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Sahtout N, Sanders DAR. Biophysical and biochemical characterization of the thioredoxin system from Colwellia psychrerythraea. Proteins 2024; 92:370-383. [PMID: 37909486 DOI: 10.1002/prot.26627] [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: 07/17/2023] [Revised: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
The thioredoxin system is a ubiquitous oxidoreductase system consisting of the enzyme thioredoxin reductase, the protein thioredoxin, and the cofactor nicotinamide adenine dinucleotide phosphate. The system has been comprehensively studied from many organisms, such as Escherichia coli; however, structural and functional analysis of this system from psychrophilic bacteria has not been as extensive. In this study, the thioredoxin system proteins of a psychrophilic bacterium, Colwellia psychrerythraea, were characterized using biophysical and biochemical techniques. Analysis of the complete genome sequence of the C. psychrerythraea thioredoxin system suggested the presence of a putative thioredoxin reductase and at least three thioredoxin. In this study, these identified putative thioredoxin system components were cloned, overexpressed, purified, and characterized. Our studies have indicated that the thioredoxin system proteins from E. coli were more stable than those from C. psychrerythraea. Consistent with these results, kinetic assays indicated that the thioredoxin reductase from E. coli had a higher optimal temperature than that from C. psychrerythraea.
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Affiliation(s)
- Naheda Sahtout
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Ma D, Wang G, Zhu J, Mu W, Dou D, Liu F. Green Leaf Volatile Trans-2-Hexenal Inhibits the Growth of Fusarium graminearum by Inducing Membrane Damage, ROS Accumulation, and Cell Dysfunction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5646-5657. [PMID: 35481379 DOI: 10.1021/acs.jafc.2c00942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fusarium graminearum, the main agent of Fusarium head blight (FHB), can cause serious yield loss and secrete mycotoxins to contaminate grain. Here, the biological activity of trans-2-hexenal (T2H) against F. graminearum was determined and its mode of action (MOA) was investigated. Furthermore, surface plasmon resonance with liquid chromatography-tandem mass spectrometry (SPR-LC-MS/MS), bioinformatic analysis, and gene knockout technique were combined to identify the binding proteins of T2H in F. graminearum cells. T2H exhibited satisfactory inhibitory activity against F. graminearum in vitro. Good lipophilicity greatly enhanced the affinity of T2H to F. graminearum mycelia and further caused membrane damage. The FgTRR (thioredoxin reductase) gene negatively regulates the sensitivity of F. graminearum to T2H by reducing the generation of reactive oxygen species (ROS) induced by T2H. Two mutant strains with FgSLX1 (structure-specific endonuclease subunit) and FgCOPB (coatomer subunit β) genes knockout showed decreased sensitivity to T2H, suggesting that these two genes may be involved in the antimicrobial activity of T2H. Taken together, T2H can inhibit F. graminearum growth by multiple MOAs and can be used as a biofumigant to control the occurrence of FHB in the field.
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Affiliation(s)
- Dicheng Ma
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Guoxian Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Jiamei Zhu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Wei Mu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Daolong Dou
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Feng Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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Structural analysis revealed a novel conformation of the NTRC reductase domain from Chlamydomonas reinhardtii. J Struct Biol 2021; 214:107829. [PMID: 34974142 DOI: 10.1016/j.jsb.2021.107829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/07/2021] [Accepted: 12/27/2021] [Indexed: 11/20/2022]
Abstract
In plant chloroplasts, thiol regulation is driven by two systems. One relies on the activity of thioredoxins through their light dependent reduction by ferredoxin via a ferredoxin-thioredoxin reductase (FTR). In the other system, a NADPH-dependent redox regulation is driven by a NADPH-thioredoxin reductase C (NTRC). While the thioredoxin system has been deeply studied, a more thorough understanding of the function of this plant specific NTRC is desirable. NTRC is a single polypeptide harbouring a thioredoxin domain (Trx) at the C-terminus of a NADPH-dependent Thioredoxin reductase (TrxR). To provide functional and structural insights, we studied the crystal structure of the TrxR domain of the NTRC from Chlamydomonas reinhardtii (CrNTRC, Cre01.g054150.t1.2) and its Cys136Ser (C136S) mutant, which is characterized by the mutation of the resolving cysteine in the active site of the TrxR domain. Furthermore, we confirmed the role of NTRC as electron donor for 2-Cys peroxiredoxin (PRX) also in C. reinhardtii. The structural data of TrxR were employed to develop a scheme of action which addresses electron transfer between TrxR and Trx of NTRC and between NTRC and its substrates.
