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YDC1/YPL087W Single Page Format

This page provides an alternative format to the SGD Locus Summary Page. Note that additional information may be available on or linked from the standard format SGD Locus Summary page.

Contents

Names and Identifiers GO Annotations Pathways Summary Paragraph Mutant Phenotypes Interactions Homologs Protein Info (physical properties, transcript info) PDB Homologs (protein structure info) Motifs Genome-wide Expression (and other large-scale analyses) Locus History (misc. notes) Sequence Retrieval and Analysis Map and Displays Localization Community Annotation Literature Guide

Sequence Coordinates   ChrXVI: 383452 to 384405 CDS: 383452 - 384405 Click on map for expanded view SGD ORF map GBrowse

SGD Locus Page

Names and Identifiers [TOP] [NEXT]
Standard Name	Systematic Name	Alias	Feature Type	SGDID
YDC1	YPL087W		ORF, Verified	S000006008
This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community. Gene name reserved on: 1999-11-03. Gene name expires on 2000-11-03.
Description
Alkaline dihydroceramidase, involved in sphingolipid metabolism; preferentially hydrolyzes dihydroceramide to a free fatty acid and dihydrosphingosine; has a minor reverse activity

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By ceramidase activity Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78        IDA : Inferred from Direct Assay Assigned on 2002-11-01 SGD hydrolase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0378 Assigned on 2007-05-23 UniProtKB hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR008901 Assigned on 2007-05-23 UniProtKB
Biological Process Annotation(s) Reference(s) Evidence Assigned By ceramide biosynthetic process Schorling S, et al. (2001) Lag1p and Lac1p are essential for the Acyl-CoA-dependent ceramide synthase reaction in Saccharomyces cerevisae. Mol Biol Cell 12(11):3417-27        IGI : Inferred from Genetic Interaction with SGD:LAG1, SGD:LAC1 Assigned on 2010-02-02 SGD ceramide metabolic process Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78        IMP : Inferred from Mutant Phenotype Assigned on 2002-11-01 SGD DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR008901 Assigned on 2007-05-23 UniProtKB vacuolar protein catabolic process Huttenhower C and Troyanskaya OG (2009) Prediction of Gene Ontology annotations by integrating high-throughput datasets    RCA : Reviewed Computational Analysis Assigned on 2009-08-06 bioPIXIE_MEFIT
Cellular Component Annotation(s) Reference(s) Evidence Assigned By Golgi apparatus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0333 Assigned on 2008-02-14 UniProtKB Golgi membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR008901 Assigned on 2009-06-17 UniProtKB endoplasmic reticulum Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78        IDA : Inferred from Direct Assay Assigned on 2002-11-01 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0256 Assigned on 2007-05-23 UniProtKB endoplasmic reticulum membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR008901 Assigned on 2009-06-17 UniProtKB integral to membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR008901 Assigned on 2007-05-23 UniProtKB GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0812 Assigned on 2007-05-23 UniProtKB GOA curators and UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.      IEA : Inferred from Electronic Annotation with EBI:SL-9909 Assigned on 2009-10-01 UniProtKB membrane GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0472 Assigned on 2007-05-23 UniProtKB

Pathways [TOP] [NEXT]
sphingolipid metabolism

Summary Paragraph [TOP] [NEXT]

SUMMARY PARAGRAPH for YDC1/YPL087W for YDC1 About sphingolipid metabolism Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannose-(inositol phosphate)2-ceramide (M(IP)2C)(1). In the yeast plasma membrane sphingolipids concentrate with ergosterol to form lipid rafts, specialized membrane microdomains implicated in a variety of cellular processes, including sorting of membrane proteins and lipids, as well as organizing and regulating signaling cascades (2). Intermediates in sphingolipid biosynthesis have been shown to play important roles as signaling molecules and growth regulators. Sphingolipid long chain bases (LCBs), dihydrosphingosine (DHS) and phytosphingosine (PHS), have been implicated as secondary messengers in signaling pathways that regulate heat stress response (3, 4). Other intermediates, phytoceramide and long-chain base phosphates (LCBPs), have been shown to be components of the tightly-controlled ceramide/LCBP rheostat, which regulates cell growth (5). Since phosphoinositol-containing sphingolipids are unique to fungi, the sphingolipid biosynthesis pathway is considered a target for antifungal drugs (6, 7). Last Updated: 2007-10-05

Basic References [TOP]

