Abstract
Comparative genomics allows comparison of different proteins that execute presumably identical functions in different organisms. In contrast to paralogues, orthologues per definition perform the same function and interact with the same partners and, consequently, should display conservation in all these properties. We have employed 20 fungal genomes to analyse key components of the high osmolarity glycerol signalling pathway of Saccharomyces cerevisiae. Among the proteins scrutinised are a complete phosphotransfer module, a MAP kinase, two scaffold proteins, one of which is also a MAPKK, and two transcription factors. Sequence alignments, domain structure and size analysis, combined with the rich information available in the literature, allowed us to probe previous structural and functional studies and to generate hypotheses for future experimental studies. Although certain domains are too highly conserved across fungal species for meaningful comparative studies, others, like interaction domains, can be studied in closely related species. Moreover, putative functionally relevant sites for protein modifications can be identified in such comparative studies. We provide several relevant examples and present a number of previously un(der)characterised domains of potential functional significance in osmosensing and signal transduction. We propose that any functional protein analysis in fungi should make use of the unique resource that fungal genome sequences offer.
Similar content being viewed by others
References
Alepuz PM, Jovanovic A, Reiser V, Ammerer G (2001) Stress-induced MAP kinase Hog1 is part of transcription activation complexes. Mol Cell 7:767–777
Alepuz PM, de Nadal E, Zapater M, Ammerer G, Posas F (2003) Osmostress-induced transcription by Hot1 depends on a Hog1-mediated recruitment of the RNA Pol II. EMBO J 22:2433–2442
Alonso-Monge R, Navarro-Garcia F, Roman E, Negredo AI, Eisman B, Nombela C, Pla J (2003) The Hog1 mitogen-activated protein kinase is essential in the oxidative stress response and chlamydospore formation in Candida albicans. Eukaryot Cell 2:351–361
Aravind L, Ponting CP (1999) The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins. FEMS Microbiol Lett 176:111–116
Attwood TK, Croning MD, Flower DR, Lewis AP, Mabey JE, Scordis P, Selley JN, Wright W (2000) PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Res 28:225–227
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam protein families database. Nucleic Acids Res 30:276–280
Bell M, Capone R, Pashtan I, Levitzki A, Engelberg D (2001) Isolation of hyperactive mutants of the MAPK p38/Hog1 that are independent of MAPK kinase activation. J Biol Chem 276:25351–25358
Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O’Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R (2004) Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 68:1–108
Brachat S, Dietrich FS, Voegeli S, Zhang Z, Stuart L, Lerch A, Gates K, Gaffney T, Philippsen P (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4:R45
Catlett NL, Yoder OC, Turgeon BG (2003) Whole-genome analysis of two-component signal transduction genes in fungal pathogens. Eukaryot Cell 2:1151–1161
Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71–76
de Nadal E, Alepuz PM, Posas F (2002) Dealing with osmostress through MAP kinase activation. EMBO Rep 3:735–740
de Nadal E, Casadome L, Posas F (2003) Targeting the MEF2-like transcription factor Smp1 by the stress-activated Hog1 mitogen-activated protein kinase. Mol Cell Biol 23:229–237
Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304–307
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 JM, 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 JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel 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 JL (2004) Genome evolution in yeasts. Nature 430:35–44
Dutta R, Inouye M (2000) GHKL, an emergent ATPase/kinase superfamily. Trends Biochem Sci 25:24–28
Dutta R, Qin L, Inouye M (1999) Histidine kinases: diversity of domain organization. Mol Microbiol 34:633–640
Elion EA (2000) Pheromone response, mating and cell biology. Curr Opin Microbiol 3:573–581
Fabre E, Muller H, Therizols P, Lafontaine I, Dujon B, Fairhead C (2004) Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing and subtelomeres. Mol Biol Evol 22:856–873
Furukawa K, Hoshi Y, Maeda T, Nakajima T, Abe K (2005) Aspergillus nidulans HOG pathway is activated only by two-component signalling pathway in response to osmotic stress. Mol Microbiol 56 (in press)