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Chun HL, Chang YJ, Park HH. Crystal structure of the cofactor-free form of thioredoxin reductase from Acinetobacter baumannii. FEBS Lett 2021; 595:1977-1986. [PMID: 34118067 DOI: 10.1002/1873-3468.14149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 11/09/2022]
Abstract
Thioredoxin reductase (TrxR) is a central component in the thioredoxin system by involving in catalyzing the reduction of thioredoxin, which is critical for organism survival. Because this system is essential, it is a promising target for novel antimicrobial agents. Herein, we solved the 1.9 Å high-resolution structure of TrxR from Acinetobacter baumannii Thioredoxin reductase (AbTrxR), which is a Gram-negative, pathogenic bacterium and a drug-resistant superbug. AbTrxR was cofactor-free and formed a dimer in solution. AbTrxR contained a longer dimerization loop2 and a shorter β7 -β8 connecting loop than other TrxRs. AbTrxR cofactor-free form exhibited a flavin-oxidizing (FO) conformation, whose NADPH domain was located close to the dimeric interface. This structural information might be helpful for development of new antibiotic agents targeting superbugs.
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Affiliation(s)
- Hye Lin Chun
- College of Pharmacy, Chung-Ang University, Seoul, Korea.,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea
| | - Ye Ji Chang
- College of Pharmacy, Chung-Ang University, Seoul, Korea.,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, Korea.,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea
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Li CC, Yang MJ, Yang J, Kang M, Li T, He LH, Song YJ, Zhu YB, Zhao NL, Zhao C, Huang Q, Mou XY, Li H, Tong AP, Tang H, Bao R. Structural and biochemical analysis of 1-Cys peroxiredoxin ScPrx1 from Saccharomyces cerevisiae mitochondria. Biochim Biophys Acta Gen Subj 2020; 1864:129706. [PMID: 32805320 DOI: 10.1016/j.bbagen.2020.129706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND ScPrx1 is a yeast mitochondrial 1-Cys peroxiredoxins (Prx), a type of Prx enzyme which require thiol-containing reducing agents to resolve its peroxidatic cysteine. ScPrx1 plays important role in protection against oxidative stress. Mitochondrial thioredoxin ScTrx3 and glutathione have been reported to be the physiological electron donor for ScPrx1. However, the mechanism underlying their actions, especially the substrate recognition of ScPrx1 requires additional elucidation. METHODS The structure of ScPrx1 was obtained through crystallization experiments. The oligomeric state of ScPrx1 was monitored by Blue-Native PAGE. Mutations were generated by the QuikChange PCR-based method. The ScPrx1 activity assay was carried out by measuring the change of 340 nm absorption of the NADPH oxidation. RESULTS ScPrx1 exist as a homodimer in solution. The structure adopts a typical Prx-fold core which is preceded by an N-terminal β-hairpin and has a C-terminal extension. Mutations (Glu94Ala, Arg198Ala and Trp126) close to the active site could enhance the catalytic efficiency of ScPrx1 while His83Ala and mutations on α4-β6 region exhibited reduced activity. The biochemical data also show that the deletion or mutations on ScPrx1 C-terminal have 2-4.56 fold increased activity. CONCLUSION We inferred that conformational changes of ScPrx1 C-terminal segment were important for its reaction, and the α4-β6 loop regions around the ScPrx1 active sites were important for the catalytic function of ScPrx1. Collectively, these structural features provides a basis for understanding the diverse reductant species usage in different 1-Cys Prxs.
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Affiliation(s)
- Chang-Cheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Mei-Jia Yang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Jing Yang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Mei Kang
- Department of Laboratory medicine, West, China Hospital, Sichuan University
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Li-Hui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Ying-Jie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Yi-Bo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Ning-Lin Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Chang Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Qin Huang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Xing-Yu Mou
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Hong Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Ai-Ping Tong
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Hong Tang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West, China Hospital, Sichuan University and Collaborative Innovation Center.
