Figure 1
Structure of the Hrdc domain of the SGS protein

Figure taken from the PDB database: http://www.rcsb.org/pdb/index.html
PDB ID: 1D8B
Primary citation Liu et al., 1999.
 

MORE INFO
SUPPRESSION OF ILLEGITAMATE RECOMBINATION
    In sgs1 mutants an increase in illegitimate recombination via the RAD52 and Hdf1 homologous recombination pathway is observed ( Yamagata, 1998).  This suggests that sgs1 suppresses illegitimate recombination by regulating the Rad52 and Hdf1 homologous recombination pathways (Yamagata, 1998).

RNA POLYMERASE II TRANSCRIPTION
     Defects in the synthesis of RNAII polymerase transcripts were observed in sgs1, srs1 double mutants (Lee, 1999).  This suggests that sgs1 and srs2 interact with RNA polymerase II.  Lee et al. (1999) propose that srs1 and sgs1 help DNA unwind during RNA polymerase II transcription.  When srs1 and sgs1 are not present, the DNA does not unwind as rapidly.  Failure to unwind causes the RNA polymerase to pause which results in double stranded breaks (DSB) that are fixed by homologous recombination.  Fixing DSB with homologous recombination would account for the deletions seen in the rDNA.

INTERACTION WITH TOPOISOMERASES
     The N terminus of the sgs1 protein binds to topoisomerase III (topIII) ( Bennett, 2001).  Topoisomerases relieve the super coiling found during DNA replication, due to the unwinding of the DNA helicases, by snipping and later rejoining super coiled DNA (Griffiths, 1999).
    Cells with mutant sgs1 copies also show an increase in chromosome missegreation (Watt, 1995).  SGS1 interacts with topII during chromosome segregation (Watt, 1995).

PREMATURE DEATH-CELL CYCLE CHECK POINTS
    SGS1 also plays a role in cell cycle checkpoints.  Frei et al. (2000) suggest that sgs1 interacts upstream of Rad53 in the S cell cycle check point.  They suggest that sgs1 normally halts the progression past the S stage when there is a stalled replication fork.  Mutant sgs1 yeast sometimes fail to activate the S checkpoint when there is a stalled replication fork.
    McVey et al. (2001) suggest that the early cell death of sgs1 mutants can be attributed to two causes.  One is the arrest of the cell cycle at the G2/M checkpoint and the other is an arrest in the G1 stage due to causes seen in normal age related senesence.  McVey et al. (2001) propose that when sgs1 is not present, the cell causes DSBs and then uses homologous recombination to fix stalled replication forks.  When the DSBs or the homologous recombination complex can not be resolved the cell cycle is arrested in the G2/M check point.  When this happens the cell dies as a small bud is beginning to come off the mother cell.  Occasionally the cell overlooks the DNA damage and continues into mitosis.  When this happens the cells die in the next few generations due to the irreparable damage caused by the DSBs.
    When cells arrest in the G1 stage it is usually accompanied by fragmentation of the nucleolus ( Guarente, 1997) and an accumulation of extra chromosomal regions (ERC) (McVey, 2001).   In sgsI mutants this seems to occur about 60% sooner than in wild type cells (Guarente, 1997).  This is thought to be the result of the hyperrecombination and increased homologous recombination seen in sgs1 mutants ( McVey, 2001).

BLOOM’S SYNDROME
     Bloom’s syndrome is a human disease caused by mutations in the BLM gene ( Watt, 1996).  Mutations in the BLM gene result in growth retardation, increased incidence of cancer, and genomic instability (Watt, 1996).  Unlike the other homologous genes to BLM, BLM and SGS1 share a highly charged N terminus (Watt, 1996).  SGS1 mutants are being used to model bloom’s disease in yeast.
For a picture of homologous sections between the bloom's syndrome gene and sgs1 go to Figure 1 of the following article by Watt et al. (1996):
http://journals.bmn.com/journals/list/render?uid=JCUB.bb6308&node=TOC%40%40JCUB%4011%4018%4011_18
 

WERNER’S SYNDROME
     Werner’s syndrome is a human disease caused by a mutation in the WRN gene (Guarente, 1997).  The main characteristic of Werner’s syndrome is premature aging (Guarente, 1997).  SGS1 is homologous to the WRN gene and thus is also being used as  way to model Werner’s disease (Guarente, 1997).
 

UNANNOTATED GENE
BASIC INFO
SGD: http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=YJU3
    Id: gene: YJU3; ORF: YK1094W
Swiss Port: http://www.expasy.ch/cgi-bin/niceprot.pl?P28321
    Id: P287321
YPD: http://www.proteome.com/databases/YPD/reports/YJU3.html
    Genbank Id: CAA81932

