PEP4/YPL154C Summary Help

Standard Name PEP4 1, 2, 3, 4, 5, 6, 7
Systematic Name YPL154C
Alias PHO9 , PRA1 , yscA
Feature Type ORF, Verified
Description Vacuolar aspartyl protease (proteinase A); required for posttranslational precursor maturation of vacuolar proteinases; important for protein turnover after oxidative damage; plays a protective role in acetic acid induced apoptosis; synthesized as a zymogen, self-activates (8, 9, 10, 11, 12, 13, 14, 15 and see Summary Paragraph)
Name Description carboxyPEPtidase Y-deficient 16, 17
Chromosomal Location
ChrXVI:260931 to 259714 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -95 cM
Gene Ontology Annotations All PEP4 GO evidence and references
  View Computational GO annotations for PEP4
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 8 genes
Classical genetics
reduction of function
Large-scale survey
72 total interaction(s) for 50 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 19
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 3
  • Biochemical Activity: 1
  • Reconstituted Complex: 1

Genetic Interactions
  • Dosage Lethality: 1
  • Dosage Rescue: 1
  • Negative Genetic: 8
  • Phenotypic Enhancement: 16
  • Phenotypic Suppression: 11
  • Synthetic Growth Defect: 2
  • Synthetic Rescue: 6

Expression Summary
Length (a.a.) 405
Molecular Weight (Da) 44,499
Isoelectric Point (pI) 4.54
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXVI:260931 to 259714 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -95 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1218 260931..259714 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000006075

PEP4 encodes the vacuolar protease proteinase A, which initiates the maturation and activation of the other vacuolar hydrolases (13, 12, 16 and reviewed in 18). Direct cleavage targets of Pep4p include carboxypeptidase Y (Prc1p), proteinase B (Prb1p), and aminopeptidase I (Lap4p) (8, 19, 20, 21). In the vacuole, Pep4p has non-protease targets such as the plasma membrane transporters Pma1p and Pdr5p and the alkaline phosphatase Pho8p (22, 23, 24, 25, 26, 27, 16). Under acetic acid or hydrogen peroxide treatment, Pep4p migrates out of the vacuole into the cytoplasm and mediates mitochondrial and nucleoporin degradation (28, 29). Proteinase A is also required for the processes of chronological aging, apoptosis, and formation of the transcription regulatory complex SLIK/SALSA (14, 28, 30). Pep4p proteolytic activity is most efficient at acidic pH and the enzyme preferentially cleaves between two adjacent hydrophobic residues (31, 32). Pep4p proteolysis is inhibited by pepstatin, diazoacetyl-DL-norleucine methyl ester (DAN), 1,2-epoxy-3-(4-nitro-phenoxy) propane (EPNP), and IA(3). The last of these, IA(3), is an endogenous and highly selective inhibitor encoded by PAI3 (33, 34, 35). IA(3) specificity is accomplished through Pep4p acting as a folding template for the inhibitor, thus stabilizing protein conformation and interaction (36).

Pep4p is synthesized as an inactive precursor, preproPrA, that is delivered to the ER via the early secretory pathway. In the ER, the precursor protein is glycosylated and an amino-terminal signal peptide is cleaved off, yielding proPrA (37). proPrA is then delivered to the Golgi where it is further modified. The sorting receptor Pep1p helps mediate the final vacuolar delivery of Pep4p through recognition of an N-terminal vacuolar sorting signal (37, 38). Maturation of the zymogen to mature PrA can occur either through the direct action of proteinase B (39, 40) or by autocatalytic cleavage which results in an intermediate form of the protein known as pseudoPrA (11, 8, 41, 10, and reviewed in 18). Expression of PEP4 is regulated by nitrogen catabolite repression by the GATA-family transcription factors Gln3p, Gat1p, and Dal80p (42). Loss of Pep4p activity leads to a shortened lifespan, and PEP4 is essential under conditions of nutrient starvation (14, 43). Homozygous diploid pep4 mutants are defective in sporulation (44, 45, 46). Pep4p homologs have been identified in protozoa and other fungi (47, 48, 49, 50). Proteinase A is also closely related to mammalian aspartyl proteases, such as pepsin, renin, chymosin, and cathepsin D (12, 13, and reviewed in 18). The potential manipulation of proteinase A for use in strains for industrial applications has also been investigated (51, 52).