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Structure, Mechanism, and Inhibition of Aspergillus fumigatus Thioredoxin Reductase. Antimicrob Agents Chemother 2019; 63:AAC.02281-18. [PMID: 30642940 DOI: 10.1128/aac.02281-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 12/29/2018] [Indexed: 12/27/2022] Open
Abstract
Aspergillus fumigatus infections are associated with high mortality rates and high treatment costs. Limited available antifungals and increasing antifungal resistance highlight an urgent need for new antifungals. Thioredoxin reductase (TrxR) is essential for maintaining redox homeostasis and presents as a promising target for novel antifungals. We show that ebselen [2-phenyl-1,2-benzoselenazol-3(2H)-one] is an inhibitor of A. fumigatus TrxR (Ki = 0.22 μM) and inhibits growth of Aspergillus spp., with in vitro MIC values of 16 to 64 µg/ml. Mass spectrometry analysis demonstrates that ebselen interacts covalently with a catalytic cysteine of TrxR, Cys148. We also present the X-ray crystal structure of A. fumigatus TrxR and use in silico modeling of the enzyme-inhibitor complex to outline key molecular interactions. This provides a scaffold for future design of potent and selective antifungal drugs that target TrxR, improving the potency of ebselen toward inhbition of A. fumigatus growth.
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May HC, Yu JJ, Guentzel MN, Chambers JP, Cap AP, Arulanandam BP. Repurposing Auranofin, Ebselen, and PX-12 as Antimicrobial Agents Targeting the Thioredoxin System. Front Microbiol 2018; 9:336. [PMID: 29556223 PMCID: PMC5844926 DOI: 10.3389/fmicb.2018.00336] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 02/12/2018] [Indexed: 01/23/2023] Open
Abstract
As microbial resistance to drugs continues to rise at an alarming rate, finding new ways to combat pathogens is an issue of utmost importance. Development of novel and specific antimicrobial drugs is a time-consuming and expensive process. However, the re-purposing of previously tested and/or approved drugs could be a feasible way to circumvent this long and costly process. In this review, we evaluate the U.S. Food and Drug Administration tested drugs auranofin, ebselen, and PX-12 as antimicrobial agents targeting the thioredoxin system. These drugs have been shown to act on bacterial, fungal, protozoan, and helminth pathogens without significant toxicity to the host. We propose that the thioredoxin system could serve as a useful therapeutic target with broad spectrum antimicrobial activity.
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Affiliation(s)
- Holly C. May
- South Texas Center for Emerging Infectious Disease, University of Texas at San Antonio, San Antonio, TX, United States
- Center for Excellence in Infection Genomics, University of Texas at San Antonio, San Antonio, TX, United States
| | - Jieh-Juen Yu
- South Texas Center for Emerging Infectious Disease, University of Texas at San Antonio, San Antonio, TX, United States
- Center for Excellence in Infection Genomics, University of Texas at San Antonio, San Antonio, TX, United States
| | - M. N. Guentzel
- South Texas Center for Emerging Infectious Disease, University of Texas at San Antonio, San Antonio, TX, United States
- Center for Excellence in Infection Genomics, University of Texas at San Antonio, San Antonio, TX, United States
| | - James P. Chambers
- South Texas Center for Emerging Infectious Disease, University of Texas at San Antonio, San Antonio, TX, United States
- Center for Excellence in Infection Genomics, University of Texas at San Antonio, San Antonio, TX, United States
| | - Andrew P. Cap
- United States Army Institute for Surgical Research, San Antonio Military Medical Center, San Antonio, TX, United States
| | - Bernard P. Arulanandam
- South Texas Center for Emerging Infectious Disease, University of Texas at San Antonio, San Antonio, TX, United States
- Center for Excellence in Infection Genomics, University of Texas at San Antonio, San Antonio, TX, United States
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Targeting Candida spp. to develop antifungal agents. Drug Discov Today 2018; 23:802-814. [PMID: 29353694 DOI: 10.1016/j.drudis.2018.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/09/2017] [Accepted: 01/04/2018] [Indexed: 01/15/2023]
Abstract
Invasive fungal infections are a complex challenge throughout the world because of their high incidence, mainly in critically ill patients, and high mortality rates. The antifungal agents currently available are limited; thus, there is a need for the rapid development of new drugs. In silico methods are a modern strategy to explore interactions between new compounds and specific fungal targets, but they depend on precise genetic information. Here, we discuss the main Candida spp. target genes, including information about null mutants, virulence, cytolocalization, co-regulatory genes, and compounds that are related to protein expression. These data will provide a basis for the future in silico development of antifungal drugs.
