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Exploration of yeast alkali metal cation/H+ antiporters: Sequence and structure comparison

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Abstract

TheSaccharomyces cerevisiae genome contains three genes encoding alkali metal cation/H+ antiporters (Nha1p, Nhx1p, Kha1p) that differ in cell localization, substrate specificity and physiological function. Systematic genome sequencing of other yeast species revealed highly conserved homologous ORFs in all of them. We compared the yeast sequences both at DNA and protein levels. The subfamily of yeast endosomal/prevacuolar Nhx1 antiporters is closely related to mammalian plasma membrane NHE proteins and to both plasma membrane and vacuolar plant antiporters. The high sequence conservation within this subfamily of yeast antiporters suggests that Nhx1p is of great importance in cell physiology. Yeast Kha1 proteins probably belong to the same subfamily as bacterial antiporters, whereas Nha1 proteins form a distinct subfamily.

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Abbreviations

aa:

amino acid

ORF:

open reading frame

tmd(s):

transmembrane domain(s)

Cal :

Candida albicans

Cgl :

Candida glabrata

Ctr :

Candida tropicalis

Dha :

Debaryomyces hansenii var.hansenii

Kla :

Kluyveromyces lactis

Pan :

Pichia (Hansenula) anomala

Pso :

Pichia sorbitophila

Sba :

Saccharomyces bayanus

Sca :

Saccharomyces castellii

Sce :

Saccharomyces cerevisiae

Sku :

Saccharomyces kudriavzevii

Smi :

Saccharomyces mikatae

Spa :

Saccharomyces paradoxus

Spo :

Schizosaccharomyces pombe

Yli :

Yarrowia lipolytica

Zro :

Zygosaccharomyces rouxii

References

  • Ali R., Brett C.L., Mukherjee S., Rao R.: Inhibition of sodium/proton exchange by a Rab-GTPase-activating protein regulates endosomal traffic in yeast.J.Biol.Chem.279, 4498–4506 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Andre B.: An overview of membrane transport proteins inSaccharomyces cerevisiae.Yeast11, 1575–1611 (1995).

    Article  PubMed  CAS  Google Scholar 

  • Baňuelos M.A., Sychrová H., Bleykasten-Grosshans C., Souciet J.-L., Potier S.: The Nha1 antiporter ofSaccharomyces cerevisiae mediates sodium and potassium efflux.Microbiology144, 2749–2758 (1998).

    Article  PubMed  Google Scholar 

  • Baňuelos M.A., Ramos J., Calero F., Braun V., Potier S.: Cation/H+ antiporters mediate potassium and sodium fluxes inPichia sorbitophila. Cloning of thePsNHA1 andPsNHA2 genes and expression inSaccharomyces cerevistae.Yeast19, 1365–1372 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Blumwald E.: Sodium transport and salt tolerance in plants.Curr.Opin.Cell Biol.12, 431–434 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Blumwald E., Aharon G.S., Apse M.P.: Sodium transport in plant cells.Biochim.Biophys.Acta1465, 140–151 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Bowers K., Levi B.P., Patel F.I., Stevens T.H.: The sodium/proton exchanger Nhx1p is required for endosomal protein trafficking in the yeastSaccharomyces cerevisiae.Mol.Biol.Cell.11, 4277–4294 (2000).

    PubMed  CAS  Google Scholar 

  • Brett C.L., Donowitz M., Rao R.: Evolutionary origins of eukaryotic sodium/proton exchangers.Am.J.Physiol.Cell Physiol.288, C223-C239 (2005a).

    Article  PubMed  CAS  Google Scholar 

  • Brett C.L., Tukaye D.N., Mukherjee S., Rao R.: The yeast endosomal Na+(K+)/H+ exchanger Nhx1 regulates cellular pH to control vesicle trafficking.Mol.Biol.Cell.16, 1396–1405 (2005b).

    Article  PubMed  CAS  Google Scholar 

  • Cherry J.M., Adler C., Ball C., Chervitz S.A., Dwight S.S., Hester E.T., Jia Y.K., Juvik G., Roe T., Schroeder M., Weng S.A., Botstein D.: SGD:Saccharomyces genome database.Nucl.Acids Res.26, 73–79 (1998).

    Article  PubMed  CAS  Google Scholar 

  • Cliften P., Sudarsanam P., Desikan A., Fulton L., Fulton B., Majors J., Waterston R., Cohen B.A., Johnston M.: Finding functional features inSaccharomyces genomes by phylogenetic footprinting.Science301, 71–76 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Devereux J., Haeberli P., Smithies O.: A comprehensive set of sequence analysis programs for the VAX.Nucl.Acids Res.12, 387–395 (1984).

    Article  PubMed  CAS  Google Scholar 

  • Dibrov P., Smith J.J., Young P.G., Fliegel L.: Identification and localization of thesod2 gene product in fission yeast.FEBS Lett.405, 119–124 (1997).

