Molecular characterization of central cytoplasmic loop in Aspergillus nidulans AstA transporter
Abstract
AstA (alternative sulfate transporter) belongs to a large, but poorly characterized, Dal5 family of allantoate permeases of the Major Facilitator Superfamily. The astA gene has been cloned from an IAM 2006 Japanese strain of Aspergillus nidulans by complementation of a sulfate permease-deficient mutant. In this study we show that conserved lysine residues in Central Cytoplasmic Loop (CCL) of the AstA protein may participate in anion selectivity, and control kinetic properties of the AstA transporter. A three-dimensional model containing four clustered lysine residues was created, showing a novel substrate-interacting structure in Major Facilitator Superfamily transporters. The assimilation constant (Kτ) of wild type AstA protein is 85 μM, while Vmax/mg of DW of AstA is twice that of the main sulfate transporter SB per mg of dry weight (DW) of mycelium (1.53 vs. 0.85 nmol/min, respectively). Amino acid substitutions in CCL did not abolish sulfate uptake, but affected its kinetic parameters. Mutants affected in the lysine residues forming the postulated sulfate-interacting pocket in AstA were able to grow and uptake sulfate, indicating that CCL is not crucial for sulfate transportation. However, these mutants exhibited altered values of Kτ and Vmax, suggesting that CCL is involved in control of the transporter activity.
References
Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, Iwata S (2003) Structure and mechanism of the lactose permease of Eschelichia coli. Science 301:610–615. https://doi.org/10.1126/science.1088196
Alper SL, Sharma AK (2013) The SLC26 gene family of anion transporters and channels. Mol Aspects Med 34:494-515. https://doi.org/10.1016/j.mam.2012.07.009
Altschul SF, Lipman DJ (1990) Protein database searches for multiple alignments. Proc Natl Acad. Sci USA 87:5509-5513.
Arst HN. Jr (1968) Genetic analysis of the first steps of sulphate metabolism in Aspergillus nidulans. Nature 219:268–270. https://doi:10.1038/219268a0
Biswas C, Djordjevic JT, Zuo X, Boles E, Jolliffe KA, Sorrell TC, Chen SC (2013) Functional characterization of the hexose transporter Hxt13p: an efflux pump that mediates resistance to miltefosine in yeast. Fungal Genet Biol 61:23-32. https://doi.org/10.1016/j.fgb.2013.09.005
Blikstad C, Dahlström KM, Salminen TA, Widersten M (2014) Substrate scope and selectivity in offspring to an enzyme subjected to directed evolution. FEBS J. 281:2387-2398. https://doi.org/10.1111/febs.12791
Blodgett DM, De Zutter JK, Levine KB, Karim P, Carruthers A (2007) Structural basis of GLUT1 inhibition by cytoplasmic ATP. J Gen Physiol 130:157-168. https://doi.org/10.1085/jgp.200709818
Bourne Y, Dannenberg J, Pollmann V, Marchot P, Pongs O (2001) Immunocytochemical localization and crystal structure of human frequenin (neuronal calcium sensor 1). J Biol Chem 276:11949-11955. https://doi.org/10.1074/jbc.M009373200
Bowler MW, Montgomery MG, Leslie AG, Walker JE (2006) How azide inhibits ATP hydrolysis by the F-ATPases. Proc Natl Acad Sci U S A 103:8646-8649. https://doi.org/10.1073/pnas.0602915103
Cerqueira GC., Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato, SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2014). The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res 42: D705-710. https://doi.org/10.1093/nar/gkt1029
Clutterbuck AJ (1994) Linkage map and locus list. Prog Ind Microbiol 29:791-824.
Dang S, Sun L, Huang Y, Lu F, Liu Y, Gong H, Wang J, Yan N (2010) Structure of a fucose transporter in an outward-open conformation. Nature 467:734-738. https://doi.org/10.1038/nature09406
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. https://doi.org/10.1093/nar/gkh340
Ethayathulla AS, Yousef MS, Amin A, Leblanc G, Kaback HR (2014) Structure-based mechanism for Na+/melibiose symport by MelB. Nature Commun 5:3009. https://doi.org/10.1038/ncomms4009
Frillingos S, Sahin-Tóth M, Wu J, Kaback HR (1998) Cys-scanning mutagenesis: a novel approach to structure function relationships in polytopic membrane proteins. FASEB J. 12:1281-1299. https://doi.org/10.1096/fasebj.12.13.1281
Gems DH, Clutterbuck AJ (1993) Co-transformation with autonomously-replicating helper plasmids facilitates gene cloning from an Aspergillus nidulans gene library. Curr Genet 24:520-524.
