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Li B, Liang J, Baniasadi HR, Kurihara S, Phillips MA, Michael AJ. Functional identification of bacterial spermine, thermospermine, norspermine, norspermidine, spermidine, and N 1-aminopropylagmatine synthases. J Biol Chem 2024; 300:107281. [PMID: 38588807 PMCID: PMC11107197 DOI: 10.1016/j.jbc.2024.107281] [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: 03/14/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024] Open
Abstract
Spermine synthase is an aminopropyltransferase that adds an aminopropyl group to the essential polyamine spermidine to form tetraamine spermine, needed for normal human neural development, plant salt and drought resistance, and yeast CoA biosynthesis. We functionally identify for the first time bacterial spermine synthases, derived from phyla Bacillota, Rhodothermota, Thermodesulfobacteriota, Nitrospirota, Deinococcota, and Pseudomonadota. We also identify bacterial aminopropyltransferases that synthesize the spermine same mass isomer thermospermine, from phyla Cyanobacteriota, Thermodesulfobacteriota, Nitrospirota, Dictyoglomota, Armatimonadota, and Pseudomonadota, including the human opportunistic pathogen Pseudomonas aeruginosa. Most of these bacterial synthases were capable of synthesizing spermine or thermospermine from the diamine putrescine and so possess also spermidine synthase activity. We found that most thermospermine synthases could synthesize tetraamine norspermine from triamine norspermidine, that is, they are potential norspermine synthases. This finding could explain the enigmatic source of norspermine in bacteria. Some of the thermospermine synthases could synthesize norspermidine from diamine 1,3-diaminopropane, demonstrating that they are potential norspermidine synthases. Of 18 bacterial spermidine synthases identified, 17 were able to aminopropylate agmatine to form N1-aminopropylagmatine, including the spermidine synthase of Bacillus subtilis, a species known to be devoid of putrescine. This suggests that the N1-aminopropylagmatine pathway for spermidine biosynthesis, which bypasses putrescine, may be far more widespread than realized and may be the default pathway for spermidine biosynthesis in species encoding L-arginine decarboxylase for agmatine production. Some thermospermine synthases were able to aminopropylate N1-aminopropylagmatine to form N12-guanidinothermospermine. Our study reveals an unsuspected diversification of bacterial polyamine biosynthesis and suggests a more prominent role for agmatine.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jue Liang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Hamid R Baniasadi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Shin Kurihara
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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2
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Vasseur CM, Karunasegaram D, Seebeck FP. Structure and Substrate Specificity of S-Methyl Thiourocanate Hydratase. ACS Chem Biol 2024; 19:718-724. [PMID: 38389448 DOI: 10.1021/acschembio.3c00745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a common cofactor in enzyme-catalyzed reactions that involve hydride transfers. In contrast, urocanase and urocanase-like enzymes use NAD+ for covalent electrophilic catalysis. Deciphering avenues by which this unusual catalytic strategy has diversified by evolution may point to approaches for the design of novel enzymes. In this report, we describe the S-methyl thiourocanate hydratase (S-Me-TUC) from Variovorax sp. RA8 as a novel member of this small family of NAD+-dependent hydratases. This enzyme catalyzes the 1,4-addition of water to S-methyl thiourocanate as the second step in the catabolism of S-methyl ergothioneine. The crystal structure of this enzyme in complex with the cofactor and a product analogue identifies critical sequence motifs that explain the narrow and nonoverlapping substrate scopes of S-methyl thiourocanate-, urocanate-, thiourocanate-, and Nτ-methyl urocanate-specific hydratases. The discovery of a S-methyl ergothioneine catabolic pathway also suggests that S-methylation or alkylation may be a significant activity in the biology of ergothioneine.
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Affiliation(s)
- Camille M Vasseur
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, Basel 4002, Switzerland
| | - Dishani Karunasegaram
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, Basel 4002, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, Basel 4002, Switzerland
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3
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Jamabo M, Mahlalela M, Edkins AL, Boshoff A. Tackling Sleeping Sickness: Current and Promising Therapeutics and Treatment Strategies. Int J Mol Sci 2023; 24:12529. [PMID: 37569903 PMCID: PMC10420020 DOI: 10.3390/ijms241512529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Human African trypanosomiasis is a neglected tropical disease caused by the extracellular protozoan parasite Trypanosoma brucei, and targeted for eradication by 2030. The COVID-19 pandemic contributed to the lengthening of the proposed time frame for eliminating human African trypanosomiasis as control programs were interrupted. Armed with extensive antigenic variation and the depletion of the B cell population during an infectious cycle, attempts to develop a vaccine have remained unachievable. With the absence of a vaccine, control of the disease has relied heavily on intensive screening measures and the use of drugs. The chemotherapeutics previously available for disease management were plagued by issues such as toxicity, resistance, and difficulty in administration. The approval of the latest and first oral drug, fexinidazole, is a major chemotherapeutic achievement for the treatment of human African trypanosomiasis in the past few decades. Timely and accurate diagnosis is essential for effective treatment, while poor compliance and resistance remain outstanding challenges. Drug discovery is on-going, and herein we review the recent advances in anti-trypanosomal drug discovery, including novel potential drug targets. The numerous challenges associated with disease eradication will also be addressed.
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Affiliation(s)
- Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, South Africa; (M.J.); (M.M.)
| | - Maduma Mahlalela
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, South Africa; (M.J.); (M.M.)
| | - Adrienne L. Edkins
- Department of Biochemistry and Microbiology, Biomedical Biotechnology Research Centre (BioBRU), Rhodes University, Makhanda 6139, South Africa;
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, South Africa; (M.J.); (M.M.)
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4
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Li B, Liang J, Phillips MA, Michael AJ. Neofunctionalization of S-adenosylmethionine decarboxylase into pyruvoyl-dependent L-ornithine and L-arginine decarboxylases is widespread in bacteria and archaea. J Biol Chem 2023; 299:105005. [PMID: 37399976 PMCID: PMC10407285 DOI: 10.1016/j.jbc.2023.105005] [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: 05/15/2023] [Revised: 06/12/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
S-adenosylmethionine decarboxylase (AdoMetDC/SpeD) is a key polyamine biosynthetic enzyme required for conversion of putrescine to spermidine. Autocatalytic self-processing of the AdoMetDC/SpeD proenzyme generates a pyruvoyl cofactor from an internal serine. Recently, we discovered that diverse bacteriophages encode AdoMetDC/SpeD homologs that lack AdoMetDC activity and instead decarboxylate L-ornithine or L-arginine. We reasoned that neofunctionalized AdoMetDC/SpeD homologs were unlikely to have emerged in bacteriophages and were probably acquired from ancestral bacterial hosts. To test this hypothesis, we sought to identify candidate AdoMetDC/SpeD homologs encoding L-ornithine and L-arginine decarboxylases in bacteria and archaea. We searched for the anomalous presence of AdoMetDC/SpeD homologs in the absence of its obligatory partner enzyme spermidine synthase, or the presence of two AdoMetDC/SpeD homologs encoded in the same genome. Biochemical characterization of candidate neofunctionalized genes confirmed lack of AdoMetDC activity, and functional presence of L-ornithine or L-arginine decarboxylase activity in proteins from phyla Actinomycetota, Armatimonadota, Planctomycetota, Melainabacteria, Perigrinibacteria, Atribacteria, Chloroflexota, Sumerlaeota, Omnitrophota, Lentisphaerota, and Euryarchaeota, the bacterial candidate phyla radiation and DPANN archaea, and the δ-Proteobacteria class. Phylogenetic analysis indicated that L-arginine decarboxylases emerged at least three times from AdoMetDC/SpeD, whereas L-ornithine decarboxylases arose only once, potentially from the AdoMetDC/SpeD-derived L-arginine decarboxylases, revealing unsuspected polyamine metabolic plasticity. Horizontal transfer of the neofunctionalized genes appears to be the more prevalent mode of dissemination. We identified fusion proteins of bona fide AdoMetDC/SpeD with homologous L-ornithine decarboxylases that possess two, unprecedented internal protein-derived pyruvoyl cofactors. These fusion proteins suggest a plausible model for the evolution of the eukaryotic AdoMetDC.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jue Liang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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5
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Islam A, Shaukat Z, Newman DL, Hussain R, Ricos MG, Dibbens L, Gregory SL. Chromosomal Instability Causes Sensitivity to Polyamines and One-Carbon Metabolism. Metabolites 2023; 13:metabo13050642. [PMID: 37233683 DOI: 10.3390/metabo13050642] [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: 04/17/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023] Open
Abstract
Aneuploidy, or having a disrupted genome, is an aberration commonly found in tumours but rare in normal tissues. It gives rise to proteotoxic stress as well as a stereotypical oxidative shift, which makes these cells sensitive to internal and environmental stresses. Using Drosophila as a model, we investigated the changes in transcription in response to ongoing changes to ploidy (chromosomal instability, CIN). We noticed changes in genes affecting one-carbon metabolism, specifically those affecting the production and use of s-adenosyl methionine (SAM). The depletion of several of these genes has led to cell death by apoptosis in CIN cells but not in normal proliferating cells. We found that CIN cells are particularly sensitive to SAM metabolism at least partly because of its role in generating polyamines. Feeding animals spermine was seen to rescue the cell death caused by the loss of SAM synthase in CIN tissues. The loss of polyamines led to decreased rates of autophagy and sensitivity to reactive oxygen species (ROS), which we have shown to contribute significantly to cell death in CIN cells. These findings suggest that a well-tolerated metabolic intervention such as polyamine inhibition has the potential to target CIN tumours via a relatively well-characterised mechanism.