    Article  PubMed  CAS  Google Scholar 

  • Dibrov P., Young P.G., Fliegel L.: Functional analysis of amino acid residues essential for activity in the Na+/H+ exchanger of fission yeast.Biochemistry37, 8282–8288 (1998).

    Article  PubMed  CAS  Google Scholar 

  • Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., Lafontaine I., de Montigny J., Marck C., Neuveglise C., Talla E., Goffard N., Frangeul L., Aigle M., Anthouard V., Babour A., Barbe V., Barnay S., Blanchin S., Beckerich J.M., Beyne E., Bleykasten C., Boisrame A., Boyer J., Cattolico L., Confanioleri F., De Daruvar A., Despons L., Fabre E., Fairhead C., Ferry-Dumazet H., Groppi A., Hantraye F., Hennequin C., Jauniaux N., Joyet P., Kachouri R., Kerrest A., Koszul R., Lemaire M., Lesur I., Ma L., Muller H., Nicaud J.M., Nikolski M., Oztas S., Ozier-Kalogeropoulos O., Pellenz S., Potier S., Richard G.F., Straub M.L., Suleau A., Swennen D., Tekaia F., Wesolowski-Loovel M., Westhof E., Wirth B., Zeniou-Meyer M., Zivanovic I., Bolotin-Fukuhara M., Thierry A., Bouchier C., Caudron B., Scarpelli C., Gaillardin C., Weissenbach J., Wincker P., Souciet J.-L.: Genome evolution in yeasts.Nature430, 35–44 (2004).

    Article  PubMed  Google Scholar 

  • Fukuda A., Nakamura A., Tagiri A., Tanaka H., Miyao A., Hirochika H., Tanaka Y.: Function, intracellular localization and the importance in salt tolerance of a vaculoar Na+/H+ antiporter from rice.Plant Cell Physiol.45, 146–159 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Gerchman Y., Rimon A., Venturi M., Padan E.: Oligomerization of NhaA, the Na+/H+ antiporter ofEscherichia coli in the membrane and its functional and structural consequences.Biochemistry40, 3403–3412 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Gilstring C.F., Ljungdahl P.O.: A method for determining thein vivo topology of yeast polytopic membrane proteins demonstrates that Gap1p fully integrates into the membrane independently of Shr3p.J.Biol.Chem.275, 31488–31495 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Hofmann K., Stoffel W.: TMbase — a database of membrane spanning segments.Biol.Chem.Hoppe-Seyler374, 166–175 (1993).

    Google Scholar 

  • Iwaki T., Higashida Y., Tsuji H., Tamai Y., Watanabe Y.: Characterization of a second gene (ZSOD22) of Na+/H+ antiporter from salt-tolerant yeastZygosaccharomyces rouxii and functional expression ofZSOD2 andZSOD22 inSaccharomyces cerevisiae.Yeast14, 1167–1174 (1998).

    Article  PubMed  CAS  Google Scholar 

  • Jia Z.P., McCullough N., Martel R., Hemminngsens S., Young P.G.: Gene amplification at a locus encoding a putative Na+/H+ antiporter confers sodium and lithium tolerance in fission yeast.EMBO J.11, 1631–1640 (1992).

    PubMed  CAS  Google Scholar 

  • Kamauchi S., Mitsui K., Ujike S., Haga M., Nakamura N., Inoue H., Sakajo S., Ueda M., Tanaka A., Kanazawa H.: Structurally and functionally conserved domains in the diverse hydrophilic carboxy-terminal halves of various yeast and fungal Na+/H+ antiporters (Nhalp).J.Biochem.131, 821–831 (2002).

    PubMed  CAS  Google Scholar 

  • Kellis M., Patterson N., Endrizzi M., Birren B., Lander E.S.: Sequencing and comparison of yeast species to identify genes and regulatory elements.Nature423, 241–254 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Kinclová O., Potier S., Sychrová H.: TheZygosaccharomyces rouxii strain CBS732 contains only one copy of theHOG1 and theSOD2 genes.J.Biotechnol.88, 151–158 (2001a).

    Article  PubMed  Google Scholar 

  • Kinclová O., Ramos J., Potier S., Sychrová H.: Functional study of theSaccharomyces cerevisiae Nhalp C-terminus.Mol.Microbiol.40, 656–668 (2001b).

    Article  PubMed  Google Scholar 

  • Kinclová O., Potier S., Sychrová H.: Difference in substrate specificity divides the yeast alkali-metal-cation/H+ antiporters into two subfamilies.Microbiology148, 1225–1232 (2002).

    PubMed  Google Scholar 

  • Kinclová-Zimmermannová O., Flegelová H., Sychrová H.: Rice Na+/H+-antiporter Nhx1 partially complements the alkali-metal-cation sensitivity of yeast strains lacking three sodium transporters.Folia Microbiol.49, 519–525 (2004).

