental Neurobiology, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Katsuhiko Mikoshiba
- Laboratories for Developmental Neurobiology, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan.
| |
Collapse
|
15
|
Lozada-Ramírez JD, Sánchez-Ferrer A, García-Carmona F. Recombinant S-adenosylhomocysteine hydrolase from Thermotoga maritima: cloning, overexpression, characterization, and thermal purification studies. Appl Biochem Biotechnol 2013; 170:639-53. [PMID: 23588970 DOI: 10.1007/s12010-013-0218-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 04/01/2013] [Indexed: 01/24/2023]
Abstract
S-Adenosylhomocysteine hydrolase (SAHase) encoded by sahase gene is a determinant when catalyzing the reversible conversion of adenosine and homocysteine to S-adenosylhomocysteine in most living organisms. The sahase gene was isolated from the genome of the highly thermostable anaerobic bacteria Thermotoga maritima, and then it was cloned, characterized, overexpressed using Escherichia coli, and partially purified by thermal precipitation. The thermal purification of the recombinant SAHase resulted in changes in the circular dichroism spectra. As a result of this analysis, it was possible to determine the structural changes in the composition of the α-helix and β-sheet content of the recombinant enzyme after purification. Moreover, a predicted secondary structure and 3D structural model was rendered by comparative molecular modeling to further understand the molecular function of this protein including its attractive biotechnological use.
Collapse
Affiliation(s)
- J D Lozada-Ramírez
- Department of Chemical and Biological Sciences, School of Sciences, Universidad de las Américas Puebla, Santa Catarina Mártir Cholula 72820, Puebla, México.
| | | | | |
Collapse
|
16
|
Kim JH, Lee YG, Yoo S, Oh J, Jeong D, Song WK, Yoo BC, Rhee MH, Park J, Cha SH, Hong S, Cho JY. Involvement of Src and the actin cytoskeleton in the antitumorigenic action of adenosine dialdehyde. Biochem Pharmacol 2013; 85:1042-56. [DOI: 10.1016/j.bcp.2013.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/28/2012] [Accepted: 01/18/2013] [Indexed: 01/06/2023]
|
17
|
Corrales RM, Leiba J, Cohen-Gonsaud M, Molle V, Kremer L. Mycobacterium tuberculosis S-adenosyl-l-homocysteine hydrolase is negatively regulated by Ser/Thr phosphorylation. Biochem Biophys Res Commun 2012. [PMID: 23178568 DOI: 10.1016/j.bbrc.2012.11.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
S-Adenosylhomocysteine hydrolase (SahH) is known as an ubiquitous player in methylation-based process that maintains the intracellular S-adenosylhomocysteine (SAH) and S-adenosylmethionine (SAM) equilibrium. Given its crucial role in central metabolism in both eukaryotes and prokaryotes, it is assumed that SahH must be regulated, albeit little is known regarding molecular mechanisms governing its activity. We report here that SahH from Mycobacterium tuberculosis can be phosphorylated by mycobacterial Ser/Thr protein kinases and that phosphorylation negatively affects its enzymatic activity. Mass spectrometric analyses and site-directed mutagenesis identified Thr2 and Thr221 as the two phosphoacceptors. SahH_T2D, SahH_T221D and SahH_T2D/T221D, designed to mimic constitutive phosphorylation, exhibited markedly decreased activity compared to the wild-type enzyme. Both residues are fully conserved in other mycobacterial SahH orthologues, suggesting that SahH phosphorylation on Thr2 and Thr221 may represent a novel and presumably more general mechanism of regulation of the SAH/SAM balance in mycobacteria.