Hiramoto F, Nomura N, Furumai T, Igarashi Y, Oki T (2005) Pradimicin resistance of yeast is caused by a mutation of the putative N-glycosylation sites of osmosensor protein sln1. Biosci Biotechnol Biochem 69:238–241
Hohmann S (2002) Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66:300–372
Hull CM, Heitman J (2002) Genetics of Cryptococcus neoformans. Annu Rev Genet 36:557–615
Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S (2004) The diploid genome sequence of Candida albicans. Proc Natl Acad Sci USA 101:7329–7334
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241–254
Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617–624
Koszul R, Caburet S, Dujon B, Fischer G (2004) Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J 23:234–243
Krantz M, Becit E, Hohmann S (2006) Comparative genomics of the HOG-signalling system in fungi. Curr Genet DOI 10.1007/s00294-005-0038-x
Lafontaine I, Fischer G, Talla E, Dujon B (2004) Gene relics in the genome of the yeast Saccharomyces cerevisiae. Gene 335:1–17
Langkjaer RB, Cliften PF, Johnston M, Piskur J (2003) Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421:848–852
Maeda T, Wurgler-Murphy SM, Saito H (1994) A two-component system that regulates an osmosensing MAP kinase cascade in yeast. Nature 369:242–245
Mapes J, Ota IM (2004) Nbp2 targets the Ptc1-type 2C Ser/Thr phosphatase to the HOG MAPK pathway. Embo J 23:302–311
Marles JA, Dahesh S, Haynes J, Andrews BJ, Davidson AR (2004) Protein-protein interaction affinity plays a crucial role in controlling the Sho1p-mediated signal transduction pathway in yeast. Mol Cell 14:813–823
Moller S, Croning MD, Apweiler R (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17:646–653
Nelson B, Parsons AB, Evangelista M, Schaefer K, Kennedy K, Ritchie S, Petryshen TL, Boone C (2004) Fus1p interacts with components of the HOG1p mitogen-activated protein kinase and Cdc42p morphogenesis signaling pathways to control cell fusion during yeast mating. Genetics 166:67–77
O’Rourke SM, Herskowitz I (1998) The Hog1 MAPK prevents cross talk between the HOG and pheromone response MAPK pathways in Saccharomyces cerevisiae. Genes Dev 12:2874–2886
O’Rourke SM, Herskowitz I, O’Shea EK (2002) Yeast go the whole HOG for the hyperosmotic response. Trends Genet 18:405–412
Ostrander DB, Gorman JA (1999) The extracellular domain of the Saccharomyces cerevisiae Sln1p membrane osmolarity sensor is necessary for kinase activity. J Bacteriol 181:2527–2534
Pascual-Ahuir A, Posas F, Serrano R, Proft M (2001) Multiple levels of control regulate the yeast cAMP-response element-binding protein repressor Sko1p in response to stress. J Biol Chem 276:37373–37378
Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183:63–98
Porter SW, West AH (2005) A common docking site for response regulators on the yeast phosphorelay protein YPD1. Biochim Biophys Acta 1748:138–145
Porter SW, Xu Q, West AH (2003) Ssk1p response regulator binding surface on histidine-containing phosphotransfer protein Ypd1p. Eukaryot Cell 2:27–33
Posas F, Saito H (1997) Osmotic activation of the HOG MAPK pathway via Ste11p MAPKKK: scaffold role of Pbs2p MAPKK. Science 276:1702–1705
Posas F, Saito H (1998) Activation of the yeast SSK2 MAP kinase kinase kinase by the SSK1 two-component response regulator. EMBO J 17:1385–1394
Posas F, Wurgler-Murphy SM, Maeda T, Witten EA, Thai TC, Saito H (1996) Yeast HOG1 MAP kinase cascade is regulated by a multistep phosphorelay mechanism in the SLN1-YPD1-SSK1 “two-component” osmosensor. Cell 86:865–875
Proft M, Struhl K (2002) Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell 9:1307–1317
Proft M, Pascual-Ahuir A, de Nadal E, Arino J, Serrano R, Posas F (2001) Regulation of the Sko1 transcriptional repressor by the Hog1 MAP kinase in response to osmotic stress. EMBO J 20:1123–1133
Raitt DC, Posas F, Saito H (2000) Yeast Cdc42 GTPase and Ste20 PAK-like kinase regulate Sho1-dependent activation of the Hog1 MAPK pathway. EMBO J 19:4623–4631
Ramezani-Rad M (2003) The role of adaptor protein Ste50-dependent regulation of the MAPKKK Ste11 in multiple signalling pathways of yeast. Curr Genet 43:161–170
Reiser V, Salah SM, Ammerer G (2000) Polarized localization of yeast Pbs2 depends on osmostress, the membrane protein Sho1 and Cdc42. Nat Cell Biol 2:620–627
Reiser V, Raitt DC, Saito H (2003) Yeast osmosensor Sln1 and plant cytokinin receptor Cre1 respond to changes in turgor pressure. J Cell Biol 161:1035–1040