    Article  Google Scholar 

  • Kumar S., Tamura K., Jakobsen I.B., Nei M.: MEGA2: molecular evolutionary genetics analysis software.Bioinformatics17, 1244–1245 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Kyte J., Doolittle R.F.: A simple method for displaying the hydropathic character of a protein.J.Mol.Biol.157, 105–132 (1982).

    Article  PubMed  CAS  Google Scholar 

  • Mansour M.F., Salama K.H.A., Al Mutawa M.M.: Transport proteins and salt tolerance in plants.Plant Sci.164, 891–900 (2003).

    Article  CAS  Google Scholar 

  • Marešova L., Sychrova H.: Physiological characterization ofSaccharomyces cerevisiae khal deletion mutants.Mol.Microbiol.55, 588–600 (2005).

    Article  PubMed  CAS  Google Scholar 

  • McGuffin L.J., Bryson K., Jones D.T.: The PSIPRED protein structure prediction server.Bioinformatics16, 404–405 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Mewes H.W., Hani J., Pfeiffer F., Frishman D.: MIPS: a database for protein sequences and complete genomes.Nucl.Acids Res.26, 33–37 (1998).

    Article  PubMed  Google Scholar 

  • Mitsui K., Kamauchi S., Nakamura N., Inoue H., Kanazawa H.: A conserved domain in the tail region of theSaccharomyces cerevisiae Na+/H+ antiporter (Nha1p) plays important roles in localization and salinity-resistant cell-growth.J.Biochem.135, 139–148 (2004a).

    Article  PubMed  CAS  Google Scholar 

  • Mitsui K., Ochi F., Nakamura N., Doi Y., Inoue H., Kanazawa H.: A novel membrane protein capable of binding the Na+/H+ antiporter (Nha1p) enhances the salinity-resistant cell growth ofSaccharomyces cerevisiae.J.Biol.Chem.279, 12438–12447 (2004b).

    Article  PubMed  CAS  Google Scholar 

  • Nass R., Rao R.: Novel localization of a Na+/H+ exchanger in a late endosomal compartment of yeast — implications for vacuole biogenesis.J.Biol.Chem.273, 21054–21060 (1998).

    Article  PubMed  CAS  Google Scholar 

  • Nass R., Rao R.: The yeast endosomal Na+/H+ exchanger, Nhxl, confers osmotolerance following acute hypertonic shock.Microbiology145, 3221–3228 (1999).

    PubMed  CAS  Google Scholar 

  • Nass R., Cunningham K.W., Rao R.: Intracellular sequestration of sodium by a novel Na+/H+ exchanger in yeast is enhanced by mutations in the plasma membrane H+-ATPase.J.Biol.Chem.272, 26145–26152 (1997).

    Article  PubMed  CAS  Google Scholar 

  • Nehrke K., Melvin J.E.: The NHX family of Na+-H+ exchangers inCaenorhabditis elegans.J.Biol.Chem.277, 29036–29044 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Nelissen B., De Wachter R., Goffeau A.: Classification of all putative permeases and other membrane plurispanners of the major facilitator superfamily encoded by the complete genome of Saccharomyces cerevisiae.FEMS Microbiol.Rev.21, 113–134 (1997).

    Article  PubMed  CAS  Google Scholar 

  • Orlowski J., Grinstein S.: Na+/H+ exchangers of mammalian cells.J.Biol.Chem.272, 22373–22376 (1997).

    Article  PubMed  CAS  Google Scholar 

  • Orlowski J., Grinstein S.: Diversity of the mammalian sodium/proton exchanger SLC9 gene family.Pflugers Arch.447, 549–565 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Paulsen I.T., Sliwinski M.K., Nelissen B., Goffeau A., Saier M.H.: Unified inventory of established and putative transporters encoded within the complete genome ofSaccharomyces cerevisiae.FEBS Lett.430, 116–125 (1998).

    Article  PubMed  CAS  Google Scholar 

  • Proft M., Struhl K.: MAP kinase-mediated stress relief that precedes and regulates the timing of transcriptional induction.Cell118, 351–361 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Ramirez J., Ramirez O., Saldana C., Coria R., Peña A.: ASaccharomyces cerevisiae mutant lacking a K+/H+ exchanger.J.Bacteriol.180, 5860–5865 (1998).

    PubMed  CAS  Google Scholar 

  • Ren Q., Kang K.H., Paulsen I.T.: Transport DB: a relational database of cellular membrane transport systems.Nucl.Acids Res.32, D284-D288 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez-Navarro A.: Potassium transport in fungi and plants.Biochim.Biophys.Acta1469, 1–30 (2000).