Collapse
Affiliation(s)
- Rosa Milagros Corrales
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université Montpellier 2, CNRS, UMR 5235, case 107, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | | | | | | | | |
Collapse
|
18
|
Jeong W, Kim J, Ahn SE, Lee SI, Bazer FW, Han JY, Song G. AHCYL1 is mediated by estrogen-induced ERK1/2 MAPK cell signaling and microRNA regulation to effect functional aspects of the avian oviduct. PLoS One 2012; 7:e49204. [PMID: 23145124 PMCID: PMC3492294 DOI: 10.1371/journal.pone.0049204] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 10/07/2012] [Indexed: 12/18/2022] Open
Abstract
S-adenosylhomocysteine hydrolase-like protein 1 (AHCYL1), also known as IP(3) receptor-binding protein released with IP(3) (IRBIT), regulates IP(3)-induced Ca(2+) release into the cytoplasm of cells. AHCYL1 is a critical regulator of early developmental stages in zebrafish, but little is known about the function of AHCYL1 or hormonal regulation of expression of the AHCYL1 gene in avian species. Therefore, we investigated differential expression profiles of the AHCYL1 gene in various adult organs and in oviducts from estrogen-treated chickens. Chicken AHCYL1 encodes for a protein of 540 amino acids that is highly conserved and has considerable homology to mammalian AHCYL1 proteins (>94% identity). AHCYL1 mRNA was expressed abundantly in various organs of chickens. Further, the synthetic estrogen agonist induced AHCYL1 mRNA and protein predominantly in luminal and glandular epithelial cells of the chick oviduct. In addition, estrogen activated AHCYL1 through the ERK1/2 signal transduction cascade and that activated expression of AHCYL1 regulated genes affecting oviduct development in chicks as well as calcium release in epithelial cells of the oviduct. Also, microRNAs, miR-124a, miR-1669, miR-1710 and miR-1782 influenced AHCYL1 expression in vitro via its 3'-UTR which suggests that post-transcriptional events are involved in the regulation of AHCYL1 expression in the chick oviduct. In conclusion, these results indicate that AHCYL1 is a novel estrogen-stimulated gene expressed in epithelial cells of the chicken oviduct that likely affects growth, development and calcium metabolism of the mature oviduct of hens via an estrogen-mediated ERK1/2 MAPK cell signaling pathway.
Collapse
Affiliation(s)
- Wooyoung Jeong
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jinyoung Kim
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Suzie E. Ahn
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Sang In Lee
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Fuller W. Bazer
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Center for Animal Biotechnology and Genomics and Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
| | - Jae Yong Han
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Gwonhwa Song
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- * E-mail:
| |
Collapse
|
19
|
Acharya P, Pallavi R, Chandran S, Chakravarti H, Middha S, Acharya J, Kochar S, Kochar D, Subudhi A, Boopathi AP, Garg S, Das A, Tatu U. A glimpse into the clinical proteome of human malaria parasites Plasmodium falciparum and Plasmodium vivax. Proteomics Clin Appl 2012; 3:1314-25. [PMID: 21136953 DOI: 10.1002/prca.200900090] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Malaria causes a worldwide annual mortality of about a million people. Rapidly evolving drug-resistant species of the parasite have created a pressing need for the identification of new drug targets and vaccine candidates. By developing fractionation protocols to enrich parasites from low-parasitemia patient samples, we have carried out the first ever proteomics analysis of clinical isolates of early stages of Plasmodium falciparum (Pf) and P. vivax. Patient-derived malarial parasites were directly processed and analyzed using shotgun proteomics approach using high-sensitivity MS for protein identification. Our study revealed about 100 parasite-coded gene products that included many known drug targets such as Pf hypoxanthine guanine phosphoribosyl transferase, Pf L-lactate dehydrogenase, and Plasmepsins. In addition, our study reports the expression of several parasite proteins in clinical ring stages that have never been reported in the ring stages of the laboratory-cultivated parasite strain. This proof-of-principle study represents a noteworthy step forward in our understanding of pathways elaborated by the parasite within the malaria patient and will pave the way towards identification of new drug and vaccine targets that can aid malaria therapy.