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9
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Unprecedented pathway of reducing equivalents in a diflavin-linked disulfide oxidoreductase. Proc Natl Acad Sci U S A 2017; 114:12725-12730. [PMID: 29133410 DOI: 10.1073/pnas.1713698114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavoproteins participate in a wide variety of physiologically relevant processes that typically involve redox reactions. Within this protein superfamily, there exists a group that is able to transfer reducing equivalents from FAD to a redox-active disulfide bridge, which further reduces disulfide bridges in target proteins to regulate their structure and function. We have identified a previously undescribed type of flavin enzyme that is exclusive to oxygenic photosynthetic prokaryotes and that is based on the primary sequence that had been assigned as an NADPH-dependent thioredoxin reductase (NTR). However, our experimental data show that the protein does not transfer reducing equivalents from flavins to disulfides as in NTRs but functions in the opposite direction. High-resolution structures of the protein from Gloeobacter violaceus and Synechocystis sp. PCC6803 obtained by X-ray crystallography showed two juxtaposed FAD molecules per monomer in redox communication with an active disulfide bridge in a variant of the fold adopted by NTRs. We have tentatively named the flavoprotein "DDOR" (diflavin-linked disulfide oxidoreductase) and propose that its activity is linked to a thiol-based transfer of reducing equivalents in bacterial membranes. These findings expand the structural and mechanistic repertoire of flavoenzymes with oxidoreductase activity and pave the way to explore new protein engineering approaches aimed at designing redox-active proteins for diverse biotechnological applications.
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10
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Parsonage D, Sheng F, Hirata K, Debnath A, McKerrow JH, Reed SL, Abagyan R, Poole LB, Podust LM. X-ray structures of thioredoxin and thioredoxin reductase from Entamoeba histolytica and prevailing hypothesis of the mechanism of Auranofin action. J Struct Biol 2016; 194:180-90. [PMID: 26876147 PMCID: PMC5003402 DOI: 10.1016/j.jsb.2016.02.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/29/2022]
Abstract
The anti-arthritic gold-containing drug Auranofin is lethal to the protozoan intestinal parasite Entamoeba histolytica, the causative agent of human amebiasis, in both culture and animal models of the disease. A putative mechanism of Auranofin action proposes that monovalent gold, Au(I), released from the drug, can bind to the redox-active dithiol group of thioredoxin reductase (TrxR). Au(I) binding in the active site is expected to prevent electron transfer to the downstream substrate thioredoxin (Trx), thus interfering with redox homeostasis in the parasite. To clarify the molecular mechanism of Auranofin action in more detail, we determined a series of atomic resolution X-ray structures for E. histolytica thioredoxin (EhTrx) and thioredoxin reductase (EhTrxR), the latter with and without Auranofin. Only the disulfide-bonded form of the active site dithiol (Cys(140)-Cys(143)) was invariably observed in crystals of EhTrxR in spite of the addition of reductants in various crystallization trials, and no gold was found associated with these cysteines. Non-catalytic Cys(286) was identified as the only site of modification, but further mutagenesis studies using the C286Q mutant demonstrated that this site was not responsible for inhibition of EhTrxR by Auranofin. Interestingly, we obtained both of the catalytically-relevant conformations of this bacterial-like, low molecular weight TrxR in crystals without requiring an engineered disulfide linkage between Cys mutants of TrxR and Trx (as was originally done with Escherichia coli TrxR and Trx). We note that the -CXXC- catalytic motif, even if reduced, would likely not provide space sufficient to bind Au(I) by both cysteines of the dithiol group.
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Affiliation(s)
- Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Fang Sheng
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ken Hirata
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA; Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Anjan Debnath
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - James H McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Department of Pathology, University of California San Diego, La Jolla, CA, USA; Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ruben Abagyan
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Larissa M Podust
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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Godoy JSR, Kioshima ÉS, Abadio AKR, Felipe MSS, de Freitas SM, Svidzinski TIE. Structural and functional characterization of the recombinant thioredoxin reductase from Candida albicans as a potential target for vaccine and drug design. Appl Microbiol Biotechnol 2015; 100:4015-25. [DOI: 10.1007/s00253-015-7223-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/01/2015] [Accepted: 12/03/2015] [Indexed: 11/24/2022]
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12
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Abadio AKR, Kioshima ES, Leroux V, Martins NF, Maigret B, Felipe MSS. Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus. PLoS One 2015; 10:e0142926. [PMID: 26569405 PMCID: PMC4646694 DOI: 10.1371/journal.pone.0142926] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/28/2015] [Indexed: 11/27/2022] Open
Abstract
The prevalence of invasive fungal infections worldwide has increased in the last decades. The development of specific drugs targeting pathogenic fungi without producing collateral damage to mammalian cells is a daunting pharmacological challenge. Indeed, many of the toxicities and drug interactions observed with contemporary antifungal therapies can be attributed to “nonselective” interactions with enzymes or cell membrane systems found in mammalian host cells. A computer-aided screening strategy against the TRR1 protein of Paracoccidioides lutzii is presented here. Initially, a bank of commercially available compounds from Life Chemicals provider was docked to model by virtual screening simulations. The small molecules that interact with the model were ranked and, among the best hits, twelve compounds out of 3,000 commercially-available candidates were selected. These molecules were synthesized for validation and in vitro antifungal activity assays for Paracoccidioides lutzii and P. brasiliensis were performed. From 12 molecules tested, 3 harbor inhibitory activity in antifungal assays against the two pathogenic fungi. Corroborating these findings, the molecules have inhibitory activity against the purified recombinant enzyme TRR1 in biochemical assays. Therefore, a rational combination of molecular modeling simulations and virtual screening of new drugs has provided a cost-effective solution to an early-stage medicinal challenge. These results provide a promising technique to the development of new and innovative drugs.