Last updated: 2011-02-07 Contact SGD

References cited on this page View Complete Literature Guide for PEP4
1) Fassler, J.  (1992) Personal Communication, Mortimer Map Edition 11
2) Jones, E.  (1985) Personal Communication, Mortimer Map Edition 9
3) Petitjean, A. and Tatchell, K.  (1989) Personal Communication, Mortimer Map Edition 10
4) Schweizer, E.  (1989) Personal Communication, Mortimer Map Edition 10
5) Stearns, T. and Botstein, D.  (1989) Personal Communication, Mortimer Map Edition 10
6) Sumrada, R. and Cooper, T.  (1992) Personal Communication, Mortimer Map Edition 11
7) Yoshida, K.  (1989) Personal Communication, Mortimer Map Edition 10
8) Rupp S and Wolf DH  (1995) Biogenesis of the yeast vacuole (lysosome). The use of active-site mutants of proteinase yscA to determine the necessity of the enzyme for vacuolar proteinase maturation and proteinase yscB stability. Eur J Biochem 231(1):115-25
9) van den Hazel HB, et al.  (1993) The propeptide is required for in vivo formation of stable active yeast proteinase A and can function even when not covalently linked to the mature region. J Biol Chem 268(24):18002-7
10) van den Hazel HB, et al.  (1992) Autoactivation of proteinase A initiates activation of yeast vacuolar zymogens. Eur J Biochem 207(1):277-83
11) Wolff AM, et al.  (1996) Vacuolar and extracellular maturation of Saccharomyces cerevisiae proteinase A. Yeast 12(9):823-32
12) Ammerer G, et al.  (1986) PEP4 gene of Saccharomyces cerevisiae encodes proteinase A, a vacuolar enzyme required for processing of vacuolar precursors. Mol Cell Biol 6(7):2490-9
13) Woolford CA, et al.  (1986) The PEP4 gene encodes an aspartyl protease implicated in the posttranslational regulation of Saccharomyces cerevisiae vacuolar hydrolases. Mol Cell Biol 6(7):2500-10
14) Marques M, et al.  (2006) The Pep4p vacuolar proteinase contributes to the turnover of oxidized proteins but PEP4 overexpression is not sufficient to increase chronological lifespan in Saccharomyces cerevisiae. Microbiology 152(Pt 12):3595-605
15) Pereira H, et al.  (2013) The protective role of yeast cathepsin D in acetic acid-induced apoptosis depends on ANT (Aac2p) but not on the voltage-dependent channel (Por1p). FEBS Lett 587(2):200-5
16) Jones EW, et al.  (1982) PEP4 gene function is required for expression of several vacuolar hydrolases in Saccharomyces cerevisiae. Genetics 102(4):665-77
17) Jones EW  (1977) Proteinase mutants of Saccharomyces cerevisiae. Genetics 85(1):23-33
18) Parr CL, et al.  (2007) The structure and function of Saccharomyces cerevisiae proteinase A. Yeast 24(6):467-80
19) Zubenko GS, et al.  (1983) Mutations in PEP4 locus of Saccharomyces cerevisiae block final step in maturation of two vacuolar hydrolases. Proc Natl Acad Sci U S A 80(2):510-4
20) Hemmings BA, et al.  (1981) Mutant defective in processing of an enzyme located in the lysosome-like vacuole of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 78(1):435-9
21) Klionsky DJ, et al.  (1992) Aminopeptidase I of Saccharomyces cerevisiae is localized to the vacuole independent of the secretory pathway. J Cell Biol 119(2):287-99
22) Gong X and Chang A  (2001) A mutant plasma membrane ATPase, Pma1-10, is defective in stability at the yeast cell surface. Proc Natl Acad Sci U S A 98(16):9104-9
23) Tutulan-Cunita AC, et al.  (2005) Involvement of Saccharomyces cerevisiae Pdr5p ATP-Binding Cassette Transporter in Calcium Homeostasis. Biosci Biotechnol Biochem 69(4):857-60
24) Decottignies A, et al.  (1999) Casein kinase I-dependent phosphorylation and stability of the yeast multidrug transporter Pdr5p. J Biol Chem 274(52):37139-46
25) Egner R, et al.  (1995) Endocytosis and vacuolar degradation of the plasma membrane-localized Pdr5 ATP-binding cassette multidrug transporter in Saccharomyces cerevisiae. Mol Cell Biol 15(11):5879-87
26) Campbell CL and Thorsness PE  (1998) Escape of mitochondrial DNA to the nucleus in yme1 yeast is mediated by vacuolar-dependent turnover of abnormal mitochondrial compartments. J Cell Sci 111 ( Pt 16)():2455-64
27) Klionsky DJ and Emr SD  (1989) Membrane protein sorting: biosynthesis, transport and processing of yeast vacuolar alkaline phosphatase. EMBO J 8(8):2241-50