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Affiliation(s)
- Anowarul Islam
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia 2 Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia 3 School of Biological Sciences, University of Adelaide, Adelaide 5006, Australia
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Zeeshan Shaukat
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - David L Newman
- School of Biological Sciences, University of Adelaide, Adelaide 5006, Australia
| | - Rashid Hussain
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Michael G Ricos
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Leanne Dibbens
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Stephen L Gregory
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia 2 Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia 3 School of Biological Sciences, University of Adelaide, Adelaide 5006, Australia
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Functional polyamine metabolic enzymes and pathways encoded by the virosphere. Proc Natl Acad Sci U S A 2023; 120:e2214165120. [PMID: 36802435 PMCID: PMC9992855 DOI: 10.1073/pnas.2214165120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Viruses produce more viruses by manipulating the metabolic and replication systems of their host cells. Many have acquired metabolic genes from ancestral hosts and use the encoded enzymes to subvert host metabolism. The polyamine spermidine is required for bacteriophage and eukaryotic virus replication, and herein, we have identified and functionally characterized diverse phage- and virus-encoded polyamine metabolic enzymes and pathways. These include pyridoxal 5'-phosphate (PLP)-dependent ornithine decarboxylase (ODC), pyruvoyl-dependent ODC and arginine decarboxylase (ADC), arginase, S-adenosylmethionine decarboxylase (AdoMetDC/speD), spermidine synthase, homospermidine synthase, spermidine N-acetyltransferase, and N-acetylspermidine amidohydrolase. We identified homologs of the spermidine-modified translation factor eIF5a encoded by giant viruses of the Imitervirales. Although AdoMetDC/speD is prevalent among marine phages, some homologs have lost AdoMetDC activity and have evolved into pyruvoyl-dependent ADC or ODC. The pelagiphages that encode the pyruvoyl-dependent ADCs infect the abundant ocean bacterium Candidatus Pelagibacter ubique, which we have found encodes a PLP-dependent ODC homolog that has evolved into an ADC, indicating that infected cells would contain both PLP- and pyruvoyl-dependent ADCs. Complete or partial spermidine or homospermidine biosynthetic pathways are found encoded in the giant viruses of the Algavirales and Imitervirales, and in addition, some viruses of the Imitervirales can release spermidine from the inactive N-acetylspermidine. In contrast, diverse phages encode spermidine N-acetyltransferase that can sequester spermidine into its inactive N-acetyl form. Together, the virome-encoded enzymes and pathways for biosynthesis and release or biochemical sequestration of spermidine or its structural analog homospermidine consolidate and expand evidence supporting an important and global role of spermidine in virus biology.
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7
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Islam A, Shaukat Z, Hussain R, Gregory SL. One-Carbon and Polyamine Metabolism as Cancer Therapy Targets. Biomolecules 2022; 12:biom12121902. [PMID: 36551330 PMCID: PMC9775183 DOI: 10.3390/biom12121902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer metabolic reprogramming is essential for maintaining cancer cell survival and rapid replication. A common target of this metabolic reprogramming is one-carbon metabolism which is notable for its function in DNA synthesis, protein and DNA methylation, and antioxidant production. Polyamines are a key output of one-carbon metabolism with widespread effects on gene expression and signaling. As a result of these functions, one-carbon and polyamine metabolism have recently drawn a lot of interest for their part in cancer malignancy. Therapeutic inhibitors that target one-carbon and polyamine metabolism have thus been trialed as anticancer medications. The significance and future possibilities of one-carbon and polyamine metabolism as a target in cancer therapy are discussed in this review.
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Affiliation(s)
- Anowarul Islam
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Zeeshan Shaukat
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Rashid Hussain
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Stephen L. Gregory
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Correspondence: ; Tel.: +61-0466987583
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8
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Barra L, Awakawa T, Abe I. Noncanonical Functions of Enzyme Cofactors as Building Blocks in Natural Product Biosynthesis. JACS AU 2022; 2:1950-1963. [PMID: 36186570 PMCID: PMC9516700 DOI: 10.1021/jacsau.2c00391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Enzymes involved in secondary metabolite biosynthetic pathways have typically evolutionarily diverged from their counterparts functioning in primary metabolism. They often catalyze diverse and complex chemical transformations and are thus a treasure trove for the discovery of unique enzyme-mediated chemistries. Besides major natural product classes, such as terpenoids, polyketides, and ribosomally or nonribosomally synthesized peptides, biosynthetic investigations of noncanonical natural product biosynthetic pathways often reveal functionally distinct enzyme chemistries. In this Perspective, we aim to highlight challenges and opportunities of biosynthetic investigations on noncanonical natural product pathways that utilize primary metabolites as building blocks, otherwise generally considered as enzyme cofactors. A focus is made on the discovered chemical and enzymological novelties.
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Affiliation(s)
- Lena Barra
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Takayoshi Awakawa
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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9
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Unraveling the genetics of polyamine metabolism in barley for senescence-related crop improvement. Int J Biol Macromol 2022; 221:585-603. [PMID: 36075308 DOI: 10.1016/j.ijbiomac.2022.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 12/25/2022]
Abstract
We explored the polyamine (PA) metabolic pathway genes in barley (Hv) to understand plant development and stress adaptation in Gramineae crops with emphasis on leaf senescence. Bioinformatics and functional genomics tools were utilized for genome-wide identification, comprehensive gene features, evolution, development and stress effects on the expression of the polyamine metabolic pathway gene families (PMGs). Three S-adenosylmethionine decarboxylases (HvSAMDCs), two ornithine decarboxylases (HvODCs), one arginine decarboxylase (HvADC), one spermidine synthase (HvSPDS), two spermine synthases (HvSPMSs), five copper amine oxidases (HvCuAOs) and seven polyamine oxidases (HvPAOs) members of PMGs were identified and characterized in barley. All the HvPMG genes were found to be distributed on all chromosomes of barley. The phylogenetic and comparative assessment revealed that PA metabolic pathway is highly conserved in plants and the prediction of nine H. vulgare miRNAs (hvu-miR) target sites, 18 protein-protein interactions and 961 putative CREs in the promoter region were discerned. Gene expression of HvSAMDC3, HvCuAO7, HvPAO4 and HvSPMS1 was apparent at every developmental stage. SPDS/SPMS gene family was found to be the most responsive to induced leaf senescence. This study provides a reference for the functional investigation of the molecular mechanism(s) that regulate polyamine metabolism in plants as a tool for future breeding decision management systems.
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Carter NS, Kawasaki Y, Nahata SS, Elikaee S, Rajab S, Salam L, Alabdulal MY, Broessel KK, Foroghi F, Abbas A, Poormohamadian R, Roberts SC. Polyamine Metabolism in Leishmania Parasites: A Promising Therapeutic Target. Med Sci (Basel) 2022; 10:24. [PMID: 35645240 PMCID: PMC9149861 DOI: 10.3390/medsci10020024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 12/30/2022] Open
Abstract
Parasites of the genus Leishmania cause a variety of devastating and often fatal diseases in humans and domestic animals worldwide. The need for new therapeutic strategies is urgent because no vaccine is available, and treatment options are limited due to a lack of specificity and the emergence of drug resistance. Polyamines are metabolites that play a central role in rapidly proliferating cells, and recent studies have highlighted their critical nature in Leishmania. Numerous studies using a variety of inhibitors as well as gene deletion mutants have elucidated the pathway and routes of transport, revealing unique aspects of polyamine metabolism in Leishmania parasites. These studies have also shed light on the significance of polyamines for parasite proliferation, infectivity, and host-parasite interactions. This comprehensive review article focuses on the main polyamine biosynthetic enzymes: ornithine decarboxylase, S-adenosylmethionine decarboxylase, and spermidine synthase, and it emphasizes recent discoveries that advance these enzymes as potential therapeutic targets against Leishmania parasites.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sigrid C. Roberts
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR 97123, USA; (N.S.C.); (Y.K.); (S.S.N.); (S.E.); (S.R.); (L.S.); (M.Y.A.); (K.K.B.); (F.F.); (A.A.); (R.P.)