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Affiliation(s)
| | - Erika Seki Kioshima
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
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13
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The structural basis of an NADP⁺-independent dithiol oxidase in FK228 biosynthesis. Sci Rep 2014; 4:4145. [PMID: 24553401 PMCID: PMC4894451 DOI: 10.1038/srep04145] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 02/05/2014] [Indexed: 01/06/2023] Open
Abstract
The disulfide bond is unusual in natural products and critical for thermal stability, cell permeability and bioactivity. DepH from Chromobacterium violaceum No. 968 is an FAD-dependent enzyme responsible for catalyzing the disulfide bond formation of FK228, an anticancer prodrug approved for the treatment of cutaneous T-cell lymphoma. Here we report the crystal structures of DepH and DepH complexed with a substrate analogue S,S'-dimethyl FK228 at 1.82 Å and 2.00 Å, respectively. Structural and biochemical analyses revealed that DepH, in contrast to the well characterized low molecular weight thioredoxin reductases (LMW TrxRs), is an NADP+-independent dithiol oxidase. DepH not only lacks a conserved GGGDXAXE motif necessary for NADP+ binding in the canonical LMW TrxRs, but also contains a 11-residue sequence which physically impedes the binding of NADP+. These observations explain the difference between NADP+-independent small molecule dithiol oxidases and NADP+-dependent thioredoxin reductases and provide insights for understanding the catalytic mechanism of dithiol oxidases involved in natural product biosynthesis.
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Kirkensgaard KG, Hägglund P, Shahpiri A, Finnie C, Henriksen A, Svensson B. A novel twist on molecular interactions between thioredoxin and nicotinamide adenine dinucleotide phosphate-dependent thioredoxin reductase. Proteins 2013; 82:607-19. [PMID: 24123219 DOI: 10.1002/prot.24437] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/19/2013] [Accepted: 09/26/2013] [Indexed: 12/31/2022]
Abstract
The ubiquitous disulfide reductase thioredoxin (Trx) regulates several important biological processes such as seed germination in plants. Oxidized cytosolic Trx is regenerated by nicotinamide adenine dinucleotide phosphate (NADPH)-dependent thioredoxin reductase (NTR) in a multistep transfer of reducing equivalents from NADPH to Trx via a tightly NTR-bound flavin. Here, interactions between NTR and Trx are predicted by molecular modelling of the barley NTR:Trx complex (HvNTR2:HvTrxh2) and probed by site directed mutagenesis. Enzyme kinetics analysis reveals mutants in a loop of the flavin adenine dinucleotide (FAD)-binding domain of HvNTR2 to strongly affect the interaction with Trx. In particular, Trp42 and Met43 play key roles for recognition of the endogenous HvTrxh2. Trx from Arabidopsis thaliana is also efficiently recycled by HvNTR2 but turnover in this case appears to be less dependent on these two residues, suggesting a distinct mode for NTR:Trx recognition. Comparison between the HvNTR2:HvTrxh2 model and the crystal structure of the Escherichia coli NTR:Trx complex reveals major differences in interactions involving the FAD- and NADPH-binding domains as supported by our experiments. Overall, the findings suggest that NTR:Trx interactions in different biological systems are fine-tuned by multiple intermolecular contacts.