28) Pereira C, et al.  (2010) Mitochondrial degradation in acetic acid-induced yeast apoptosis: the role of Pep4 and the ADP/ATP carrier. Mol Microbiol 76(6):1398-410
29) Mason DA, et al.  (2005) Increased nuclear envelope permeability and Pep4p-dependent degradation of nucleoporins during hydrogen peroxide-induced cell death. FEMS Yeast Res 5(12):1237-51
30) Spedale G, et al.  (2010) Identification of Pep4p as the protease responsible for formation of the SAGA-related SLIK protein complex. J Biol Chem 285(30):22793-9
31) Sorensen SO, et al.  (1994) pH-dependent processing of yeast procarboxypeptidase Y by proteinase A in vivo and in vitro. Eur J Biochem 220(1):19-27
32) Dreyer T  (1989) Substrate specificity of proteinase yscA from saccharomyces cerevisiae. Carlsberg Res Commun 54(3):85-97
33) Meussdoerffer F, et al.  (1980) Purification and properties of proteinase A from yeast. J Biol Chem 255(24):12087-93
34) Schu P and Wolf DH  (1991) The proteinase yscA-inhibitor, IA3, gene. Studies of cytoplasmic proteinase inhibitor deficiency on yeast physiology. FEBS Lett 283(1):78-84
35) Padron-Garcia JA, et al.  (2009) Quantitative structure activity relationship of IA3-like peptides as aspartic proteinase inhibitors. Proteins 75(4):859-69
36) Li M, et al.  (2000) The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix. Nat Struct Biol 7(2):113-7
37) Klionsky DJ, et al.  (1988) Intracellular sorting and processing of a yeast vacuolar hydrolase: proteinase A propeptide contains vacuolar targeting information. Mol Cell Biol 8(5):2105-16
38) Westphal V, et al.  (1996) Multiple pathways for vacuolar sorting of yeast proteinase A. J Biol Chem 271(20):11865-70
39) Hirsch HH, et al.  (1992) Biogenesis of the yeast vacuole (lysosome). Proteinase yscB contributes molecularly and kinetically to vacuolar hydrolase-precursor maturation. Eur J Biochem 207(3):867-76
40) Mechler B, et al.  (1988) Biogenesis of the yeast lysosome (vacuole): biosynthesis and maturation of proteinase yscB. EMBO J 7(6):1705-10
41) Woolford CA, et al.  (1993) Phenotypic analysis of proteinase A mutants. Implications for autoactivation and the maturation pathway of the vacuolar hydrolases of Saccharomyces cerevisiae. J Biol Chem 268(12):8990-8
42) Coffman JA and Cooper TG  (1997) Nitrogen GATA factors participate in transcriptional regulation of vacuolar protease genes in Saccharomyces cerevisiae. J Bacteriol 179(17):5609-13
43) Teichert U, et al.  (1989) Lysosomal (vacuolar) proteinases of yeast are essential catalysts for protein degradation, differentiation, and cell survival. J Biol Chem 264(27):16037-45
44) Zubenko GS and Jones EW  (1981) Protein degradation, meiosis and sporulation in proteinase-deficient mutants of Saccharomyces cerevisiae. Genetics 97(1):45-64
45) Mechler B and Wolf DH  (1981) Analysis of proteinase A function in yeast. Eur J Biochem 121(1):47-52
46) Kaneko Y, et al.  (1982) Identification of the genetic locus for the structural gene and a new regulatory gene for the synthesis of repressible alkaline phosphatase in Saccharomyces cerevisiae. Mol Cell Biol 2(2):127-37
47) Williams RA, et al.  (2006) Cysteine peptidases CPA and CPB are vital for autophagy and differentiation in Leishmania mexicana. Mol Microbiol 61(3):655-74
48) Bae JH, et al.  (2005) Cloning and characterization of the Hansenula polymorpha PEP4 gene encoding proteinase A. Yeast 22(1):13-9
49) Komeda T, et al.  (2002) Construction of protease-deficient Candida boidinii strains useful for recombinant protein production: cloning and disruption of proteinase A gene (PEP4) and proteinase B gene (PRBI). Biosci Biotechnol Biochem 66(3):628-31
50) Vazquez-Laslop N, et al.  (1996) Characterization of a vacuolar protease in Neurospora crassa and the use of gene RIPing to generate protease-deficient strains. J Biol Chem 271(36):21944-9
51) Guo ZP, et al.  (2010) Improving the performance of industrial ethanol-producing yeast by expressing the aspartyl protease on the cell surface. Yeast 27(12):1017-27
52) Wang ZY, et al.  (2007) Over-expression of GSH1 gene and disruption of PEP4 gene in self-cloning industrial brewer's yeast. Int J Food Microbiol 119(3):192-9