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11
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Sumi MP, Guru SA, Mir R, Bhat MA, Sahu S, Girish MP, Saxena A. Molecular evaluation of exon 8 cystathionine rs5742905T T>C gene polymorphism and determination of its frequency, distribution pattern, and association with susceptibility to Coronary Artery Disease. In North Indian Population. Cardiovasc Hematol Disord Drug Targets 2021; 21:115-122. [PMID: 33719952 DOI: 10.2174/1871529x21666210315121027] [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: 05/07/2020] [Revised: 01/04/2021] [Accepted: 01/18/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The protein coded by cystathionine β synthase (CBS) gene act as a catalyzer, converts homocysteine to cystathionine. Impairment of CBS gene leads to homocystinuria by cystathionine β synthase deficiency which is linked to Coronary Artery Disease. A number of polymorphisms study have been performed in cystathione β synthase gene. In the current study we planned to analyze the influence of CBS T833C gene polymorphism and its association with Coronary Artery Disease development and its progression in the north Indian population. MATERIALS AND METHOD The present study comprises 100 angiographically confirmed CAD patients and 100 age and sex-matched healthy controls. A ≥ 50% luminal stenosis at one major coronary artery was considered for the inclusion criteria of the cases. The investigation of T833C polymorphism in the CBS gene was performed by PCR- RFLP technique. RESULT In result, we found that homozygous mutant (CC ) and heterozygous (TC) genotypes of CBS T833C gene polymorphism, were significantly higher in CAD patients as compared to healthy subjects. We also observed a substantial increased CAD risk exists in dominant, codominant inheritance and allele specific models for the CBS T833C gene polymorphism. We, analyzed the differential distribution with respect to disease severity, but there was no significant association (p=0.96). CONCLUSION In conclusion, this study demonstrates that CBS T833C gene polymorphism plays a key role in developing coronary artery disease and its progression.
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Affiliation(s)
- Mamta P Sumi
- Department of Biochemistry, Maulana Azad Medical College, University of Delhi. India
| | - Sameer Ahmad Guru
- Department of Biochemistry and Multidisciplinary Research Unit (MRU), MAMC, University of Delhi. India
| | - Rashid Mir
- Prince Fahd Bin Sultan Research chair, Department of Medical Lab Technology, Faculty of Applied Medical Sciences, University of Tabuk . Saudi Arabia
| | - Musadiq A Bhat
- Institute of Pharmacology and Toxicology-Neuropharmacology, University of Zurich Winterthurerstrasse, Zurich. Switzerland
| | - Samantak Sahu
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Science. India
| | - M P Girish
- iDepartment of Cardiology, GB Pant Hospital, University of Delhi. India
| | - Alpana Saxena
- Department of Biochemistry, Maulana Azad Medical College, University of Delhi. India
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12
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Zou D, Li L, Min Y, Ji A, Liu Y, Wei X, Wang J, Wen Z. Biosynthesis of a Novel Bioactive Metabolite of Spermidine from Bacillus amyloliquefaciens: Gene Mining, Sequence Analysis, and Combined Expression. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:267-274. [PMID: 33356220 DOI: 10.1021/acs.jafc.0c07143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Spermidine is a biologically active polyamine with extensive application potential in functional foods. However, previously reported spermidine titers by biosynthesis methods are relatively low, which hinders its industrial application. To improve the spermidine titer, key genes affecting the spermidine production were mined to modify Bacillus amyloliquefaciens. Genes of S-adenosylmethionine decarboxylase (speD) and spermidine synthase (speE) from different microorganisms were expressed and compared in B. amyloliquefaciens. Therein, the speD from Escherichia coli and speE from Saccharomyces cerevisiae were confirmed to be optimal for spermidine synthesis, respectively. Gene and amino acid sequence analysis further confirmed the function of speD and speE. Then, these two genes were co-expressed to generate a recombinant strain B. amyloliquefaciens HSAM2(PDspeD-SspeE) with a spermidine titer of 105.2 mg/L, improving by 11.0-fold compared with the control (HSAM2). Through optimization of the fermentation medium, the spermidine titer was increased to 227.4 mg/L, which was the highest titer among present reports. Moreover, the consumption of the substrate S-adenosylmethionine was consistent with the accumulation of spermidine, which contributed to understanding its synthesis pattern. In conclusion, two critical genes for spermidine synthesis were obtained, and an engineering B. amyloliquefaciens strain was constructed for enhanced spermidine production.
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Affiliation(s)
- Dian Zou
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Li
- Guangdong Key Laboratory of Agricultural Products Processing, Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510610, China
| | - Yu Min
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Anying Ji
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingli Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xuetuan Wei
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Zhiyou Wen
- Department of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011, United States
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Plett JM, Plett KL, Wong-Bajracharya J, de Freitas Pereira M, Costa MD, Kohler A, Martin F, Anderson IC. Mycorrhizal effector PaMiSSP10b alters polyamine biosynthesis in Eucalyptus root cells and promotes root colonization. THE NEW PHYTOLOGIST 2020; 228:712-727. [PMID: 32562507 DOI: 10.1111/nph.16759] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Pathogenic microbes are known to manipulate the defences of their hosts through the production of secreted effector proteins. More recently, mutualistic mycorrhizal fungi have also been described as using these secreted effectors to promote host colonization. Here we characterize a mycorrhiza-induced small secreted effector protein of 10 kDa produced by the ectomycorrhizal fungus Pisolithus albus, PaMiSSP10b. We demonstrate that PaMiSSP10b is secreted from fungal hyphae, enters the cells of its host, Eucalyptus grandis, and interacts with an S-adenosyl methionine decarboxylase (AdoMetDC) in the polyamine pathway. Plant polyamines are regulatory molecules integral to the plant immune system during microbial challenge. Using biochemical and transgenic approaches we show that expression of PaMiSSP10b influences levels of polyamines in the plant roots as it enhances the enzymatic activity of AdoMetDC and increases the biosynthesis of higher polyamines. This ultimately favours the colonization success of P. albus. These results identify a new mechanism by which mutualistic microbes are able to manipulate the host´s enzymatic pathways to favour colonization.
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Johanna Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Maíra de Freitas Pereira
- INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA GrandEst Nancy, Université de Lorraine, Champenoux, 54280, France
- Bolsista do CNPq, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maurício Dutra Costa
- Bolsista do CNPq, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Annegret Kohler
- INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA GrandEst Nancy, Université de Lorraine, Champenoux, 54280, France
| | - Francis Martin
- INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA GrandEst Nancy, Université de Lorraine, Champenoux, 54280, France
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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14
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Brooks W. An Epigenetics-Based Hypothesis of Autoantigen Development in Systemic Lupus Erythematosus. EPIGENOMES 2020; 4:epigenomes4020006. [PMID: 34968240 PMCID: PMC8594704 DOI: 10.3390/epigenomes4020006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/20/2020] [Indexed: 11/16/2022] Open
Abstract
Currently, we have a limited understanding of mechanisms leading to systemic lupus erythematosus, but we know that genetics, environmental factors, and epigenetics contribute to the disease. One common aspect of the various environmental triggers is that they can cause cellular stress. When extraordinary stress occurs, such as viral activation, a cell's response can include increased nucleolar volume and activity to produce more machinery (e.g., ribosomes) to help the cell recover. However, nucleolar expansion can disrupt the epigenetic control in neighboring heterochromatin that comprises the nucleolar shell. This disruption can open underlying vulnerabilities that provoke an autoimmune reaction. Here, we review the "X chromosome-nucleolus nexus" hypothesis, which explains how nucleolar stress can disrupt epigenetically silenced chromatin, especially the neighboring inactive X chromosome (aka the nucleolar satellite). Chromatin disruption can lead to the expression of sequestered DNA, such as Alu elements and fully functional LINE-1 reverse transcriptase genes. In addition, Alu transcripts can disrupt the nucleolar structural integrity, leading to nucleolar disintegration. Such disintegration can leave nucleolar components and products in autoantigenic forms, such as abnormal conformations or incomplete macromolecular assemblies. Recent research on DNA sensing pathways can now be incorporated into the hypothesis to provide further details explaining how autoantibodies to endogenous nucleic acids arise.