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Affiliation(s)
- Kristine G Kirkensgaard
- Enzyme and Protein Chemistry Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; The Protein Chemistry Group, Carlsberg Laboratory, DK-1799 København V, Denmark
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Mu Y, Lian FM, Teng YB, Ao J, Jiang YL, He YX, Chen Y, Zhou CZ, Chen X. The N-terminal β-sheet of peroxiredoxin 4 in the large yellow croaker Pseudosciaena crocea is involved in its biological functions. PLoS One 2013; 8:e57061. [PMID: 23451146 PMCID: PMC3581551 DOI: 10.1371/journal.pone.0057061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/16/2013] [Indexed: 11/29/2022] Open
Abstract
Peroxiredoxins (Prxs) are thiol-specific antioxidant proteins that exhibit peroxidase and peroxynitrite reductase activities involved in the reduction of reactive oxygen species. The peroxiredoxin Prx4 from the large yellow croaker Pseudosciaena crocea is a typical 2-Cys Prx with an N-terminal signal peptide. We solved the crystal structure of Prx4 at 1.90 Å and revealed an N-terminal antiparallel β-sheet that contributes to the dimer interface. Deletion of this β-sheet decreased the in vitro peroxidase activity to about 50% of the wild-type. In vivo assays further demonstrated that removal of this β-sheet led to some impairment in the ability of Prx4 to negatively regulate nuclear factor-κB (NF-κB) activity and to perform its role in anti-bacterial immunity. These results provide new insights into the structure and function relationship of a peroxiredoxin from bony fish.
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Affiliation(s)
- Yinnan Mu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, People’s Republic of China
| | - Fu-Ming Lian
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yan-Bin Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Jingqun Ao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, People’s Republic of China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yong-Xing He
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- * E-mail: (XC) (CZ); (C-ZZ) (XC)
| | - Xinhua Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, People’s Republic of China
- * E-mail: (XC) (CZ); (C-ZZ) (XC)
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Lian FM, Yu J, Ma XX, Yu XJ, Chen Y, Zhou CZ. Structural snapshots of yeast alkyl hydroperoxide reductase Ahp1 peroxiredoxin reveal a novel two-cysteine mechanism of electron transfer to eliminate reactive oxygen species. J Biol Chem 2012; 287:17077-17087. [PMID: 22474296 DOI: 10.1074/jbc.m112.357368] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Peroxiredoxins (Prxs) are thiol-specific antioxidant proteins that protect cells against reactive oxygen species and are involved in cellular signaling pathways. Alkyl hydroperoxide reductase Ahp1 belongs to the Prx5 subfamily and is a two-cysteine (2-Cys) Prx that forms an intermolecular disulfide bond. Enzymatic assays and bioinformatics enabled us to re-assign the peroxidatic cysteine (C(P)) to Cys-62 and the resolving cysteine (C(R)) to Cys-31 but not the previously reported Cys-120. Thus Ahp1 represents the first 2-Cys Prx with a peroxidatic cysteine after the resolving cysteine in the primary sequence. We also found the positive cooperativity of the substrate t-butyl hydroperoxide binding to Ahp1 homodimer at a Hill coefficient of ∼2, which enabled Ahp1 to eliminate hydroperoxide at much higher efficiency. To gain the structural insights into the catalytic cycle of Ahp1, we determined the crystal structures of Ahp1 in the oxidized, reduced, and Trx2-complexed forms at 2.40, 2.91, and 2.10 Å resolution, respectively. Structural superposition of the oxidized to the reduced form revealed significant conformational changes at the segments containing C(P) and C(R). An intermolecular C(P)-C(R) disulfide bond crossing the A-type dimer interface distinguishes Ahp1 from other typical 2-Cys Prxs. The structure of the Ahp1-Trx2 complex showed for the first time how the electron transfers from thioredoxin to a peroxidase with a thioredoxin-like fold. In addition, site-directed mutagenesis in combination with enzymatic assays suggested that the peroxidase activity of Ahp1 would be altered upon the urmylation (covalently conjugated to ubiquitin-related modifier Urm1) of Lys-32.
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Affiliation(s)
- Fu-Ming Lian
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jiang Yu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiao-Xiao Ma
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiao-Jie Yu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.