Collapse
Affiliation(s)
- Pragyan Acharya
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Oncoepigenomics: making histone lysine methylation count. Eur J Med Chem 2012; 56:179-94. [PMID: 22975593 DOI: 10.1016/j.ejmech.2012.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/01/2012] [Accepted: 08/04/2012] [Indexed: 12/30/2022]
Abstract
Increasing studies show that methylation of histone lysine residues is implicated in the development and progression of varying disease states such as schizophrenia, diabetes, and multiple human cancers. Targeting the specific enzymes responsible for these processes has fueled global investigation into the understanding and correction of epigenetic pathology. This review aims to assemble a timely account of the current progress against chromatin-modifying histone lysine methyltransferases (KMTs) and demethylases (KDMs) to inform ongoing and future efforts into this promising field. In particular, we report on their role in tumor growth and progression and the development of small molecules that modulate these enzymes.
Collapse
|
21
|
Martinet N, Michel BY, Bertrand P, Benhida R. Small molecules DNAmethyltransferasesinhibitors. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00194a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
This review describes current knowledge concerning DNA methyltransferases (DNMT) biology and the two main classes of DNMT inhibtors.
Collapse
Affiliation(s)
- Nadine Martinet
- Laboratoire de Chimie des Molécules Bioactives et des Arômes
- UMR 6001 CNRS
- Institut de Chimie de Nice
- Université de Nice-Sophia Antipolis
- 06108 Nice Cedex 2
| | - Benoît Y. Michel
- Laboratoire de Chimie des Molécules Bioactives et des Arômes
- UMR 6001 CNRS
- Institut de Chimie de Nice
- Université de Nice-Sophia Antipolis
- 06108 Nice Cedex 2
| | - Philippe Bertrand
- Laboratory of reactivity and synthesis of natural substances
- UMR 6514 Poitiers
- France
| | - Rachid Benhida
- Laboratoire de Chimie des Molécules Bioactives et des Arômes
- UMR 6001 CNRS
- Institut de Chimie de Nice
- Université de Nice-Sophia Antipolis
- 06108 Nice Cedex 2
| |
Collapse
|
22
|
Lee S, Doxey AC, McConkey BJ, Moffatt BA. Nuclear targeting of methyl-recycling enzymes in Arabidopsis thaliana is mediated by specific protein interactions. MOLECULAR PLANT 2012; 5:231-48. [PMID: 21976714 DOI: 10.1093/mp/ssr083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Numerous transmethylation reactions are required for normal plant growth and development. S-adenosylhomocysteine hydrolase (SAHH) and adenosine kinase (ADK) act coordinately to recycle the by-product of these reactions, S-adenosylhomocysteine (SAH) that would otherwise competitively inhibit methyltransferase (MT) activities. Here, we report on investigations to understand how the SAH produced in the nucleus is metabolized by SAHH and ADK. Localization analyses using green fluorescent fusion proteins demonstrated that both enzymes are capable of localizing to the cytoplasm and the nucleus, although no obvious nuclear localization signal was found in their sequences. Deletion analysis revealed that a 41-amino-acid segment of SAHH (Gly(150)-Lys(190)) is required for nuclear targeting of this enzyme. This segment is surface exposed, shows unique sequence conservation patterns in plant SAHHs, and possesses additional features of protein-protein interaction motifs. ADK and SAHH interact in Arabidopsis via this segment and also interact with an mRNA cap MT. We propose that the targeting of this complex is directed by the nuclear localization signal of the MT; other MTs may similarly target SAHH/ADK to other subcellular compartments to ensure uninterrupted transmethylation.