Rep M, Reiser V, Gartner U, Thevelein JM, Hohmann S, Ammerer G, Ruis H (1999a) Osmotic stress-induced gene expression in Saccharomyces cerevisiae requires Msn1p and the novel nuclear factor Hot1p. Mol Cell Biol 19:5474–5485
Rep M, Reiser V, Holzmüller U, Thevelein JM, Hohmann S, Ammerer G, Ruis H (1999b) Osmotic stress-induced gene expression in Saccharomyces cerevisiae requires Msn1p and the novel nuclear factor Hot1p. Mol Cell Biol 19:5474–5485
Rep M, Krantz M, Thevelein JM, Hohmann S (2000) The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J Biol Chem 275:8290–8300
Rep M, Proft M, Remize F, Tamas M, Serrano R, Thevelein JM, Hohmann S (2001) The Saccharomyces cerevisiae Sko1p transcription factor mediates HOG pathway-dependent osmotic regulation of a set of genes encoding enzymes implicated in protection from oxidative damage. Mol Microbiol 40:1067–1083
Saito H, Tatebayashi K (2004) Regulation of the osmoregulatory HOG MAPK cascade in yeast. J Biochem (Tokyo) 136:267–272
Santos JL, Shiozaki K (2001) Fungal histidine kinases. Sci STKE 2001:RE1
Seet BT, Pawson T (2004) MAPK signaling: Sho business. Curr Biol 14:R708–710
Sharma P, Mondal AK (2005) Evidence that C-terminal non-kinase domain of Pbs2p has a role in high osmolarity-induced nuclear localization of Hog1p. Biochem Biophys Res Commun 328:906–913
Sheikh-Hamad D, Gustin MC (2004) MAP kinases and the adaptive response to hypertonicity: functional preservation from yeast to mammals. Am J Physiol Renal Physiol 287:F1102–1110
Smith DA, Nicholls S, Morgan BA, Brown AJ, Quinn J (2004) A conserved stress-activated protein kinase regulates a core stress response in the human pathogen Candida albicans. Mol Biol Cell 15:4179–4190
Suzuki M, Brenner SE (1995) Classification of multi-helical DNA-binding domains and application to predict the DBD structures of sigma factor, LysR, OmpR/PhoB, CENP-B, Rapl, and Xy1S/Ada/AraC. FEBS Lett 372:215–221
Tao W, Malone CL, Ault AD, Deschenes RJ, Fassler JS (2002) A cytoplasmic coiled-coil domain is required for histidine kinase activity of the yeast osmosensor, SLN1. Mol Microbiol 43:459–473
Tatebayashi K, Takekawa M, Saito H (2003) A docking site determining specificity of Pbs2 MAPKK for Ssk2/Ssk22 MAPKKKs in the yeast HOG pathway. Embo J 22:3624–3634
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Westfall PJ, Ballon DR, Thorner J (2004) When the stress of your environment makes you go HOG wild. Science 306:1511–1512
White SH, von Heijne G (2004) The machinery of membrane protein assembly. Curr Opin Struct Biol 14:397–404
Wolanin PM, Thomason PA, Stock JB (2002) Histidine protein kinases: key signal transducers outside the animal kingdom. Genome Biol 3:REVIEWS3013
von Heijne G (1989) Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature 341:456–458
Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O’Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Dusterhoft A, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Benito J, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P, Cerrutti L (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871–880
Xu Q, West AH (1999) Conservation of structure and function among histidine-containing phosphotransfer (HPt) domains as revealed by the crystal structure of YPD1. J Mol Biol 292:1039–1050
Xu Q, Porter SW, West AH (2003) The Yeast YPD1/SLN1 Complex. Insights into molecular recognition in two-component signaling systems. Struct (Camb) 11:1569–1581
Yaakov G, Bell M, Hohmann S, Engelberg D (2003) Combination of two activating mutations in one HOG1 gene forms hyperactive enzymes that induce growth arrest. Mol Cell Biol 23:4826–4840
Yaku H, Mizuno T (1997) The membrane-located osmosensory kinase, EnvZ, that contains a leucine zipper-like motif functions as a dimer in Escherichia coli. FEBS Lett 417:409–413
Zarrinpar A, Bhattacharyya RP, Nittler MP, Lim WA (2004) Sho1 and Pbs2 act as coscaffolds linking components in the yeast high osmolarity MAP kinase pathway. Mol Cell 14:825–832
Acknowledgements
This work was supported by the QUASI EC-funded project (contract LSHG-CT2003–530203). SH is a recipient of a research position from the Swedish Research Council.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by J. Hasek
Rights and permissions
About this article
Cite this article
Krantz, M., Becit, E. & Hohmann, S. Comparative analysis of HOG pathway proteins to generate hypotheses for functional analysis. Curr Genet 49, 152–165 (2006). https://doi.org/10.1007/s00294-005-0039-9
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00294-005-0039-9