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17
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Obiero J, Sanders DAR. Design of Deinococcus radiodurans thioredoxin reductase with altered thioredoxin specificity using computational alanine mutagenesis. Protein Sci 2011; 20:1021-9. [PMID: 21465613 DOI: 10.1002/pro.635] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/22/2011] [Accepted: 03/22/2011] [Indexed: 11/06/2022]
Abstract
In this study, the X-ray crystal structure of the complex between Escherichia coli thioredoxin reductase (EC TrxR) and its substrate thioredoxin (Trx) was used as a guide to design a Deinococcus radiodurans TrxR (DR TrxR) mutant with altered Trx specificity. Previous studies have shown that TrxRs have higher affinity for cognate Trxs (same species) than that for Trxs from different species. Computational alanine scanning mutagenesis and visual inspection of the EC TrxR-Trx interface suggested that only four residues (F81, R130, F141, and F142) account for the majority of the EC TrxR-Trx interface stability. Individual replacement of equivalent residues in DR TrxR (M84, K137, F148, and F149) with alanine resulted in drastic changes in binding affinity, confirming that the four residues account for most of TrxR-Trx interface stability. When M84 and K137 were changed to match equivalent EC TrxR residues (K137R and M84F), the DR TrxR substrate specificity was altered from its own Trx to that of EC Trx. The results suggest that a small subset of the TrxR-Trx interface residues is responsible for the majority of Trx binding affinity and species-specific recognition.
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Affiliation(s)
- Josiah Obiero
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK S7N5C9, Canada
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Abadio AKR, Kioshima ES, Teixeira MM, Martins NF, Maigret B, Felipe MSS. Comparative genomics allowed the identification of drug targets against human fungal pathogens. BMC Genomics 2011; 12:75. [PMID: 21272313 PMCID: PMC3042012 DOI: 10.1186/1471-2164-12-75] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 01/27/2011] [Indexed: 11/16/2022] Open
Abstract
Background The prevalence of invasive fungal infections (IFIs) has increased steadily worldwide in the last few decades. Particularly, there has been a global rise in the number of infections among immunosuppressed people. These patients present severe clinical forms of the infections, which are commonly fatal, and they are more susceptible to opportunistic fungal infections than non-immunocompromised people. IFIs have historically been associated with high morbidity and mortality, partly because of the limitations of available antifungal therapies, including side effects, toxicities, drug interactions and antifungal resistance. Thus, the search for alternative therapies and/or the development of more specific drugs is a challenge that needs to be met. Genomics has created new ways of examining genes, which open new strategies for drug development and control of human diseases. Results In silico analyses and manual mining selected initially 57 potential drug targets, based on 55 genes experimentally confirmed as essential for Candida albicans or Aspergillus fumigatus and other 2 genes (kre2 and erg6) relevant for fungal survival within the host. Orthologs for those 57 potential targets were also identified in eight human fungal pathogens (C. albicans, A. fumigatus, Blastomyces dermatitidis, Paracoccidioides brasiliensis, Paracoccidioides lutzii, Coccidioides immitis, Cryptococcus neoformans and Histoplasma capsulatum). Of those, 10 genes were present in all pathogenic fungi analyzed and absent in the human genome. We focused on four candidates: trr1 that encodes for thioredoxin reductase, rim8 that encodes for a protein involved in the proteolytic activation of a transcriptional factor in response to alkaline pH, kre2 that encodes for α-1,2-mannosyltransferase and erg6 that encodes for Δ(24)-sterol C-methyltransferase. Conclusions Our data show that the comparative genomics analysis of eight fungal pathogens enabled the identification of four new potential drug targets. The preferred profile for fungal targets includes proteins conserved among fungi, but absent in the human genome. These characteristics potentially minimize toxic side effects exerted by pharmacological inhibition of the cellular targets. From this first step of post-genomic analysis, we obtained information relevant to future new drug development.
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Oliveira MA, Discola KF, Alves SV, Medrano FJ, Guimarães BG, Netto LES. Insights into the specificity of thioredoxin reductase-thioredoxin interactions. A structural and functional investigation of the yeast thioredoxin system. Biochemistry 2010; 49:3317-26. [PMID: 20235561 DOI: 10.1021/bi901962p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The enzymatic activity of thioredoxin reductase enzymes is endowed by at least two redox centers: a flavin and a dithiol/disulfide CXXC motif. The interaction between thioredoxin reductase and thioredoxin is generally species-specific, but the molecular aspects related to this phenomenon remain elusive. Here, we investigated the yeast cytosolic thioredoxin system, which is composed of NADPH, thioredoxin reductase (ScTrxR1), and thioredoxin 1 (ScTrx1) or thioredoxin 2 (ScTrx2). We showed that ScTrxR1 was able to efficiently reduce yeast thioredoxins (mitochondrial and cytosolic) but failed to reduce the human and Escherichia coli thioredoxin counterparts. To gain insights into this specificity, the crystallographic structure of oxidized ScTrxR1 was solved at 2.4 A resolution. The protein topology of the redox centers indicated the necessity of a large structural rearrangement for FAD and thioredoxin reduction using NADPH. Therefore, we modeled a large structural rotation between the two ScTrxR1 domains (based on the previously described crystal structure, PDB code 1F6M ). Employing diverse approaches including enzymatic assays, site-directed mutagenesis, amino acid sequence alignment, and structure comparisons, insights were obtained about the features involved in the species-specificity phenomenon, such as complementary electronic parameters between the surfaces of ScTrxR1 and yeast thioredoxin enzymes and loops and residues (such as Ser(72) in ScTrx2). Finally, structural comparisons and amino acid alignments led us to propose a new classification that includes a larger number of enzymes with thioredoxin reductase activity, neglected in the low/high molecular weight classification.