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Affiliation(s)
- Wesley Brooks
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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15
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Sánchez-Jiménez F, Medina MÁ, Villalobos-Rueda L, Urdiales JL. Polyamines in mammalian pathophysiology. Cell Mol Life Sci 2019; 76:3987-4008. [PMID: 31227845 PMCID: PMC11105599 DOI: 10.1007/s00018-019-03196-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 02/07/2023]
Abstract
Polyamines (PAs) are essential organic polycations for cell viability along the whole phylogenetic scale. In mammals, they are involved in the most important physiological processes: cell proliferation and viability, nutrition, fertility, as well as nervous and immune systems. Consequently, altered polyamine metabolism is involved in a series of pathologies. Due to their pathophysiological importance, PA metabolism has evolved to be a very robust metabolic module, interconnected with the other essential metabolic modules for gene expression and cell proliferation/differentiation. Two different PA sources exist for animals: PA coming from diet and endogenous synthesis. In the first section of this work, the molecular characteristics of PAs are presented as determinant of their roles in living organisms. In a second section, the metabolic specificities of mammalian PA metabolism are reviewed, as well as some obscure aspects on it. This second section includes information on mammalian cell/tissue-dependent PA-related gene expression and information on crosstalk with the other mammalian metabolic modules. The third section presents a synthesis of the physiological processes described as modulated by PAs in humans and/or experimental animal models, the molecular bases of these regulatory mechanisms known so far, as well as the most important gaps of information, which explain why knowledge around the specific roles of PAs in human physiology is still considered a "mysterious" subject. In spite of its robustness, PA metabolism can be altered under different exogenous and/or endogenous circumstances so leading to the loss of homeostasis and, therefore, to the promotion of a pathology. The available information will be summarized in the fourth section of this review. The different sections of this review also point out the lesser-known aspects of the topic. Finally, future prospects to advance on these still obscure gaps of knowledge on the roles on PAs on human physiopathology are discussed.
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Affiliation(s)
- Francisca Sánchez-Jiménez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain
- UNIT 741, CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain
| | - Miguel Ángel Medina
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain
- UNIT 741, CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain
| | - Lorena Villalobos-Rueda
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain
| | - José Luis Urdiales
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain.
- UNIT 741, CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain.
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16
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A polyamine-independent role for S-adenosylmethionine decarboxylase. Biochem J 2019; 476:2579-2594. [DOI: 10.1042/bcj20190561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 11/17/2022]
Abstract
AbstractThe only known function of S-adenosylmethionine decarboxylase (AdoMetDC) is to supply, with its partner aminopropyltransferase enzymes such as spermidine synthase (SpdSyn), the aminopropyl donor for polyamine biosynthesis. Polyamine spermidine is probably essential for the growth of all eukaryotes, most archaea and many bacteria. Two classes of AdoMetDC exist, the prokaryotic class 1a and 1b forms, and the eukaryotic class 2 enzyme, which is derived from an ancient fusion of two prokaryotic class 1b genes. Herein, we show that ‘eukaryotic' class 2 AdoMetDCs are found in bacteria and are enzymatically functional. However, the bacterial AdoMetDC class 2 genes are phylogenetically limited and were likely acquired from a eukaryotic source via transdomain horizontal gene transfer, consistent with the class 2 form of AdoMetDC being a eukaryotic invention. We found that some class 2 and thousands of class 1b AdoMetDC homologues are present in bacterial genomes that also encode a gene fusion of an N-terminal membrane protein of the Major Facilitator Superfamily (MFS) class of transporters and a C-terminal SpdSyn-like domain. Although these AdoMetDCs are enzymatically functional, spermidine is absent, and an entire fusion protein or its SpdSyn-like domain only, does not biochemically complement a SpdSyn deletion strain of E. coli. This suggests that the fusion protein aminopropylates a substrate other than putrescine, and has a role outside of polyamine biosynthesis. Another integral membrane protein found clustered with these genes is DUF350, which is also found in other gene clusters containing a homologue of the glutathionylspermidine synthetase family and occasionally other polyamine biosynthetic enzymes.
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17
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Patel MM, Volkov OA, Leija C, Lemoff A, Phillips MA. A dual regulatory circuit consisting of S-adenosylmethionine decarboxylase protein and its reaction product controls expression of the paralogous activator prozyme in Trypanosoma brucei. PLoS Pathog 2018; 14:e1007404. [PMID: 30365568 PMCID: PMC6221367 DOI: 10.1371/journal.ppat.1007404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/07/2018] [Accepted: 10/12/2018] [Indexed: 01/12/2023] Open
Abstract
Polyamines are essential for cell growth of eukaryotes including the etiologic agent of human African trypanosomiasis (HAT), Trypanosoma brucei. In trypanosomatids, a key enzyme in the polyamine biosynthetic pathway, S-adenosylmethionine decarboxylase (TbAdoMetDC) heterodimerizes with a unique catalytically-dead paralog called prozyme to form the active enzyme complex. In higher eukaryotes, polyamine metabolism is subject to tight feedback regulation by spermidine-dependent mechanisms that are absent in trypanosomatids. Instead, in T. brucei an alternative regulatory strategy based on TbAdoMetDC prozyme has evolved. We previously demonstrated that prozyme protein levels increase in response to loss of TbAdoMetDC activity. Herein, we show that prozyme levels are under translational control by monitoring incorporation of deuterated leucine into nascent prozyme protein. We furthermore identify pathway factors that regulate prozyme mRNA translation. We find evidence for a regulatory feedback mechanism in which TbAdoMetDC protein and decarboxylated AdoMet (dcAdoMet) act as suppressors of prozyme translation. In TbAdoMetDC null cells expressing the human AdoMetDC enzyme, prozyme levels are constitutively upregulated. Wild-type prozyme levels are restored by complementation with either TbAdoMetDC or an active site mutant, suggesting that TbAdoMetDC possesses an enzyme activity-independent function that inhibits prozyme translation. Depletion of dcAdoMet pools by three independent strategies: inhibition/knockdown of TbAdoMetDC, knockdown of AdoMet synthase, or methionine starvation, each cause prozyme upregulation, providing independent evidence that dcAdoMet functions as a metabolic signal for regulation of the polyamine pathway in T. brucei. These findings highlight a potential regulatory paradigm employing enzymes and pseudoenzymes that may have broad implications in biology. Trypanosoma brucei is a single-celled eukaryotic pathogen and the causative agent of human African trypanosomiasis (HAT). Polyamines are organic polycations that are essential for growth in T. brucei to facilitate protein translation and to maintain redox homeostasis. The pathway is the target of eflornithine, a current frontline therapy for treatment of HAT. Polyamine biosynthetic enzymes are regulated at multiple levels in mammals (e.g. transcription, translation and protein turnover), but in contrast, T. brucei lacks these mechanisms. Instead in T. brucei a central enzyme in polyamine metabolism called AdoMetDC must form a complex with a sister protein (termed a pseudoenzyme) to be active. Herein, we show that cellular levels of this sister protein we call prozyme are in turn feedback regulated by both AdoMetDC and by its reaction product in response to cell treatments that reduce pathway output. This regulatory paradigm highlights how pseudoenzymes can evolve to play an important role in metabolic pathway regulation and in organismal fitness.
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Affiliation(s)
- Manish M. Patel
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Oleg A. Volkov
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Christopher Leija
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
- * E-mail:
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18
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Zabala-Letona A, Arruabarrena-Aristorena A, Martín-Martín N, Fernandez-Ruiz S, Sutherland JD, Clasquin M, Tomas-Cortazar J, Jimenez J, Torres I, Quang P, Ximenez-Embun P, Bago R, Ugalde-Olano A, Loizaga-Iriarte A, Lacasa-Viscasillas I, Unda M, Torrano V, Cabrera D, van Liempd SM, Cendon Y, Castro E, Murray S, Revandkar A, Alimonti A, Zhang Y, Barnett A, Lein G, Pirman D, Cortazar AR, Arreal L, Prudkin L, Astobiza I, Valcarcel-Jimenez L, Zuñiga-García P, Fernandez-Dominguez I, Piva M, Caro-Maldonado A, Sánchez-Mosquera P, Castillo-Martín M, Serra V, Beraza N, Gentilella A, Thomas G, Azkargorta M, Elortza F, Farràs R, Olmos D, Efeyan A, Anguita J, Muñoz J, Falcón-Pérez JM, Barrio R, Macarulla T, Mato JM, Martinez-Chantar ML, Cordon-Cardo C, Aransay AM, Marks K, Baselga J, Tabernero J, Nuciforo P, Manning BD, Marjon K, Carracedo A. mTORC1-dependent AMD1 regulation sustains polyamine metabolism in prostate cancer. Nature 2017; 547:109-113. [PMID: 28658205 PMCID: PMC5505479 DOI: 10.1038/nature22964] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 05/04/2017] [Indexed: 02/07/2023]
Abstract
Activation of the PTEN-PI3K-mTORC1 pathway consolidates metabolic programs that sustain cancer cell growth and proliferation. Here we show that mechanistic target of rapamycin complex 1 (mTORC1) regulates polyamine dynamics, a metabolic route that is essential for oncogenicity. By using integrative metabolomics in a mouse model and human biopsies of prostate cancer, we identify alterations in tumours affecting the production of decarboxylated S-adenosylmethionine (dcSAM) and polyamine synthesis. Mechanistically, this metabolic rewiring stems from mTORC1-dependent regulation of S-adenosylmethionine decarboxylase 1 (AMD1) stability. This novel molecular regulation is validated in mouse and human cancer specimens. AMD1 is upregulated in human prostate cancer with activated mTORC1. Conversely, samples from a clinical trial with the mTORC1 inhibitor everolimus exhibit a predominant decrease in AMD1 immunoreactivity that is associated with a decrease in proliferation, in line with the requirement of dcSAM production for oncogenicity. These findings provide fundamental information about the complex regulatory landscape controlled by mTORC1 to integrate and translate growth signals into an oncogenic metabolic program.