Collapse
Affiliation(s)
- Sanghyun Lee
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | | | | | | |
Collapse
|
23
|
Paliwal SK, Verma AN, Paliwal S. Neglected disease - african sleeping sickness: recent synthetic and modeling advances. Sci Pharm 2011; 79:389-428. [PMID: 21886894 PMCID: PMC3163371 DOI: 10.3797/scipharm.1012-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 05/10/2011] [Indexed: 01/21/2023] Open
Abstract
Human African Trypanosomiasis (HAT) also called sleeping sickness is caused by subspecies of the parasitic hemoflagellate Trypanosoma brucei that mostly occurs in sub-Saharan Africa. The current chemotherapy of the human trypanosomiases relies on only six drugs, five of which have been developed more than 30 years ago, have undesirable toxic side effects and most of them show drug-resistance. Though development of new anti-trypanosomal drugs seems to be a priority area research in this area has lagged far behind. The given review mainly focus upon the recent synthetic and computer based approaches made by various research groups for the development of newer anti-trypanosomal analogues which may have improved efficacy and oral bioavailability than the present ones. The given paper also attempts to investigate the relationship between the various physiochemical parameters and anti-trypanosomal activity that may be helpful in development of potent anti-trypanosomal agents against sleeping sickness.
Collapse
|
24
|
Lin JH, Chang CW, Wu ZH, Tseng WL. Colorimetric Assay for S-Adenosylhomocysteine Hydrolase Activity and Inhibition Using Fluorosurfactant-Capped Gold Nanoparticles. Anal Chem 2010; 82:8775-9. [DOI: 10.1021/ac102020n] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jia-Hui Lin
- Department of Chemistry, National Sun Yat-sen University, Taiwan, and National Sun Yat-sen University−Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan
| | - Chung-Wei Chang
- Department of Chemistry, National Sun Yat-sen University, Taiwan, and National Sun Yat-sen University−Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan
| | - Zong-Han Wu
- Department of Chemistry, National Sun Yat-sen University, Taiwan, and National Sun Yat-sen University−Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, National Sun Yat-sen University, Taiwan, and National Sun Yat-sen University−Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan
| |
Collapse
|
25
|
Huthmacher C, Hoppe A, Bulik S, Holzhütter HG. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC SYSTEMS BIOLOGY 2010; 4:120. [PMID: 20807400 PMCID: PMC2941759 DOI: 10.1186/1752-0509-4-120] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 08/31/2010] [Indexed: 12/20/2022]
Abstract
BACKGROUND Despite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances to antimalarials are widely spread. Hence, new antimalarial drugs are urgently needed. RESULTS Here, we present a computational analysis of the metabolism of Plasmodium falciparum, the deadliest malaria pathogen. We assembled a compartmentalized metabolic model and predicted life cycle stage specific metabolism with the help of a flux balance approach that integrates gene expression data. Predicted metabolite exchanges between parasite and host were found to be in good accordance with experimental findings when the parasite's metabolic network was embedded into that of its host (erythrocyte). Knock-out simulations identified 307 indispensable metabolic reactions within the parasite. 35 out of 57 experimentally demonstrated essential enzymes were recovered and another 16 enzymes, if additionally the assumption was made that nutrient uptake from the host cell is limited and all reactions catalyzed by the inhibited enzyme are blocked. This predicted set of putative drug targets, shown to be enriched with true targets by a factor of at least 2.75, was further analyzed with respect to homology to human enzymes, functional similarity to therapeutic targets in other organisms and their predicted potency for prophylaxis and disease treatment. CONCLUSIONS The results suggest that the set of essential enzymes predicted by our flux balance approach represents a promising starting point for further drug development.