    PubMed  CAS  Google Scholar 

  • Saier M.H.: A functional-phylogenetic classification system for transmembrane solute transporters.Microbiol.Mol.Biol.Rev.64, 354–366 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Shi H.Z., Ishitani M., Kim C.S., Zhu J.K.: TheArabidopsis thaliana salt tolerance geneSOS1 encodes a putative Na+/H+ antiporter.Proc.Nat.Acad.Sci.USA97, 6896–6901 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Simon E., Clotet J., Calero F., Ramos J., Arino J.: A screening for high copy supressors of thesit4 hal3 synthetically lethal phenotype reveals a role for the yeast Nha1 antiporter in cell cycle regulation.J.Biol.Chem.276, 29740–29747 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Simon E., Barcelo A., Arino J.: Mutagenesis analysis of the yeast Nhal Na+/H+ antiporter carboxy-terminal tail reveals residues required for function in cell cycle.FEBS Lett.545, 239–245 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Sonnhammer E.L., von Heijne G., Krogh A.: A hidden Markov model for predicting transmembrane helices in protein sequences.Proc.Internal.Conf.Intell.Syst.Mol.Biol.6, 175–182 (1998).

    CAS  Google Scholar 

  • Soong T.W., Yong T.F., Ramanan N., Wang Y.: TheCandida albicans antiporter geneCNH1 has a role in Na+ and H+ transport, salt tolerance, and morphogenesis.Microbiology146, 1035–1044 (2000).

    PubMed  CAS  Google Scholar 

  • Sychrová H.: Yeast as a model organism to study transport and homeostasis of alkali-metal cations.Physiol.Res.53, S91-S98 (2004).

    PubMed  Google Scholar 

  • Sychrová H., Ramírez J., Peña A.: Involvement of Nhal antiporter in regulation of intracellular pH inSaccharomyces cerevisiae.FEMS Microbiol.Lett.171, 167–172 (1999).

    Article  PubMed  Google Scholar 

  • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G.: The Clustal_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucl.Acids Res.25, 4876–4882 (1997).

    Article  PubMed  CAS  Google Scholar 

  • Tusnady G.E., Simon I.: The HMMTOP transmembrane topology prediction server.Bioinformatics17, 849–850 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Tzubery T., Rimon A., Padan E.: Mutation E252C increases drastically theKm value for Na+ and causes an alkaline shift of the pH dependence of NhaA Na+/H+ antiporter ofEscherichia coli.J.Biol.Chem.279, 3265–3272 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Velkova K., Sychrová H.: TheDebaryomyces hansenii NHA1 gene encodes a plasma membrane alkali-metal-cation antiporter with broad substrate specificity.Gene369, 27–34 (2006).

    Article  PubMed  CAS  Google Scholar 

  • Watanabe Y., Miwa S., Tamai Y.: Characterization of Na+/H+-antiporter gene closely related to the salt-tolerance of yeastZygosaccharomyces rouxii.Yeast11, 829–838 (1995).

    Article  PubMed  CAS  Google Scholar 

  • Wiebe C.A., Rieder C., Young P.G., Dibrov P., Fliegel L.: Functional analysis of amino acids of the Na+/H+ exchanger that are important for proton translocation.Mol.Cell.Biochem.254, 117–124 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Williams K.A.: Three-dimensional structure of the ion-coupled transport protein NhaA.Nature403, 112–115 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Yamaguchi T., Apse M.P., Shi H.Z., Blumwald E.: Topological analysis of a plant vacuolar Na+/H+ antiporter reveals a luminal C terminus that regulates antiporter cation selectivity.Proc.Nat.Acad.Sci.USA100, 12510–12515 (2003).

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Membrane Transport, Institute of Physiology, Academy of Sciences of the Czech Republic, 142 20, Prague, Czechia

    L. Přibylová, K. Papoušková, M. Zavřel & H. Sychrová

  2. Laboratoire de Dynamique, Evolution et Expression des Génomes de Microorganismes (FRE 2326 CNRS), Université Louis Pasteur, 67083, Strasbourg, France

    J. -L. Souciet

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  1. L. Přibylová
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  2. K. Papoušková
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  3. M. Zavřel
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  4. J. -L. Souciet
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  5. H. Sychrová
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Correspondence to H. Sychrová.

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This work was supported by theMinistry of Education, Youth and Sports of the Czech Republic (grant MŠMT LC531), by theGrant Agency of the Czech Republic (grant GA ČR 204/03/H066) and byInstitutional research project of theInstitute of Physiology (AV 0Z 501 1922). A. Kotyk and O. Kinclová-Zimmermannová are gratefully acknowledged for critical reading of the manuscript.

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Přibylová, L., Papoušková, K., Zavřel, M. et al. Exploration of yeast alkali metal cation/H+ antiporters: Sequence and structure comparison. Folia Microbiol 51, 413–424 (2006). https://doi.org/10.1007/BF02931585

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