title: cis- and trans-acting localization determinants of pH response regulator Rim13 in Saccharomyces cerevisiae.
abstract: The Rim101/PacC pathway governs adaptation to alkaline pH in many fungi. Output of the pathway is mediated by transcription factors of the Rim101/PacC family, which are activated by proteolytic cleavage. The proteolytic complex includes scaffold protein Rim20 and endosome-associated subunits of the endosomal sorting complex required for transport (ESCRT). We provide here evidence that Saccharomyces cerevisiae Rim13, the protease that is implicated in Rim101 cleavage, is associated with the Rim20-ESCRT complex, and we investigate its regulation. Rim13-GFP is dispersed in cells grown in acidic medium but forms punctate foci when cells encounter alkaline conditions. A vps4Δ mutant, which accumulates elevated levels of endosomal ESCRT, also accumulates elevated levels of Rim13-GFP foci, independently of external pH. In the vps4Δ background, mutation of ESCRT subunit Snf7 or of Rim20 blocks the formation of Rim13 foci, and we found that Rim13 and Rim20 are colocalized. The Rim13 ortholog PalB of Aspergillus nidulans has been shown to undergo ESCRT and membrane association through an N-terminal MIT domain, but Rim13 orthologs in the Saccharomyces clade lack homology to this N-terminal region. Instead, there is a clade-limited C-terminal region, and we show that point mutations in this region prevent punctate localization and impair Rim13 function. We suggest that RIM13 arose from its ancestral gene through two genome rearrangements. The ancestor lost the coding region for its MIT domain through a 5' rearrangement and acquired the coding region for the Saccharomyces-specific functional equivalent through a 3' rearrangement.
authors.affiliation: Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Shoba
authors.initials: S
authors.lastname: Subramanian
authors.forename: Carol A
authors.initials: CA
authors.lastname: Woolford
authors.forename: Jigar V
authors.initials: JV
authors.lastname: Desai
authors.forename: Frederick
authors.initials: F
authors.lastname: Lanni
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Mitchell
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D057056:Cysteine Proteases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D056827:Endosomal Sorting Complexes Required for Transport / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D010447:Peptide Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D021382:Protein Sorting Signals; D021381:Protein Transport; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D056827:Endosomal Sorting Complexes Required for Transport; D021382:Protein Sorting Signals; C489601:RIM101 protein, S cerevisiae; D012097:Repressor Proteins; C510979:Rim20 protein, S cerevisiae; C083890:SNF7 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; C107528:VPS4 protein, S cerevisiae; D057056:Cysteine Proteases; D010447:Peptide Hydrolases; C578371:Rim13 protein, S cerevisiae; D000251:Adenosine Triphosphatases