Collapse
Affiliation(s)
- Carola Huthmacher
- Institute of Biochemistry, Charité, Monbijoustraße 2, 10117 Berlin, Germany
| | - Andreas Hoppe
- Institute of Biochemistry, Charité, Monbijoustraße 2, 10117 Berlin, Germany
| | - Sascha Bulik
- Institute of Biochemistry, Charité, Monbijoustraße 2, 10117 Berlin, Germany
| | | |
Collapse
|
26
|
Musa TL, Ioerger TR, Sacchettini JC. The tuberculosis structural genomics consortium: a structural genomics approach to drug discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2009; 77:41-76. [PMID: 20663481 DOI: 10.1016/s1876-1623(09)77003-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Structural genomics is changing the way we study and understand biological systems, providing insight into the biology and life cycle of an organism at the molecular level through determination of protein structures. Structural genomics can be a particularly useful tool in the study of infectious diseases, especially to facilitate the development of new chemotherapeutics by providing a structural foundation for drug discovery. The Tuberculosis Structural Genomics Consortium (TBSGC) is applying a structural genomics approach to solving the structures of biologically and medically important proteins in the pathogenic bacterium Mycobacterium tuberculosis, adding to the scientific knowledge base essential for developing novel and effective antitubercular drugs. Tuberculosis (TB) has been declared a global health emergency by the World Health Organization (WHO). With the rise in the number of multidrug resistant (MDR) and extensively drug resistant (XDR) TB strains, the need for more effective TB treatments has become urgent. In contrast to other structural genomics projects, the TBSGC specifically prioritizes proteins based on their potential as drug targets. We describe the consortium's high-throughput (HT) structure determination pipeline that enables an efficient distribution of resources while also incorporating knowledge from several scientific fields. The success of this pipeline is illustrated in the number of successful structure solutions as demonstrated in the case studies presented in this chapter.
Collapse
Affiliation(s)
- Tracey L Musa
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
| | | | | |
Collapse
|
27
|
Reddy MCM, Kuppan G, Shetty ND, Owen JL, Ioerger TR, Sacchettini JC. Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Protein Sci 2008; 17:2134-44. [PMID: 18815415 DOI: 10.1110/ps.038125.108] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
S-adenosylhomocysteine hydrolase (SAHH) is a ubiquitous enzyme that plays a central role in methylation-based processes by maintaining the intracellular balance between S-adenosylhomocysteine (SAH) and S-adenosylmethionine. We report the first prokaryotic crystal structure of SAHH, from Mycobacterium tuberculosis (Mtb), in complex with adenosine (ADO) and nicotinamide adenine dinucleotide. Structures of complexes with three inhibitors are also reported: 3'-keto aristeromycin (ARI), 2-fluoroadenosine, and 3-deazaadenosine. The ARI complex is the first reported structure of SAHH complexed with this inhibitor, and confirms the oxidation of the 3' hydroxyl to a planar keto group, consistent with its prediction as a mechanism-based inhibitor. We demonstrate the in vivo enzyme inhibition activity of the three inhibitors and also show that 2-fluoradenosine has bactericidal activity. While most of the residues lining the ADO-binding pocket are identical between Mtb and human SAHH, less is known about the binding mode of the homocysteine (HCY) appendage of the full substrate. We report the 2.0 A resolution structure of the complex of SAHH cocrystallized with SAH. The most striking change in the structure is that binding of HCY forces a rotation of His363 around the backbone to flip out of contact with the 5' hydroxyl of the ADO and opens access to a nearby channel that leads to the surface. This complex suggests that His363 acts as a switch that opens up to permit binding of substrate, then closes down after release of the cleaved HCY. Differences in the entrance to this access channel between human and Mtb SAHH are identified.
Collapse
Affiliation(s)
- Manchi C M Reddy
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
| | | | | | | | | | | |
Collapse
|
28
|
Devogelaere B, Sammels E, De Smedt H. The IRBIT domain adds new functions to the AHCY family. Bioessays 2008; 30:642-52. [PMID: 18536033 DOI: 10.1002/bies.20772] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
During the past few years, the IRBIT domain has emerged as an important add-on of S-adenosyl-L-homocystein hydrolase (AHCY), thereby creating the new family of AHCY-like proteins. In this review, we discuss the currently available data on this new family of proteins. We describe the IRBIT domain as a unique part of these proteins and give an overview of its regulation via (de)phosphorylation and proteolysis. The second part of this review is focused on the potential functions of the AHCY-like proteins. We propose that the IRBIT domain serves as an anchor for targeting AHCY-like proteins towards cytoplasmic targets. This leads to regulation of (i) intracellular Ca2+ via the inositol 1,4,5-trisphosphate receptor (IP3R), (ii) intracellular pH via the Na+/HCO3 - cotransporters (NBCs); whereas inactivation of the IRBIT domain induces (iii) nuclear translocation and regulation of AHCY activity. Dysfunction of AHCY-like proteins will disturb these three important functions, with various biological implications.
