Shared and more specific genetic determinants and pathways underlying yeast tolerance to acetic, butyric, and octanoic acids

Mota, Marta N.; Matos, Madalena; Bahri, Nada; Sá-Correia, Isabel

doi:10.1186/s12934-024-02309-0

Table 1 Genes involved in vacuolar and vesicular function and transport

From: Shared and more specific genetic determinants and pathways underlying yeast tolerance to acetic, butyric, and octanoic acids

Gene/ORF	Description of the encoded protein function	Susceptibility
Gene/ORF	Description of the encoded protein function	C2	C4	C8
ARL1 (5,6,7)	Soluble GTPase with a role in regulation of membrane traffic. Arl1p regulates potassium influx and also plays a role in membrane organization at trans-Golgi network	+	0	+
ATG20 (4,6,7)	Sorting nexin family member. Atg20p is required for the cytoplasm-to-vacuole targeting (Cvt) pathway, endosomal sorting and selective autophagy	+	+	+
BRO1 (1,2,3,4,6)	Cytoplasmic class E vacuolar protein sorting (VPS) factor. Bro1p coordinates protein sorting and deubiquitination in the multivesicular body (MVB) pathway by recruiting Doa4p to endosomes	+	+	+
DID4 (1,2,3,4,8)	Class E Vps protein of the ESCRT-III complex. Did4p is required for sorting of integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthesized vacuolar enzymes to the vacuole. Did4p is also involved in endocytosis	+	+	0
SNF7 (1,2,3,4)	One of four subunits of the ESCRT-III complex. Snf7p is involved in the sorting of transmembrane proteins into the multivesicular body (MVB) pathway. Snf7p is recruited from the cytoplasm to endosomal membranes	+	+	+
SNF8 (1,3,4,7)	Component of the ESCRT-II complex. Snf8p is involved in glucose derepression	+	+	0
STP22 (1,3,6,7)	Component of the ESCRT-I complex	+	+	+ +
VPS1 (5,6,7,8)	Dynamin-like GTPase required for vacuolar sorting. Vps1p promotes fission of retrograde transport carriers from endosome. It is also involved in endocytosis and late Golgi-retention of some proteins	+	+	+
VPS16 (3,4,6,7)	Subunit of the HOPS and the CORVET complexes and also part of the Class C Vps complex essential for membrane docking and fusion at Golgi-to-endosome and endosome-to-vacuole protein transport stages	+	+ +	+ +
VPS20 (1,2,3,4)	Myristoylated subunit of the ESCRT-III complex. Vps20p is a cytoplasmic protein recruited to endosomal membrane	+	+	+
VPS24 (1,2,3,4)	One of four subunits of the ESCRT-III complex. Vps24p forms an endosomal sorting complex required for transport III (ESCRT-III) subcomplex with Did4p. Vps24p is also involved in the sorting of transmembrane proteins into the multivesicular body (MVB) pathway	+	+	−
VPS25 (1,3,4,7)	Component of the ESCRT-II complex	+	C4	−
VPS27 (1,3,4,5,6,8)	Ubiquitin binding protein involved in endosomal protein sorting; subunit of the ESCRT-0 complex that binds to ubiquitin. Vps27p is required for recycling Golgi proteins, forming lumenal membranes and sorting ubiquitinated proteins destined for degradation	−	+	+
VPS28 (1,3,4,7)	Component of the ESCRT-I complex	+	+	−
VPS36 (1,3,4,7)	Component of the ESCRT-II complex. Vps36p contains the GLUE domain which is involved in interactions with ESCRT-I and ubiquitin-dependent sorting of proteins into the endosome	+	−	−
VPS4 (2,3,4,5,8)	AAA-ATPase involved in multivesicular body (MVB) protein sorting. Vps4p localizes to endosomes and catalyzes ESCRT-III disassembly and membrane release	−	+ +	+
YPT6 (4,6,7)	Rab family GTPase, required for endosome-to-Golgi, intra-Golgi retrograde, and retrograde Golgi-to-ER transport	+	+	+

The table includes the list of genes, involved in vacuolar acidification, identified in this study as determinants of yeast tolerance to acetic acid (C2), butyric acid (C4), or octanoic acid (C8). The description of the encoded protein functions is based on the information at SGD. The susceptibility phenotype of each single deletion mutant was scored, after 48 h as described in Additional Files, Figure S2: ( +) if the mutant strain showed, compared with the parental strain, a slight to moderate growth inhibition, and (+ +) if no growth was observed. “0” corresponds to an absence of a detectable susceptibility phenotype. Underneath the name of each gene are indicated the functions, as defined in the PANTHER Classification System (http://pantherdb.org) used for functional analysis, to which the gene is correlated
The table includes the list of genes, involved in vacuolar and vesicular function and transport, identified in this study as determinants of yeast tolerance to acetic acid (C2), butyric acid (C4), or octanoic acid (C8)
(1) “ATP export” and “Ubiquitin-dependent protein catabolic process via the MVB sorting pathway” (C2/C4)
(2) “intraluminal vesicle formation” (C2/C4)
(3) “Late endosome to vacuole transport” (C2/C4)
(4) “Endosomal Transport” (C2/C4/C8)
(5) “Protein localization to Golgi apparatus” (C8)
(6) “Protein localization to vacuole” (C8)
(7) “Protein targeting to vacuole” (C2)
(8) “Protein retention in Golgi apparatus” (C4)

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ISSN: 1475-2859

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