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Affiliation(s)
- Amaia Zabala-Letona
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- CIBERONC
| | | | | | | | | | | | | | - Jose Jimenez
- Vall d'Hebron Institute of Oncology (VHIO), Universidad Autonoma de Barcelona, Barcelona, Spain
| | - Ines Torres
- Department of Pathology, Vall d'Hebron Hospital, Universitat Autónoma de Barcelona, Barcelona, Spain
| | | | | | - Ruzica Bago
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | | | | | | | - Miguel Unda
- Department of Urology, Basurto University Hospital, 48013, Bilbao, Spain
| | - Verónica Torrano
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- CIBERONC
| | - Diana Cabrera
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
| | | | - Ylenia Cendon
- Spanish National Cancer Research Centre, Madrid, Spain
- Medicine School, Universidad Autónoma de Madrid
| | - Elena Castro
- Spanish National Cancer Research Centre, Madrid, Spain
| | | | - Ajinkya Revandkar
- Institute of Oncology Research (IOR) and Oncology Institute of Southern Switzerland (IOSI), Bellinzona CH 6500, Switzerland
- Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne CH 1011, Switzerland
| | - Andrea Alimonti
- Institute of Oncology Research (IOR) and Oncology Institute of Southern Switzerland (IOSI), Bellinzona CH 6500, Switzerland
- Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne CH 1011, Switzerland
| | - Yinan Zhang
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | | | - Gina Lein
- AGIOS Pharmaceuticals, Cambridge, USA
| | | | - Ana R. Cortazar
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
| | - Leire Arreal
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
| | - Ludmila Prudkin
- Vall d'Hebron Institute of Oncology (VHIO), Universidad Autonoma de Barcelona, Barcelona, Spain
| | - Ianire Astobiza
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
| | | | | | | | - Marco Piva
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
| | | | | | - Mireia Castillo-Martín
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pathology, Fundação Champalimaud, Lisboa, Portugal
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology (VHIO), Universidad Autonoma de Barcelona, Barcelona, Spain
| | - Naiara Beraza
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
| | - Antonio Gentilella
- Laboratory of Metabolism and Cancer, Catalan Institute of Oncology, ICO, Bellvitge Biomedical Research Institute, IDIBELL, 08908 Barcelona, Spain
| | - George Thomas
- Laboratory of Metabolism and Cancer, Catalan Institute of Oncology, ICO, Bellvitge Biomedical Research Institute, IDIBELL, 08908 Barcelona, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII)
| | - Felix Elortza
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Rosa Farràs
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012 Valencia, Spain
| | - David Olmos
- Spanish National Cancer Research Centre, Madrid, Spain
- CNIO-IBIMA Genitourinary Cancer Unit, Medical Oncology Department, Hospitales Universitarios Virgen de la Victoria y Regional de Málaga
| | - Alejo Efeyan
- Spanish National Cancer Research Centre, Madrid, Spain
| | - Juan Anguita
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- Ikerbasque, Basque foundation for science, Bilbao, Spain
| | - Javier Muñoz
- Spanish National Cancer Research Centre, Madrid, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII)
| | - Juan M. Falcón-Pérez
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
- Ikerbasque, Basque foundation for science, Bilbao, Spain
| | - Rosa Barrio
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
| | - Teresa Macarulla
- CIBERONC
- Vall d'Hebron Institute of Oncology (VHIO), Universidad Autonoma de Barcelona, Barcelona, Spain
| | - Jose M. Mato
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Maria L. Martinez-Chantar
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ana M. Aransay
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | | | - José Baselga
- Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Josep Tabernero
- CIBERONC
- Vall d'Hebron Institute of Oncology (VHIO), Universidad Autonoma de Barcelona, Barcelona, Spain
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Universidad Autonoma de Barcelona, Barcelona, Spain
| | - Brendan D. Manning
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | | | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia Technology Park, 801 building, 48160, Derio, Spain
- CIBERONC
- Ikerbasque, Basque foundation for science, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
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19
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Extending enzyme molecular recognition with an expanded amino acid alphabet. Proc Natl Acad Sci U S A 2017; 114:2610-2615. [PMID: 28196894 DOI: 10.1073/pnas.1616816114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural enzymes are constructed from the 20 proteogenic amino acids, which may then require posttranslational modification or the recruitment of coenzymes or metal ions to achieve catalytic function. Here, we demonstrate that expansion of the alphabet of amino acids can also enable the properties of enzymes to be extended. A chemical mutagenesis strategy allowed a wide range of noncanonical amino acids to be systematically incorporated throughout an active site to alter enzymic substrate specificity. Specifically, 13 different noncanonical side chains were incorporated at 12 different positions within the active site of N-acetylneuraminic acid lyase (NAL), and the resulting chemically modified enzymes were screened for activity with a range of aldehyde substrates. A modified enzyme containing a 2,3-dihydroxypropyl cysteine at position 190 was identified that had significantly increased activity for the aldol reaction of erythrose with pyruvate compared with the wild-type enzyme. Kinetic investigation of a saturation library of the canonical amino acids at the same position showed that this increased activity was not achievable with any of the 20 proteogenic amino acids. Structural and modeling studies revealed that the unique shape and functionality of the noncanonical side chain enabled the active site to be remodeled to enable more efficient stabilization of the transition state of the reaction. The ability to exploit an expanded amino acid alphabet can thus heighten the ambitions of protein engineers wishing to develop enzymes with new catalytic properties.
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20
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Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA. Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog. eLife 2016; 5. [PMID: 27977001 PMCID: PMC5201418 DOI: 10.7554/elife.20198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 12/11/2016] [Indexed: 02/06/2023] Open
Abstract
Catalytically inactive enzyme paralogs occur in many genomes. Some regulate their active counterparts but the structural principles of this regulation remain largely unknown. We report X-ray structures of Trypanosoma brucei S-adenosylmethionine decarboxylase alone and in functional complex with its catalytically dead paralogous partner, prozyme. We show monomeric TbAdoMetDC is inactive because of autoinhibition by its N-terminal sequence. Heterodimerization with prozyme displaces this sequence from the active site through a complex mechanism involving a cis-to-trans proline isomerization, reorganization of a β-sheet, and insertion of the N-terminal α-helix into the heterodimer interface, leading to enzyme activation. We propose that the evolution of this intricate regulatory mechanism was facilitated by the acquisition of the dimerization domain, a single step that can in principle account for the divergence of regulatory schemes in the AdoMetDC enzyme family. These studies elucidate an allosteric mechanism in an enzyme and a plausible scheme by which such complex cooperativity evolved. DOI:http://dx.doi.org/10.7554/eLife.20198.001
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Affiliation(s)
- Oleg A Volkov
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lisa Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carson Ariagno
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shihua Zhong
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute,University of Texas Southwestern Medical Center, Dallas, United States
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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21
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Shi H, Mu WD, Zhang B, Meng T, Zhang ST, Zhou DS. Potential role of S-adenosylmethionine in osteosarcoma development. Onco Targets Ther 2016; 9:3653-9. [PMID: 27382303 PMCID: PMC4920229 DOI: 10.2147/ott.s101408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The metastatic form of osteosarcoma is a life threatening one since it metastasizes to the lungs. The major cause of metastatic osteosarcoma is hypomethylation of numerous genes that undergo overexpression to enable the progression of the disease. In the present study, S-adenosylmethionine (SAM), a predominant methyl donor, was administered to find out its effects on osteosarcoma progression. As evidence of tumor suppression, the SAM-treated mouse tissue was analyzed histologically, which exemplifies the control that SAM has over abnormal cell proliferation, especially on primary osteosarcoma, but it lacks positive effects on metastatic osteosarcoma. At the molecular level, the successful inhibition of primary osteosarcoma was found to be associated with a lower expression of Sox2, a protein highly expressed in osteosarcoma stem cells, along with an upregulated expression of TCTP. The data suggest that the administration of SAM has a positive role in treating primary osteosarcoma, but it has no role in suppressing metastatic osteosarcoma. The decreased expression of Sox2 together with upregulation of TCTP following SAM administration indicates that SAM has a control over primary osteosarcoma.