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Affiliation(s)
- Marcos A Oliveira
- Departamento de Biologia, Universidade Estadual Paulista, São Vicente, Brazil
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20
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Kirkensgaard KG, Hägglund P, Finnie C, Svensson B, Henriksen A. Structure of Hordeum vulgare NADPH-dependent thioredoxin reductase 2. Unwinding the reaction mechanism. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:932-41. [PMID: 19690371 PMCID: PMC2733882 DOI: 10.1107/s0907444909021817] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 06/09/2009] [Indexed: 12/24/2022]
Abstract
Thioredoxins (Trxs) are protein disulfide reductases that regulate the intracellular redox environment and are important for seed germination in plants. Trxs are in turn regulated by NADPH-dependent thioredoxin reductases (NTRs), which provide reducing equivalents to Trx using NADPH to recycle Trxs to the active form. Here, the first crystal structure of a cereal NTR, HvNTR2 from Hordeum vulgare (barley), is presented, which is also the first structure of a monocot plant NTR. The structure was determined at 2.6 A resolution and refined to an R(cryst) of 19.0% and an R(free) of 23.8%. The dimeric protein is structurally similar to the structures of AtNTR-B from Arabidopsis thaliana and other known low-molecular-weight NTRs. However, the relative position of the two NTR cofactor-binding domains, the FAD and the NADPH domains, is not the same. The NADPH domain is rotated by 25 degrees and bent by a 38% closure relative to the FAD domain in comparison with AtNTR-B. The structure may represent an intermediate between the two conformations described previously: the flavin-oxidizing (FO) and the flavin-reducing (FR) conformations. Here, analysis of interdomain contacts as well as phylogenetic studies lead to the proposal of a new reaction scheme in which NTR-Trx interactions mediate the FO to FR transformation.
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Affiliation(s)
- Kristine G. Kirkensgaard
- Carlsberg Laboratory, Denmark
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
| | - Per Hägglund
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
| | - Christine Finnie
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
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González-Siso MI, García-Leiro A, Tarrío N, Cerdán ME. Sugar metabolism, redox balance and oxidative stress response in the respiratory yeast Kluyveromyces lactis. Microb Cell Fact 2009; 8:46. [PMID: 19715615 PMCID: PMC2754438 DOI: 10.1186/1475-2859-8-46] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 08/30/2009] [Indexed: 12/04/2022] Open
Abstract
A lot of studies have been carried out on Saccharomyces cerevisiae, an yeast with a predominant fermentative metabolism under aerobic conditions, which allows exploring the complex response induced by oxidative stress. S. cerevisiae is considered a eukaryote model for these studies. We propose Kluyveromyces lactis as a good alternative model to analyse variants in the oxidative stress response, since the respiratory metabolism in this yeast is predominant under aerobic conditions and it shows other important differences with S. cerevisiae in catabolic repression and carbohydrate utilization. The knowledge of oxidative stress response in K. lactis is still a developing field. In this article, we summarize the state of the art derived from experimental approaches and we provide a global vision on the characteristics of the putative K. lactis components of the oxidative stress response pathway, inferred from their sequence homology with the S. cerevisiae counterparts. Since K. lactis is also a well-established alternative host for industrial production of native enzymes and heterologous proteins, relevant differences in the oxidative stress response pathway and their potential in biotechnological uses of this yeast are also reviewed.
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Affiliation(s)
- M Isabel González-Siso
- Department of Molecular and Cell Biology, University of A Coruña, Campus da Zapateira s/n, 15071- A Coruña, Spain.
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Bao R, Zhang Y, Lou X, Zhou CZ, Chen Y. Structural and kinetic analysis of Saccharomyces cerevisiae thioredoxin Trx1: Implications for the catalytic mechanism of GSSG reduced by the thioredoxin system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1218-23. [DOI: 10.1016/j.bbapap.2009.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 03/28/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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