Comparative analysis of HOG pathway proteins to generate hypotheses for functional analysis.
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.
Krantz
Marcus
M
Department for Cell and Molecular Biology, Göteborg University, Box 462, 40530, Göteborg, Sweden.
Becit
Evren
E
Hohmann
Stefan
S
D050976:Basic-Leucine Zipper Transcription Factors / Q000502:physiology; D004268:DNA-Binding Proteins / Q000502:physiology; D016681:Genome, Fungal; D023281:Genomics; D047908:Intracellular Signaling Peptides and Proteins; D020929:Mitogen-Activated Protein Kinase Kinases / Q000502:physiology*; D020928:Mitogen-Activated Protein Kinases / Q000502:physiology; D011494:Protein Kinases / Q000502:physiology; D012097:Repressor Proteins / Q000502:physiology; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000502:physiology*; D015398:Signal Transduction / Q000502:physiology*; D014157:Transcription Factors / Q000502:physiology
D050976:Basic-Leucine Zipper Transcription Factors; D004268:DNA-Binding Proteins; C120535:HOT1 protein, S cerevisiae; D047908:Intracellular Signaling Peptides and Proteins; D012097:Repressor Proteins; C077832:SKO1 protein, S cerevisiae; C087199:SSK1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D011494:Protein Kinases; C102035:YPD1 protein, S cerevisiae; C088589:HOG1 protein, S cerevisiae; D020928:Mitogen-Activated Protein Kinases; D020929:Mitogen-Activated Protein Kinase Kinases; C089356:PBS2 protein, S cerevisiae; C083749:SLN1 protein, S cerevisiae