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Affiliation(s)
- Hui Shi
- Department of Traumatic Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan; Department of Bone and Joint Surgery
| | - Wei-Dong Mu
- Department of Traumatic Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan
| | - Bing Zhang
- Department of Urology Surgery, Binzhou Medical University Hospital, Binzhou, Shandong, People's Republic of China
| | - Tao Meng
- Department of Bone and Joint Surgery
| | | | - Dong-Sheng Zhou
- Department of Traumatic Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan
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22
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Zhao M, Wijayasinghe YS, Bhansali P, Viola RE, Blumenthal RM. A surprising range of modified-methionyl S-adenosylmethionine analogues support bacterial growth. MICROBIOLOGY-SGM 2015; 161:674-82. [PMID: 25717169 DOI: 10.1099/mic.0.000034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
S-Adenosyl-l-methionine (AdoMet) is an essential metabolite, serving in a very wide variety of metabolic reactions. The enzyme that produces AdoMet from l-methionine and ATP (methionine adenosyltransferase, MAT) is thus an attractive target for antimicrobial agents. We previously showed that a variety of methionine analogues are MAT substrates, yielding AdoMet analogues that function in specific methyltransfer reactions. However, this left open the question of whether the modified AdoMet molecules could support bacterial growth, meaning that they functioned in the full range of essential AdoMet-dependent reactions. The answer matters both for insight into the functional flexibility of key metabolic enzymes, and for drug design strategies for both MAT inhibitors and selectively toxic MAT substrates. In this study, methionine analogues were converted in vitro into AdoMet analogues, and tested with an Escherichia coli strain lacking MAT (ΔmetK) but that produces a heterologous AdoMet transporter. Growth that yields viable, morphologically normal cells provides exceptionally robust evidence that the analogue functions in every essential reaction in which AdoMet participates. Overall, the S-adenosylated derivatives of all tested l-methionine analogues modified at the carboxyl moiety, and some others as well, showed in vivo functionality sufficient to allow good growth in both rich and minimal media, with high viability and morphological normality. As the analogues were chosen based on incompatibility with the reactions via which AdoMet is used to produce acylhomoserine lactones (AHLs) for quorum sensing, these results support the possibility of using this route to selectively interfere with AHL biosynthesis without inhibiting bacterial growth.
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Affiliation(s)
- Mojun Zhao
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | | | - Pravin Bhansali
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, University of Toledo Health Sciences Campus, Toledo, OH 43614, USA
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23
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Remaining Mysteries of Molecular Biology: The Role of Polyamines in the Cell. J Mol Biol 2015; 427:3389-406. [DOI: 10.1016/j.jmb.2015.06.020] [Citation(s) in RCA: 401] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/12/2015] [Accepted: 06/29/2015] [Indexed: 11/23/2022]
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24
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Abstract
Carbon–sulfur biological chemistry encompasses a fascinating area of biochemistry and medicinal chemistry and includes the roles that methionine and S-adenosyl-l-methionine play in cells as well as the chemistry of intracellular thiols such as glutathione. This article, based on the 2014 Bernard Belleau Award lecture, provides an overview of some of the key investigations that were undertaken in this area from a bioorganic perspective. The research has ameliorated our fundamental knowledge of several of the enzymes utilizing these sulfur-containing molecules, has led to the development of several novel 19F biophysical probes, and has explored some of the medicinal chemistry associated with these processes.
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Affiliation(s)
- John F. Honek
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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25
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Li B, Kim SH, Zhang Y, Hanfrey CC, Elliott KA, Ealick SE, Michael AJ. Different polyamine pathways from bacteria have replaced eukaryotic spermidine biosynthesis in ciliates Tetrahymena thermophila and Paramecium tetaurelia. Mol Microbiol 2015; 97:791-807. [PMID: 25994085 DOI: 10.1111/mmi.13066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2015] [Indexed: 11/28/2022]
Abstract
The polyamine spermidine is absolutely required for growth and cell proliferation in eukaryotes, due to its role in post-translational modification of essential translation elongation factor eIF5A, mediated by deoxyhypusine synthase. We have found that free-living ciliates Tetrahymena and Paramecium lost the eukaryotic genes encoding spermidine biosynthesis: S-adenosylmethionine decarboxylase (AdoMetDC) and spermidine synthase (SpdSyn). In Tetrahymena, they were replaced by a gene encoding a fusion protein of bacterial AdoMetDC and SpdSyn, present as three copies. In Paramecium, a bacterial homospermidine synthase replaced the eukaryotic genes. Individual AdoMetDC-SpdSyn fusion protein paralogues from Tetrahymena exhibit undetectable AdoMetDC activity; however, when two paralogous fusion proteins are mixed, AdoMetDC activity is restored and spermidine is synthesized. Structural modelling indicates a functional active site is reconstituted by sharing critical residues from two defective protomers across the heteromer interface. Paramecium was found to accumulate homospermidine, suggesting it replaces spermidine for growth. To test this concept, a budding yeast spermidine auxotrophic strain was found to grow almost normally with homospermidine instead of spermidine. Biosynthesis of spermidine analogue aminopropylcadaverine, but not exogenously provided norspermidine, correlated with some growth. Finally, we found that diverse single-celled eukaryotic parasites and multicellular metazoan Schistosoma worms have lost the spermidine biosynthetic pathway but retain deoxyhypusine synthase.
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Affiliation(s)
- Bin Li
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sok Ho Kim
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Anthony J Michael
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
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26
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Liao C, Wang Y, Tan X, Sun L, Liu S. Discovery of novel inhibitors of human S-adenosylmethionine decarboxylase based on in silico high-throughput screening and a non-radioactive enzymatic assay. Sci Rep 2015; 5:10754. [PMID: 26030749 PMCID: PMC5377238 DOI: 10.1038/srep10754] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/27/2015] [Indexed: 12/12/2022] Open
Abstract
Natural polyamines are small polycationic molecules essential for cell growth and development, and elevated level of polyamines is positively correlated with various cancers. As a rate-limiting enzyme of the polyamine biosynthetic pathway, S-adenosylmethionine decarboxylase (AdoMetDC) has been an attractive drug target. In this report, we present the discovery of novel human AdoMetDC (hAdoMetDC) inhibitors by coupling computational and experimental tools. We constructed a reasonable computational structure model of hAdoMetDC that is compatible with general protocols for high-throughput drug screening, and used this model in in silico screening of hAdoMetDC inhibitors against a large compound library using a battery of computational tools. We also established and validated a simple, economic, and non-radioactive enzymatic assay, which can be adapted for experimental high-throughput screening of hAdoMetDC inhibitors. Finally, we obtained an hAdoMetDC inhibitor lead with a novel scaffold. This study provides both new tools and a new lead for the developing of novel hAdoMetDC inhibitors.
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Affiliation(s)
- Chenzeng Liao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yanlin Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Xiao Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Lidan Sun
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Sen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
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27
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Choi JY, Duraisingh MT, Marti M, Ben Mamoun C, Voelker DR. From Protease to Decarboxylase: THE MOLECULAR METAMORPHOSIS OF PHOSPHATIDYLSERINE DECARBOXYLASE. J Biol Chem 2015; 290:10972-80. [PMID: 25724650 DOI: 10.1074/jbc.m115.642413] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 12/26/2022] Open
Abstract
Phosphatidylserine decarboxylase (PSDs) play a central role in the synthesis of phosphatidylethanolamine in numerous species of prokaryotes and eukaryotes. PSDs are unusual decarboxylase containing a pyruvoyl prosthetic group within the active site. The covalently attached pyruvoyl moiety is formed in a concerted reaction when the PSD proenzyme undergoes an endoproteolytic cleavage into a large β-subunit, and a smaller α-subunit, which harbors the prosthetic group at its N terminus. The mechanism of PSD proenzyme cleavage has long been unclear. Using a coupled in vitro transcription/translation system with the soluble Plasmodium knowlesi enzyme (PkPSD), we demonstrate that the post-translational processing is inhibited by the serine protease inhibitor, phenylmethylsulfonyl fluoride. Comparison of PSD sequences across multiple phyla reveals a uniquely conserved aspartic acid within an FFXRX6RX12PXD motif, two uniquely conserved histidine residues within a PXXYHXXHXP motif, and a uniquely conserved serine residue within a GS(S/T) motif, suggesting that PSDs belong to the D-H-S serine protease family. The function of the conserved D-H-S residues was probed using site-directed mutagenesis of PkPSD. The results from these mutagenesis experiments reveal that Asp-139, His-198, and Ser-308 are all essential for endoproteolytic processing of PkPSD, which occurs in cis. In addition, within the GS(S/T) motif found in all PSDs, the Gly-307 residue is also essential, but the Ser/Thr-309 is non-essential. These results define the mechanism whereby PSDs begin their biochemical existence as proteases that execute one autoendoproteolytic cleavage reaction to give rise to a mature PSD harboring a pyruvoyl prosthetic group.