Hirai T, Heymann JA, Shi D, Sarker R, Maloney PC, Subramaniam S (2002) Three-dimensional structure of a bacterial oxalate transporter. Nat Struct Biol 9:597-600. https://doi.org/10.1038/nsb821
Hoischen C, Levin J, Pitaknarongphorn S, Reizer J, Saier MH Jr (1996) Involvement of the central loop of the lactose permease of Escherichia coli in its allosteric regulation by the glucose-specific enzyme IIA of the phosphoenolpyruvate-dependent phosphotransferase system. J Bacteriol 178:6082-6086.
Holt S, Kankipati H, De Graeve S, Van Zeebroeck G, Foulquié-Moreno MR, Lindgreen S, Thevelein JM (2017) Major sulfonate transporter Soa1 in Saccharomyces cerevisiae and considerable substrate diversity in its fungal family. Nat Commun 8:14247. https://doi.org/10.1038/ncomms14247
Iancu CV, Zamoon J, Woo SB, Aleshi, A, Choe JY (2013) Crystal structure of a glucose/H+ symporter and its mechanism of action. Proc Natl Acad Sci USA 110:17862-17867. https://doi.org/10.1073/pnas.1311485110
Kasahara T, Ishiguro M, Kasahara M (2006) Eight amino acid residues in transmembrane segments of yeast glucose transporter Hxt2 are required for high affinity transport. J Biol Chem 281:18532-18538. https://doi.org/10.1074/jbc.M602123200
Kasahara T, Maeda M, Bole,s E, Kasahara M (2009) Identification of a key residue determining substrate affinity in the human glucose transporter GLUT1. Biochim Biophys Acta 1788:1051-1055. https://doi.org/10.1016/j.bbamem.2009.01.014
Kertesz MA (2001) Bacterial transporters for sulfate and organosulfur compounds. Res Microbiol 152:279-290.
Kuwano T, Shirataki C, Itoh Y (2008) Comparison between polyethylene glycol- and polyethylenimine-mediated transformation of Aspergillus nidulans. Curr Genet 54:95-103. https://doi.org/10.1007/s00294-008-0204-z
Law CJ, Maloney PC, Wang DN (2008) Ins and outs of major facilitator superfamily antiporters. Annu Rev Microbiol 62:289-305. https://doi.org/10.1146/annurev.micro.61.080706.093329
Lemieux MJ, Huan, Y, Wang DN (2004) The structural basis of substrate translocation by the Escherichia coli glycerol-3-phosphate transporter: a member of the major facilitator superfamily. Curr Opin Struct Biol 14:405-412. https://doi.org/10.1016/j.sbi.2004.06.003
Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193:265–275.
Łukaszkiewicz Z, Paszewski A (1976) Hyper-repressible operator-type mutant in sulphate permease gene of Aspergillus nidulans. Nature 259:337-338. https://doi.org/10.1038/259337a0
Mandal A, Kumar A, Singh A, Lynn AM, Kapoor K, Prasad R (2012) A key structural domain of the Candida albicans Mdr1 protein. Biochem J 445:313-322. https://doi.org/10.1042/BJ20120190
Martinelli SD (1994) Gene symbols. Prog Ind Microbiol 29:825-827.
Okano Y, Asada M, Fujimoto A, Ohtake A, Murayama K, Hsiao KJ, Choeh K, Yang Y, Cao Q, Reichardt, JK, Niihira S, Imamura T, Yamano T (2001) A genetic factorfor age-related cataract: identification and characterization of a novel galactokinase variant, 'Osaka', in Asians. Am. J. Hum. Genet. 68:1036–1042. https://doi.org/10.1086/319512
Pasrija R, Banerjee D, Prasad R (2007) Structure and function analysis of CaMdr1p, a major facilitator superfamily antifungal efflux transporter protein of Candida albicans: identification of amino acid residues critical for drug/H+ transport. Eukaryot Cell 6:443-453. https://doi.org/10.1128/EC.00315-06
Patron M, Checchetto V, Raffaello A, Teardo E, Reane DV, Mantoan M, Granatiero V, Szabo I, De Stefani D, Rizzuto R (2014) MICU1 and MICU2 finely tune the mitochondrial Ca2+ uniporter by exerting opposite effects on MCU activity. Mol Cell 53:726-737. https://doi.org/10.1016/j.molcel.2014.01.013
Paulsen IT, Brown MH, Skurray RA (1996) Proton-dependent multidrug efflux systems. Microbiol Rev 60:575–608.
Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz, Z., Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM (2013) Crystal structure of a eukaryotic phosphate transporter. Nature 496:533-536. https://doi.org/10.1038/nature12042
Piłsyk S, Natorff R, Sieńko M, Paszewski A (2007) Sulfate transport in Aspergillus nidulans: a novel gene encoding alternative sulfate transporter. Fungal Genet Biol 44:715-725. https://doi.org/10.1016/j.fgb.2006.11.007
Piłsyk S, Paszewski A (2009) Sulfate permeases - phylogenetic diversity of sulfate transport. Acta Biochim Pol 56:375-384.
Piłsyk S, Natorff R, Gawińska-Urbanowicz H, Kruszewska JS (2015) Fusarium sambucinum astA gene expressed during potato infection is a functional orthologue of Aspergillus nidulans astA. Fungal Biol 119:509-517. https://doi.org/10.1016/j.funbio.2015.02.002
Rost B, Yachdav G, Liu J (2004) The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326. https://doi.org/10.1093/nar/gkh377
Roth V (2006) Doubling Time Computing, Available from: http://www.doubling-time.com/compute.php
Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols 5:725-738. https://doi.org/10.1038/nprot.2010.5
Roy A, Yang J, Zhang, Y (2012) COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res 40, (Web Server issue):W471-7. doi: 10.1093/nar/gks372 https://doi.org/10.1093/nar/gks372
Sahin-Tóth M, le Coutre J, Kharabi D, le Maire G, Lee JC, Kaback HR (1999) Characterization of Glu126 and Arg144, two residues that are indispensable for substrate binding in the lactose permease of Escherichia coli. Biochemistry. 38:813-819. https://doi.org/10.1021/bi982200h
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press. https://doi.org/10.1016/0092-8674(90)90210-6
Sayle RA, Milner-White EJ (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci 20:374. https://doi.org/10.1016/S0968-0004(00)89080-5
Seok YJ, Sun J, Kaback HR, Peterkofsky A (1997) Topology of allosteric regulation of lactose permease. Proc Natl Acad Sci U S A. 94:13515-13519. https://doi.org/10.1073/pnas.94.25.13515
Sieńko M, Natorff R, Skoneczny M, Kruszewska J, Paszewski A, Brzywczy J (2014) Regulatory mutations affecting sulfur metabolism induce environmental stress response in Aspergillus nidulans. Fungal Genet Biol. 65:37-47. https://doi.org/10.1016/j.fgb.2014.02.001
Strelow J, Dewe W, Iversen PW, Brooks HB, Radding JA, McGee J, Weidner J (2012) "Mechanism of Action Assays for Enzymes", in G. S. Sittampalam, N. P. Coussens, H. Nelson et al. (editors), Assay Guidance Manual, Eli Lilly & Company and the National Center for Advancing Translational Sciences, 2004.
Sun L, Zeng X, Yan C, Sun X, Gong X, Rao Y, Yan N (2012) Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Nature 490:361-366. https://doi.org/10.1038/nature11524
Timson DJ, Reece RJ (2003) Functional analysis of disease-causing mutations in human galactokinase. Eur J Biochem. 270:1767-1774. https://doi.org/10.1046/j.1432-1033.2003.03538.x
Tweedie JW Segel IH (1970) Specificity of transport processes for sulfur, selenium, and molybdenum anions by filamentous fungi. Biochim Biophys Acta 196:95-106. https://doi.org/10.1016/0005-2736(70)90170-7
Weinglass AB, Kaback HR (2000) The central cytoplasmic loop of the major facilitator superfamily of transport proteins governs efficient membrane insertion. Proc Natl Acad Sci U S A. 97:8938-8943. https://doi.org/10.1073/pnas.140224497
Will A, Grassl R, Erdmenger J, Caspari T, Tanner W (1998) Alteration of substrate affinities and specificities of the Chlorella Hexose/H+ symporters by mutations and construction of chimeras. J Biol Chem. 273:11456-11462. https://doi.org/10.1074/jbc.273.19.11456
Wisedchaisri G, Park MS, Iadanza MG, Zhen H, Gonen T (2014) Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE. Nat Commun 5:4521. https://doi.org/10.1038/ncomms5521
Woodin TS Wang JL (1989) Sulfate permease of Penicillium duponti. Exp Mycol 13:380-391. https://doi.org/10.1016/0147-5975(89)90034-0
Yin Y, He X, Szewczyk P, Nguyen T, Chang G (2006) Structure of the multidrug transporter EmrD from Escherichia coli. Science 312:741-744. https://doi.org/10.1126/science.1125629
Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9:40. http://www.biomedcentral.com/content/pdf/1471-2105-9-40 https://doi.org/10.1186/1471-2105-9-40
Acta Biochimica Polonica is an OpenAccess quarterly and publishes four issues a year. All contents are distributed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY 4.0) license. Everybody may use the content following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
Copyright for all published papers © stays with the authors.
Copyright for the journal: © Polish Biochemical Society.