BASIC INFORMATION REFERENCES forYDC1/YPL087W for YDC1 1) Dickson RC and Lester RL (2002) Sphingolipid functions in Saccharomyces cerevisiae. Biochim Biophys Acta 1583(1):13-25            2) Bagnat M and Simons K (2002) Lipid rafts in protein sorting and cell polarity in budding yeast Saccharomyces cerevisiae. Biol Chem 383(10):1475-80        3) Jenkins GM, et al. (1997) Involvement of yeast sphingolipids in the heat stress response of Saccharomyces cerevisiae. J Biol Chem 272(51):32566-72        4) Ferguson-Yankey SR, et al. (2002) Mutant analysis reveals complex regulation of sphingolipid long chain base phosphates and long chain bases during heat stress in yeast. Yeast 19(7):573-86      5) Kobayashi SD and Nagiec MM (2003) Ceramide/long-chain base phosphate rheostat in Saccharomyces cerevisiae: regulation of ceramide synthesis by Elo3p and Cka2p. Eukaryot Cell 2(2):284-94        6) Nagiec MM, et al. (1997) Sphingolipid synthesis as a target for antifungal drugs. Complementation of the inositol phosphorylceramide synthase defect in a mutant strain of Saccharomyces cerevisiae by the AUR1 gene. J Biol Chem 272(15):9809-17        7) Sugimoto Y, et al. (2004) IPC synthase as a useful target for antifungal drugs. Curr Drug Targets Infect Disord 4(4):311-22        8) Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for YDC1/YPL087W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for YDC1/YPL087W

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi Candida Homologs (CGD) Candida Homologs (CandidaDB) Fungal Alignment Fungal Orthogroups Repository Ortholog Search (P-POD) PhylomeDB Synteny Viewer Yeast Gene Order Browser (YGOB) eukarYotic OrtholoGY (YOGY)

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations from Predicted Full length Translation N-term MLFSWPY C-term DETKKNN Length(aa) 317 MW(Da) 37,231 pI 7.15 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.110   Codon Adaptation Index 0.146   Frequency of Optimal Codons 0.479   Hydropathicity of Protein 0.402   Aromaticity Score 0.174	10 20 30 40 50 | | | | | MLFSWPYPEAPIEGYWGKPTSLIDWCEENYVVSPYIAEWSNTITNSIFLM TAFYSTYSAWRNKLETRYILIGMGFSLVGIGSWLFHMTLQYRYQLLDELP MLYATIIPSWSIFAETQEILIKDEKKRKESSFRIQMVISFIMCGIVTILT WIYVVVQKPAIFQVLYGILTLLVVVLSGWLTYYHVHDSFAKKNLFITMVM GMIPFVIGFICWQLDIHLCSFWIYIRRTYLALPLGVLLELHAWWHLLTGT GVYIFVVYLQYLRILTHGNPNDFLFIWRWGFFPELVRKGLPIGTSYSLEY LGPIVNTQVDDETKKNN*

Protein Structures from PDB: proteins of known structure with sequence similarity to YDC1/YPL087W, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]
Functional Analysis Expression Connection Summary Cell cycle and metabolic oscillation Cell cycle transcript profile Cyclebase Genevestigator GermOnline SPELL Microarray Search YGAC Triples Yeast Microarray Global Viewer YeastFunc	You can also search multiple datasets simultaneously using Expression Connection for expression studies or Function Junction for other large scale analyses.

Locus History (misc. notes) [TOP] [NEXT]

Nomenclature History

Standard Name	Date Standardized	Reference
YDC1	2001-02-07	Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78

Sequence Retrieval [TOP] [NEXT]
Sequence Type	Output Format
Genomic DNA	GCG | FASTA | NoHeader
Genomic DNA with 1 kb up and downstream	GCG | FASTA | NoHeader
DNA coding sequence (without introns, without flanking regions)	GCG | FASTA | NoHeader
Protein Translation of ORF	GCG | FASTA | NoHeader
6-Frame Translation(with Restriction Map)	GCG
Restriction Fragment Sizes	GCG
Sequence Analysis Tools BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YPL087W	SGD Systematic Sequence
856018	NCBI: Gene ID
NP_015238.1	NCBI: RefSeq protein version ID
NP_015238.1	NCBI: RefSeq protein version ID
6325170	NCBI: NCBI protein GI

Map and Displays [TOP] [NEXT]
Physical, Genetic Maps:	Chromosomal Feature Map	GBrowse	Combined Physical and Genetic Map	Genetic Distance vs. Physical Distance Ratios
Similarity Viewers:	Synteny Viewer	Genomic Stripe View	SAGE Results Map

Localization [TOP] [NEXT]
Localization Resources YeastRC Localization (Seattle) YGAC Triples YeastGFP DB (UCSF) at SGD

Community Annotation [TOP] [NEXT]
No community annotation available.