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Affiliation(s)
- Jae-Yeon Choi
- From the Department of Medicine, Basic Science Section, National Jewish Health, Denver, Colorado 80206
| | - Manoj T Duraisingh
- the Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Matthias Marti
- the Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Choukri Ben Mamoun
- the Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut 06520, and
| | - Dennis R Voelker
- From the Department of Medicine, Basic Science Section, National Jewish Health, Denver, Colorado 80206,
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28
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Da MX, Zhang YB, Yao JB, Duan YX. DNA methylation regulates expression of VEGF-C, and S-adenosylmethionine is effective for VEGF-C methylation and for inhibiting cancer growth. ACTA ACUST UNITED AC 2014. [PMID: 25387667 PMCID: PMC4244666 DOI: 10.1590/1414-431x20144005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA hypomethylation may activate oncogene transcription, thus promoting carcinogenesis and tumor development. S-adenosylmethionine (SAM) is a methyl donor in numerous methylation reactions and acts as an inhibitor of intracellular demethylase activity, which results in hypermethylation of DNA. The main objectives of this study were to determine whether DNA hypomethylation correlated with vascular endothelial growth factor-C (VEGF-C) expression, and the effect of SAM on VEGF-C methylation and gastric cancer growth inhibition. VEGF-C expression was assayed by Western blotting and RT-qPCR in gastric cancer cells, and by immunohistochemistry in tumor xenografts. VEGF-C methylation was assayed by bisulfite DNA sequencing. The effect of SAM on cell apoptosis was assayed by flow cytometry analyses and its effect on cancer growth was assessed in nude mice. The VEGF-C promoters of MGC-803, BGC-823, and SGC-7901 gastric cancer cells, which normally express VEGF-C, were nearly unmethylated. After SAM treatment, the VEGF-C promoters in these cells were highly methylated and VEGF-C expression was downregulated. SAM also significantly inhibited tumor growth in vitro and in vivo. DNA methylation regulates expression of VEGF-C. SAM can effectively induce VEGF-C methylation, reduce the expression of VEGF-C, and inhibit tumor growth. SAM has potential as a drug therapy to silence oncogenes and block the progression of gastric cancer.
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Affiliation(s)
- M X Da
- Department of Surgical Oncology, Gansu Provincial Hospital, Lanzhou, China
| | - Y B Zhang
- Department of Surgery, Ningxia Medical University, Yinchuan, China
| | - J B Yao
- Department of Surgical Oncology, Gansu Provincial Hospital, Lanzhou, China
| | - Y X Duan
- Department of Surgery, Ningxia Medical University, Yinchuan, China
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29
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Ravikiran B, Mahalakshmi R. Unusual post-translational protein modifications: the benefits of sophistication. RSC Adv 2014. [DOI: 10.1039/c4ra04694c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review summarizes the “seemingly bizarre”, yet naturally occurring, covalent non-disulphide cross-links in enzymatic and scaffolding proteins and their functions.
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Affiliation(s)
- Boddepalli Ravikiran
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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30
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Ramani D, De Bandt JP, Cynober L. Aliphatic polyamines in physiology and diseases. Clin Nutr 2013; 33:14-22. [PMID: 24144912 DOI: 10.1016/j.clnu.2013.09.019] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 01/01/2023]
Abstract
Aliphatic polyamines are a family of polycationic molecules derived from decarboxylation of the amino acid ornithine that classically comprise three molecules: putrescine, spermidine and spermine. In-cell polyamine homeostasis is tightly controlled at key steps of cell metabolism. Polyamines are involved in an array of cellular functions from DNA stabilization, and regulation of gene expression to ion channel function and, particularly, cell proliferation. As such, aliphatic polyamines play an essential role in rapidly dividing cells such as in the immune system and digestive tract. Because of their role in cell proliferation, polyamines are also involved in carcinogenesis, prompting intensive research into polyamine metabolism as a target in cancer therapy. More recently, another aliphatic polyamine, agmatine, the decarboxylated derivative of arginine, has been identified as a neurotransmitter in mammals, and investigations have focused on its effects in the CNS, notably as a neuroprotector in brain injury.
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Affiliation(s)
- D Ramani
- EA 4466, Faculté des Sciences Pharmaceutiques et Biologiques, Paris Descartes University, Sorbonne Paris Cité, and Clinical Chemistry Department, Hopitaux Universitaires Paris Centre, APHP, Paris, France
| | - J P De Bandt
- EA 4466, Faculté des Sciences Pharmaceutiques et Biologiques, Paris Descartes University, Sorbonne Paris Cité, and Clinical Chemistry Department, Hopitaux Universitaires Paris Centre, APHP, Paris, France.
| | - L Cynober
- EA 4466, Faculté des Sciences Pharmaceutiques et Biologiques, Paris Descartes University, Sorbonne Paris Cité, and Clinical Chemistry Department, Hopitaux Universitaires Paris Centre, APHP, Paris, France
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31
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Jiang Y, Li BQ, Zhang Y, Feng YM, Gao YF, Zhang N, Cai YD. Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins. PLoS One 2013; 8:e66678. [PMID: 23805260 PMCID: PMC3689656 DOI: 10.1371/journal.pone.0066678] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 05/09/2013] [Indexed: 12/28/2022] Open
Abstract
Most of pyruvoyl-dependent proteins observed in prokaryotes and eukaryotes are critical regulatory enzymes, which are primary targets of inhibitors for anti-cancer and anti-parasitic therapy. These proteins undergo an autocatalytic, intramolecular self-cleavage reaction in which a covalently bound pyruvoyl group is generated on a conserved serine residue. Traditional detections of the modified serine sites are performed by experimental approaches, which are often labor-intensive and time-consuming. In this study, we initiated in an attempt for the computational predictions of such serine sites with Feature Selection based on a Random Forest. Since only a small number of experimentally verified pyruvoyl-modified proteins are collected in the protein database at its current version, we only used a small dataset in this study. After removing proteins with sequence identities >60%, a non-redundant dataset was generated and was used, which contained only 46 proteins, with one pyruvoyl serine site for each protein. Several types of features were considered in our method including PSSM conservation scores, disorders, secondary structures, solvent accessibilities, amino acid factors and amino acid occurrence frequencies. As a result, a pretty good performance was achieved in our dataset. The best 100.00% accuracy and 1.0000 MCC value were obtained from the training dataset, and 93.75% accuracy and 0.8441 MCC value from the testing dataset. The optimal feature set contained 9 features. Analysis of the optimal feature set indicated the important roles of some specific features in determining the pyruvoyl-group-serine sites, which were consistent with several results of earlier experimental studies. These selected features may shed some light on the in-depth understanding of the mechanism of the post-translational self-maturation process, providing guidelines for experimental validation. Future work should be made as more pyruvoyl-modified proteins are found and the method should be evaluated on larger datasets. At last, the predicting software can be downloaded from http://www.nkbiox.com/sub/pyrupred/index.html.
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Affiliation(s)
- Yang Jiang
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, P. R. China
| | - Bi-Qing Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yuchao Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiaotong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese, Academy of Sciences, Shanghai, P.R. China
| | - Yuan-Ming Feng
- Department of Biomedical Engineering, Tianjin University, Tianjin Key Lab of Biomedical Engineering Measurement, Tianjin, P.R.China
| | - Yu-Fei Gao
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, P. R. China
- * E-mail: (YFG); (NZ); (YDC)
| | - Ning Zhang
- Department of Biomedical Engineering, Tianjin University, Tianjin Key Lab of Biomedical Engineering Measurement, Tianjin, P.R.China
- * E-mail: (YFG); (NZ); (YDC)
| | - Yu-Dong Cai
- Institiute of Systems Biology, Shanghai University, Shanghai, P. R. China
- * E-mail: (YFG); (NZ); (YDC)
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32
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Velez N, Brautigam CA, Phillips MA. Trypanosoma brucei S-adenosylmethionine decarboxylase N terminus is essential for allosteric activation by the regulatory subunit prozyme. J Biol Chem 2013; 288:5232-40. [PMID: 23288847 DOI: 10.1074/jbc.m112.442475] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human African trypanosomiasis is caused by a single-celled protozoan parasite, Trypanosoma brucei. Polyamine biosynthesis is a clinically validated target for the treatment of human African trypanosomiasis. Metabolic differences between the parasite and the human polyamine pathway are thought to contribute to species selectivity of pathway inhibitors. S-adenosylmethionine decarboxylase (AdoMetDC) catalyzes a key step in the production of the polyamine spermidine. We previously showed that trypanosomatid AdoMetDC differs from other eukaryotic enzymes in that it is regulated by heterodimer formation with a catalytically dead paralog, designated prozyme, which binds with high affinity to the enzyme and increases its activity by up to 10(3)-fold. Herein, we examine the role of specific residues involved in AdoMetDC activation by prozyme through deletion and site-directed mutagenesis. Results indicate that 12 key amino acids at the N terminus of AdoMetDC are essential for prozyme-mediated activation with Leu-8, Leu-10, Met-11, and Met-13 identified as the key residues. These N-terminal residues are fully conserved in the trypanosomatids but are absent from other eukaryotic homologs lacking the prozyme mechanism, suggesting co-evolution of these residues with the prozyme mechanism. Heterodimer formation between AdoMetDC and prozyme was not impaired by mutation of Leu-8 and Leu-10 to Ala, suggesting that these residues are involved in a conformational change that is essential for activation. Our findings provide the first insight into the mechanisms that influence catalytic regulation of AdoMetDC and may have potential implications for the development of new inhibitors against this enzyme.