Collapse
Affiliation(s)
- Benoit Devogelaere
- Laboratory of Molecular and Cellular Signalling, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Belgium
| | | | | |
Collapse
|
29
|
Mull L, Ebbs ML, Bender J. A histone methylation-dependent DNA methylation pathway is uniquely impaired by deficiency in Arabidopsis S-adenosylhomocysteine hydrolase. Genetics 2006; 174:1161-71. [PMID: 16951055 PMCID: PMC1667058 DOI: 10.1534/genetics.106.063974] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
S-adenosylhomocysteine hydrolase (SAH) is a key enzyme in the maintenance of methylation homeostasis in eukaryotes because it is needed to metabolize the by-product of transmethylation reactions, S-adenosylhomocysteine (AdoHcy), which causes by-product inhibition of methyltransferases (MTase's). Complete loss of SAH function is lethal. Partial loss of SAH function causes pleiotropic effects including developmental abnormalities and reduced cytosine methylation. Here we describe a novel partial-function missense allele of the Arabidopsis SAH1 gene that causes loss of cytosine methylation specifically in non-CG contexts controlled by the CMT3 DNA MTase and transcriptional reactivation of a silenced reporter gene, without conferring developmental abnormalities. The CMT3 pathway depends on histone H3 lysine 9 methylation (H3 mK9) to guide DNA methylation. Our results suggest that this pathway is uniquely sensitive to SAH impairment because of its requirement for two transmethylation reactions that can both be inhibited by AdoHcy. Our results further suggest that gene silencing pathways involving an interplay between histone and DNA methylation in other eukaryotes can be selectively impaired by controlled SAH downregulation.
Collapse
Affiliation(s)
- Lori Mull
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | | | | |
Collapse
|
30
|
Porcelli M, Moretti MA, Concilio L, Forte S, Merlino A, Graziano G, Cacciapuoti G. S-adenosylhomocysteine hydrolase from the archaeon Pyrococcus furiosus: biochemical characterization and analysis of protein structure by comparative molecular modeling. Proteins 2006; 58:815-25. [PMID: 15645450 DOI: 10.1002/prot.20381] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
S-adenosylhomocysteine hydrolase (AdoHcyHD) is an ubiquitous enzyme that catalyzes the breakdown of S-adenosylhomocysteine, a powerful inhibitor of most transmethylation reactions, to adenosine and L-homocysteine. AdoHcyHD from the hyperthermophilic archaeon Pyrococcus furiosus (PfAdoHcyHD) was cloned, expressed in Escherichia coli, and purified. The enzyme is thermoactive with an optimum temperature of 95 degrees C, and thermostable retaining 100% residual activity after 1 h at 90 degrees C and showing an apparent melting temperature of 98 degrees C. The enzyme is a homotetramer of 190 kDa and contains four cysteine residues per subunit. Thiol groups are not involved in the catalytic process whereas disulfide bond(s) could be present since incubation with 0.8 M dithiothreitol reduces enzyme activity. Multiple sequence alignment of hyperthermophilic AdoHcyHD reveals the presence of two cysteine residues in the N-terminus of the enzyme conserved only in members of Pyrococcus species, and shows that hyperthermophilic AdoHcyHD lack eight C-terminal residues, thought to be important for structural and functional properties of the eukaryotic enzyme. The homology-modeled structure of PfAdoHcyHD shows that Trp220, Tyr181, Tyr184, and Leu185 of each subunit and Ile244 from a different subunit form a network of hydrophobic and aromatic interactions in the central channel formed at the subunits interface. These contacts partially replace the interactions of the C-terminal tail of the eukaryotic enzyme required for tetramer stability. Moreover, Cys221 and Lys245 substitute for Thr430 and Lys426, respectively, of the human enzyme in NAD-binding. Interestingly, all these residues are fairly well conserved in hyperthermophilic AdoHcyHDs but not in mesophilic ones, thus suggesting a common adaptation mechanism at high temperatures.