Literature Guide: papers categorized by topic. [TOP]
Topics	Reference	Other Genes Addressed
16 curated references; 0 references not yet curated
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Cerantola V, et al. (2009) Aureobasidin A arrests growth of yeast cells through both ceramide intoxication and deprivation of essential inositolphosphorylceramides. Mol Microbiol 71(6):1523-37	|AUR1 |LAC1 |LAG1 |YPC1
RNA Levels and Processing	Chen AK, et al. (2009) Response of Saccharomyces cerevisiae to stress-free acidification. J Microbiol 47(1):1-8	|ACE2 |ACO1 |ARN1 |ARN2 |ARP4 |ATP1 |ATP16 |ATP2 |ATP3 |BRF1 |CAP1 |CAP2 |CBF5 |CCC2 |MORE
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Villa NY, et al. (2009) Sphingolipids function as downstream effectors of a fungal PAQR. Mol Pharmacol 75(4):866-75	|FET3 |IZH2 |NRG1 |NRG2 |PKH1 |PKH2 |TPK2 |YPC1
Regulation of Transcription	Ye Y, et al. (2009) Gaining insight into the response logic of Saccharomyces cerevisiae to heat shock by combining expression profiles with metabolic pathways. Biochem Biophys Res Commun 385(3):357-62	|ADH6 |ADH7 |AFT1 |ARA1 |ATH1 |CRD1 |DPL1 |FHL1 |GCY1 |GDB1 |GLC3 |GLG1 |GLG2 |GPH1 |MORE
Mutants/Phenotypes Strains/Constructs	Aerts AM, et al. (2008) Ydc1p ceramidase triggers organelle fragmentation, apoptosis and accelerated ageing in yeast. Cell Mol Life Sci 65(12):1933-42
Cross-species Expression Genetic Interactions Mutants/Phenotypes Non-Fungal Related Genes/Proteins Strains/Constructs	Pata MO, et al. (2008) Molecular cloning and characterization of OsCDase, a ceramidase enzyme from rice. Plant J 55(6):1000-9	|YPC1
Mutants/Phenotypes	Bishop AL, et al. (2007) Phenotypic heterogeneity can enhance rare-cell survival in 'stress-sensitive' yeast populations. Mol Microbiol 63(2):507-20	|ADE12 |ADE2 |ADH5 |AGP2 |AIM10 |AIM7 |ARE2 |ATP1 |BUD5 |CBP6 |CCE1 |CCS1 |COX6 |CSE2 |MORE
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Cerantola V, et al. (2007) Yeast sphingolipids do not need to contain very long chain fatty acids. Biochem J 401(1):205-216	|LAC1 |LAG1 |LIP1 |YPC1
Reviews	Kihara A, et al. (2007) Metabolism and biological functions of two phosphorylated sphingolipids, sphingosine 1-phosphate and ceramide 1-phosphate. Prog Lipid Res 46(2):126-44	|DPL1 |LAC1 |LAG1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |LIP1 |SUR2 |TSC10 |TSC3 |YPC1 |YSR3
Cross-species Expression Mutants/Phenotypes Non-Fungal Related Genes/Proteins	Galadari S, et al. (2006) Identification of a novel amidase motif in neutral ceramidase. Biochem J 393(Pt 3):687-95	|YPC1
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Gaigg B, et al. (2005) Synthesis of sphingolipids with very long chain fatty acids but not ergosterol is required for routing of newly synthesized plasma membrane ATPase to the cell surface of yeast. J Biol Chem 280(23):22515-22	|ACB1 |ACC1 |ARE1 |ARE2 |AYR1 |CSG2 |DPL1 |ELO1 |ERG24 |ERG3 |ERG4 |ERG5 |FEN1 |HEM1 |MORE
RNA Levels and Processing Regulation of	Lai LC, et al. (2005) Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol Cell Biol 25(10):4075-91	|AAC1 |ADE1 |ADE12 |ADE17 |ADE4 |AFR1 |AIM17 |AIM3 |AKR1 |AKR2 |ALA1 |ALD5 |ARE1 |ARN1 |MORE
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Jiang JC, et al. (2004) Suppressor analysis points to the subtle role of the LAG1 ceramide synthase gene in determining yeast longevity. Exp Gerontol 39(7):999-1009	|LAC1 |LAG1 |YPC1
Reviews	Funato K, et al. (2002) Biosynthesis and trafficking of sphingolipids in the yeast Saccharomyces cerevisiae. Biochemistry 41(51):15105-14	|ACB1 |AUR1 |CCC2 |CSG2 |DPL1 |ELO1 |FEN1 |FMP45 |IFA38 |IPT1 |ISC1 |LAC1 |LAG1 |LCB1 |MORE
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Schorling S, et al. (2001) Lag1p and Lac1p are essential for the Acyl-CoA-dependent ceramide synthase reaction in Saccharomyces cerevisae. Mol Biol Cell 12(11):3417-27	|LAC1 |LAG1 |YPC1
Function/Process Fungal Related Genes/Proteins Genetic Interactions Mutants/Phenotypes Strains/Constructs Substrates/Ligands/Cofactors	Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78	|YPC1

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