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Affiliation(s)
- Nahir Velez
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041, USA
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33
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Abstract
New drugs are urgently needed for the treatment of tropical and subtropical parasitic diseases, such as African sleeping sickness, Chagas' disease, leishmaniasis and malaria. Enzymes in polyamine biosynthesis and thiol metabolism, as well as polyamine transporters, are potential drug targets within these organisms. In the present review, the current knowledge of unique properties of polyamine metabolism in these parasites is outlined. These properties include prozyme regulation of AdoMetDC (S-adenosylmethionine decarboxylase) activity in trypanosomatids, co-expression of ODC (ornithine decarboxylase) and AdoMetDC activities in a single protein in plasmodia, and formation of trypanothione, a unique compound linking polyamine and thiol metabolism in trypanosomatids. Particularly interesting features within polyamine metabolism in these parasites are highlighted for their potential in selective therapeutic strategies.
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34
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Michael AJ. Molecular machines encoded by bacterially-derived multi-domain gene fusions that potentially synthesize,N-methylate and transfer long chain polyamines in diatoms. FEBS Lett 2011; 585:2627-34. [DOI: 10.1016/j.febslet.2011.07.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 07/21/2011] [Indexed: 11/26/2022]
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35
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Williams M, Sprenger J, Human E, Al-Karadaghi S, Persson L, Louw AI, Birkholtz LM. Biochemical characterisation and novel classification of monofunctional S-adenosylmethionine decarboxylase of Plasmodium falciparum. Mol Biochem Parasitol 2011; 180:17-26. [PMID: 21803076 DOI: 10.1016/j.molbiopara.2011.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/11/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Plasmodium falciparum like other organisms is dependent on polyamines for proliferation. Polyamine biosynthesis in these parasites is regulated by a unique bifunctional S-adenosylmethionine decarboxylase/ornithine decarboxylase (PfAdoMetDC/ODC). Only limited biochemical and structural information is available on the bifunctional enzyme due to the low levels and impurity of an instable recombinantly expressed protein from the native gene. Here we describe the high level expression of stable monofunctional PfAdoMetDC from a codon-harmonised construct, which permitted its biochemical characterisation indicating similar catalytic properties to AdoMetDCs of orthologous parasites. In the absence of structural data, far-UV CD showed that at least on secondary structure level, PfAdoMetDC corresponds well to that of the human protein. The kinetic properties of the monofunctional enzyme were also found to be different from that of PfAdoMetDC/ODC as mainly evidenced by an increased K(m). We deduced that complex formation of PfAdoMetDC and PfODC could enable coordinated modulation of the decarboxylase activities since there is a convergence of their k(cat) and lowering of their K(m). Such coordination results in the aligned production of decarboxylated AdoMet and putrescine for the subsequent synthesis of spermidine. Furthermore, based on the results obtained in this study we propose a new AdoMetDC subclass for plasmodial AdoMetDCs.
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Affiliation(s)
- Marni Williams
- Department of Biochemistry, University of Pretoria, Hatfield, South Africa
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36
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Green R, Hanfrey CC, Elliott KA, McCloskey DE, Wang X, Kanugula S, Pegg AE, Michael AJ. Independent evolutionary origins of functional polyamine biosynthetic enzyme fusions catalysing de novo diamine to triamine formation. Mol Microbiol 2011; 81:1109-24. [PMID: 21762220 DOI: 10.1111/j.1365-2958.2011.07757.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have identified gene fusions of polyamine biosynthetic enzymes S-adenosylmethionine decarboxylase (AdoMetDC, speD) and aminopropyltransferase (speE) orthologues in diverse bacterial phyla. Both domains are functionally active and we demonstrate the novel de novo synthesis of the triamine spermidine from the diamine putrescine by fusion enzymes from β-proteobacterium Delftia acidovorans and δ-proteobacterium Syntrophus aciditrophicus, in a ΔspeDE gene deletion strain of Salmonella enterica sv. Typhimurium. Fusion proteins from marine α-proteobacterium Candidatus Pelagibacter ubique, actinobacterium Nocardia farcinica, chlorobi species Chloroherpeton thalassium, and β-proteobacterium D. acidovorans each produce a different profile of non-native polyamines including sym-norspermidine when expressed in Escherichia coli. The different aminopropyltransferase activities together with phylogenetic analysis confirm independent evolutionary origins for some fusions. Comparative genomic analysis strongly indicates that gene fusions arose by merger of adjacent open reading frames. Independent fusion events, and horizontal and vertical gene transfer contributed to the scattered phyletic distribution of the gene fusions. Surprisingly, expression of fusion genes in E. coli and S. Typhimurium revealed novel latent spermidine catabolic activity producing non-native 1,3-diaminopropane in these species. We have also identified fusions of polyamine biosynthetic enzymes agmatine deiminase and N-carbamoylputrescine amidohydrolase in archaea, and of S-adenosylmethionine decarboxylase and ornithine decarboxylase in the single-celled green alga Micromonas.
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Affiliation(s)
- Robert Green
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR47UA, UK
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Wada M, Shirahata A. Conformational stabilization of rat s-adenosylmethionine decarboxylase by putrescine. Biol Pharm Bull 2011; 33:1800-5. [PMID: 21048303 DOI: 10.1248/bpb.33.1800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The activity and processing of mammalian S-adenosylmethionine decarboxylase (AdoMetDC) is stimulated by putrescine. To obtain new insights into the mechanism through which putrescine stimulates AdoMetDC, we investigated conformational changes in rat prostate AdoMetDC in the presence or absence of putrescine. We examined the reactivity of purified rat prostate AdoMetDC to the SH-reagent iodoacetic acid (IAA) and its susceptibility to proteolysis in the presence or absence of putrescine using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The activity of AdoMetDC treated with IAA in the absence of putrescine was reduced, but about 80% of its activity remained after treatment with IAA in the presence of putrescine. In the presence of putrescine, IAA incorporation was 1.9 mol IAA/mol of AdoMetDC α-subunit, while there was no incorporation of IAA in the β-subunit of AdoMetDC. In the absence of putrescine, 5.0 mol of IAA/mol of α-subunit and 0.9 mol of IAA/mol of β-subunit were incorporated. Only Cys292 and Cys310 were carboxymethylated by IAA in the presence of putrescine. In contrast, in the absence of putrescine all cysteines were carboxymethylated by IAA. In addition, putrescine slowed the rate of AdoMetDC degradation by trypsin. These results demonstrate that the conformation of AdoMetDC purified from rat prostate is stabilized by putrescine.
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Affiliation(s)
- Makiko Wada
- Faculty of Pharmaceutical Sciences, Josai University, 1–1 Keyakidai, Sakado, Saitama 350–0295, Japan.
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Abstract
This chapter provides an overview of the polyamine field and introduces the 32 other chapters that make up this volume. These chapters provide a wide range of methods, advice, and background relevant to studies of the function of polyamines, the regulation of their content, their role in disease, and the therapeutic potential of drugs targeting polyamine content and function. The methodology provided in this new volume will enable laboratories already working in this area to expand their experimental techniques and facilitate the entry of additional workers into this rapidly expanding field.
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Affiliation(s)
- Anthony E Pegg
- College of Medicine, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, PA, USA
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Luo J, Li YN, Wang F, Zhang WM, Geng X. S-adenosylmethionine inhibits the growth of cancer cells by reversing the hypomethylation status of c-myc and H-ras in human gastric cancer and colon cancer. Int J Biol Sci 2010; 6:784-95. [PMID: 21152119 PMCID: PMC2999854 DOI: 10.7150/ijbs.6.784] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 12/03/2010] [Indexed: 02/07/2023] Open
Abstract
A global DNA hypomethylation might activate oncogene transcription, thus promoting carcinogenesis and tumor development. S-Adenosylmethionine (SAM) serves as a major methyl donor in biological transmethylation events. The object of this study is to explore the influence of SAM on the status of methylation at the promoter of the oncogenes c-myc, H-ras and tumor-suppressor gene p16 (INK4a), as well as its inhibitory effect on cancer cells. The results indicated that SAM treatment inhibited cell growth in gastric cancer cells and colon cancer cells, and the inhibition efficiency was significantly higher than that in the normal cells. Under standard growth conditions, C-myc and H-ras promoters were hypomethylated in gastric cancer cells and colon cancer cells. SAM treatment resulted in a heavy methylation of these promoters, which consequently downregulated mRNA and protein levels. In contrast, there was no significant difference in mRNA and protein levels of p16 (INK4a) with and without SAM treatment. SAM can effectively inhibit the tumor cells growth by reversing the DNA hypomethylation on promoters of oncogenes, thus down-regulating their expression. With no influence on the expression of the tumor suppressor genes, such as P16, SAM could be used as a potential drug for cancer therapy.
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Affiliation(s)
- Jin Luo
- Department of biochemistry, Tianjin Medical University, Tianjin, 300070 China
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