Collapse
Affiliation(s)
- Marina Porcelli
- Dipartimento di Biochimica e Biofisica F. Cedrangolo, Seconda Università di Napoli, Naples, Italy.
| | | | | | | | | | | | | |
Collapse
|
31
|
Cui L, Fan Q, Hu Y, Karamycheva SA, Quackenbush J, Khuntirat B, Sattabongkot J, Carlton JM. Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages. Mol Biochem Parasitol 2005; 144:1-9. [PMID: 16085323 DOI: 10.1016/j.molbiopara.2005.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Accepted: 05/30/2005] [Indexed: 11/17/2022]
Abstract
Despite the significance of Plasmodium vivax as the most widespread human malaria parasite and a major public health problem, gene expression in this parasite is poorly understood. To accelerate gene discovery and facilitate the annotation phase of the P. vivax genome project, we have undertaken a transcriptome approach to study gene expression in the mixed blood stages of a P. vivax field isolate. Using a cDNA library constructed from purified blood stages, we have obtained single-pass sequences for approximately 21,500 expressed sequence tags (ESTs), the largest number of transcript tags obtained so far for this species. Cluster analysis revealed that the library is highly redundant, resulting in 5407 clusters. Clustered ESTs were searched against public protein databases for functional annotation, and more than one-third showed a significant match, the majority of these to Plasmodium falciparum proteins. The most abundant clusters were to genes encoding ribosomal proteins and proteins involved in metabolism, consistent with the predominance of trophozoites in the field isolate sample. In spite of the scarcity of other parasite stages in the field isolate, we could identify genes that are expressed in rings, schizonts and gametocytes. This study should facilitate our understanding of the gene expression in P. vivax asexual stages and provide valuable data for gene prediction and annotation of the P. vivax genome sequence.
Collapse
Affiliation(s)
- Liwang Cui
- Department of Entomology, The Pennsylvania State University, 501 ASI, University Park, PA 16802, USA.
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum. J Mol Biol 2004; 343:1007-17. [PMID: 15476817 DOI: 10.1016/j.jmb.2004.08.104] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 08/24/2004] [Accepted: 08/27/2004] [Indexed: 11/25/2022]
Abstract
The human malaria parasite Plasmodium falciparum is responsible for the death of more than a million people each year. The emergence of strains of malarial parasite resistant to conventional drug therapy has stimulated searches for antimalarials with novel modes of action. S-Adenosyl-L-homocysteine hydrolase (SAHH) is a regulator of biological methylations. Inhibitors of SAHH affect the methylation status of nucleic acids, proteins, and small molecules. P.falciparum SAHH (PfSAHH) inhibitors are expected to provide a new type of chemotherapeutic agent against malaria. Despite the pressing need to develop selective PfSAHH inhibitors as therapeutic drugs, only the mammalian SAHH structures are currently available. Here, we report the crystal structure of PfSAHH complexed with the reaction product adenosine (Ado). Knowledge of the structure of the Ado complex in combination with a structural comparison with Homo sapiens SAHH (HsSAHH) revealed that a single substitution between the PfSAHH (Cys59) and HsSAHH (Thr60) accounts for the differential interactions with nucleoside inhibitors. To examine roles of the Cys59 in the interactions with nucleoside inhibitors, a mutant PfSAHH was prepared. A replacement of Cys59 by Thr results in mutant PfSAHH, which shows HsSAHH-like nucleoside inhibitor sensitivity. The present structure should provide opportunities to design potent and selective PfSAHH inhibitors.
Collapse
|