The YBR056W-A and Its Ortholog YDR034W-B of S. cerevisiae Belonging to CYSTM Family Participate in Manganese Stress Overcoming

Abstract

The CYSTM (cysteine-rich transmembrane module) protein family comprises small molecular cysteine-rich tail-anchored membrane proteins found in many eukaryotes. The Saccharomyces cerevisiae strains carrying the CYSTM genes YDRO34W-B and YBR056W-A (MNC1) fused with GFP were used to test the expression of these genes under different stresses. The YBR056W-A (MNC1) and YDR034W-B genes are expressed under stress conditions caused by the toxic concentrations of heavy metal ions, such as manganese, cobalt, nickel, zinc, cuprum, and 2.4-dinitrophenol uncoupler. The expression level of YDR034W-B was higher than that of YBR056W-A under alkali and cadmium stresses. The Ydr034w-b-GFP and Ybr056w-a-GFP proteins differ in the cellular localization: Ydr034w-b-GFP was mainly observed in the plasma membrane and vacuolar membrane, while Ybr056w-a-GFP was observed in the cytoplasm, probably in intracellular membranes. The null-mutants in both genes demonstrated decreased cell concentration and lytic phenotype when cultivated in the presence of excess manganese. This allows for speculations about the involvement of Mnc1 and Ydr034w-b proteins in manganese stress overcoming.

Palmitoylation of CYSTM (CYSPD) proteins in yeast

“…Reports both in yeast ( 3 ) and in plants ( 9 ) suggested localizations other than the PM for some members of the CYSPD family. However, in both cases, proteins were tagged with GFP at the C terminus.…”

“…Mnc1 is a paralog of YDR034W-B, but does not have a CYSTM region as defined by Venancio et al ( 1 ), since it is not predicted to fold into a single α-helix (our unpublished observations). A role in manganese metabolism has also been proposed for Ydr034w-based both on a growth phenotype and its enhanced expression in the presence of this metal ( 3 ).…”

Genome-wide conditional degron libraries for functional genomics

“…The relationship between terminal localization signals and differential fitness of N- and C-terminally tagged strains was examined using a list of 998 validated or predicted localization signals obtained through literature curation or retrieved from the UniProt database (Bateman et al, 2023) (Table S2). The list consists of proteins with a glycosylphosphatidylinositol (GPI) anchor (De Groot et al, 2003; Gíslason et al, 2021), tail-anchored (TA) proteins (Beilharz et al, 2003; Burri and Lithgow, 2004; Lewis and Pelham, 2002; Schuldiner et al, 2008; Šimočková et al, 2008), proteins with a cysteine-rich transmembrane module (CYSTM) (Giolito et al, 2024; Venancio and Aravind, 2010; Zvonarev et al, 2023), acylated proteins (UniProt as of 19.02.2024, search for proteins with lipidation, including N-myristoylation, palmitoylation, GPI-anchor addition and prenylation), proteins with a PTS1 peroxisomal targeting signal (Nötzel et al, 2016) (UniProt as of 24.04.2024, search for proteins with motif: microbody targeting signal, C-terminal peroxisome targeting signal (PTS1), peroxisome targeting signal (PTS1), SKL peroxisome targeting motif, peroxisomal target signal 1 (PTS1) or peroxisomal targeting signal type 1), proteins with a signal peptide (SP) or a mitochondrial targeting signal (MTS) (Somashekara and Muniyappa, 2022; Weill et al, 2018; Yofe et al, 2016), proteins with nuclear localization signals (Bordonné, 2000; Hahn et al, 2008; Lee et al, 2023; Somashekara and Muniyappa, 2022) and proteins with HDEL, KKXX or KXKXX motifs identified by pattern match or retrieved from Uniprot (UniProt as of 24.04.2024, search for proteins with motif: prevents secretion from ER or di-lysine motif).…”