Name: YJU3
Chromosome: 11
Null allele: viable

DNA sequence:
        1  ATGGCTCCGT ATCCATACAA AGTGCAGACG ACAGTACCTG AACTTCAATA

      51  CGAAAACTTT GATGGTGCTA AGTTCGGGTA CATGTTCTGG CCTGTTCAAA

     101  ATGGCACCAA TGAGGTCAGA GGTAGAGTTT TACTGATTCA TGGGTTTGGC

     151  GAGTACACAA AGATTCAATT CCGGCTTATG GACCACTTAT CACTCAATGG

     201  TTACGAGTCA TTTACGTTTG ATCAAAGGGG TGCTGGTGTT ACATCGCCGG

     251  GCAGATCGAA AGGTGTAACT GATGAGTACC ATGTGTTTAA CGATCTTGAG

     301  CATTTTGTGG AGAAGAACTT GAGTGAATGT AAGGCCAAAG GCATACCCTT

     351  GTTCATGTGG GGGCATTCAA TGGGCGGTGG TATCTGCCTA AACTATGCCT

     401  GCCAAGGTAA GCACAAAAAC GAAATAAGCG GATATATCGG GTCAGGCCCA

     451  TTAATAATTT TACATCCGCA TACAATGTAT AACAAGCCGA CCCAAATTAT

     501  TGCTCCATTA TTGGCGAAAT TTTTACCAAG GGTAAGGATC GACACTGGTT

     551  TAGATCTTAA AGGAATCACA TCTGATAAAG CCTATCGTGC TTTCCTCGGA

     601  AGCGATCCTA TGTCTGTTCC ACTATATGGG TCGTTTAGGC AAATACACGA

     651  CTTTATGCAA CGTGGTGCCA AGCTCTACAA GAATGAAAAC AATTATATTC

     701  AGAAGAACTT CGCTAAAGAC AAACCCGTTA TTATTATGCA TGGACAAGAC

     751  GACACAATCA ACGATCCTAA GGGCTCTGAA AAGTTCATTC AGGACTGTCC

     801  TTCTGCTGAC AAAGAATTAA AGCTGTATCC GGGCGCAAGA CATTCGATTT

     851  TCTCACTAGA GACAGATAAA GTCTTCAACA CGGTGTTCAA TGATATGAAG

     901  CAATGGTTGG ACAAACACAC CACGACCGAA GCTAAACCAT AA

Protein sequence:
        1  MAPYPYKVQT TVPELQYENF DGAKFGYMFW PVQNGTNEVR GRVLLIHGFG

      51  EYTKIQFRLM DHLSLNGYES FTFDQRGAGV TSPGRSKGVT DEYHVFNDLE

     101  HFVEKNLSEC KAKGIPLFMW GHSMGGGICL NYACQGKHKN EISGYIGSGP

     151  LIILHPHTMY NKPTQIIAPL LAKFLPRVRI DTGLDLKGIT SDKAYRAFLG

     201  SDPMSVPLYG SFRQIHDFMQ RGAKLYKNEN NYIQKNFAKD KPVIIMHGQD

     251  DTINDPKGSE KFIQDCPSAD KELKLYPGAR HSIFSLETDK VFNTVFNDMK

     301  QWLDKHTTTE AKP

Conserved Domain Search
http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00561&version=v1.54

pfam 00561
abhydrolase, alph/beta hydrolase fold
catalytic domain found in many enzymes

ProDom
http://protein.toulouse.inra.fr/cgi-bin/ReqProdomII.pl?acc_seq0=P28321

yeast-
complete proteome peroxiase lysophospholipase chloroperoxidase synthase polymerase
    oxidoreductase non-heme

homologous proteins-
function: biotransformation enzyme that catalyzes the hydrolysis of epoxides (alkene oxides,
    oxiranes) and arene oxides to less reactive and more water soluble dihydrodiols by the trans
    addition of water
catalytic activity: epoxide + H20 = glycol

NCBI BLASTP
http://www.ncbi.nlm.nih.gov/BLAST/

abhydrolase
40-50% positives with lisophospholipases of other organisms

Kyte Doolittle Plot
 http://fasta.bioch.virginia.edu/fasta/grease.htm
J. Kyte and R. F. Doolittle (1982) J. Mol. Biol. 157:105-132

The Kyte Doolittle hydropathy plot tells you whether a protein may me a transmembrane protein.
If a peak is higher than two then the protein may be a transmembrane protein.
 

Figure 2 Kyte Doolittle Hydropathy Plot for the sgs1 protein
d
There doesn't seem to be very good evidence to suggest that the YJU3 gene encodes for a transmembrane protein.

BLASTP against other mamalian homologs
http://genome-www.stanford.edu/cgi-bin/SGD/Sacch3D/getblast?name=YJU3&db=mammal

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990).
    Basic local alignment search tool. J. Mol. Biol. 215: 403-10.
Altschul et al. (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database
    search programs. Nucl. Acids Res. 25: 3389-3402.
 

46% positive with human lysophospholipase homolog
44% positive with Mouse cyclophilin C-associated protein
44% positive with Mouse mama gene product

PULLING IT ALL TOGETHER
   The data suggest that YJU3 may be a  abhydrolase protein and a lysophospholipase protein.  Experiments should be created and performed to test this possibility.
 

References
Bennett, Richard J. and James C. Wang. September 25, 2001. Association of yeast DNA
    topoisomerase III and Sgs1 DNA helicase: Studies of fusion proteins. PNAS (USA) 98(20):
    11108-11113. http://www.jbc.org/cgi/content/abstract/275/35/26898?ijkey=12NNavZs9ppNo

Frei, Christian and Susan M. Gasser. January 2000. The yeast Sgs1p helicase acts upstream of
    Rad53p in the DNA replication checkpoint and colocalizes with Rad53p in S-phase-specific
    foci. Genes and Dev. 14(1): 81-96.http://www.genesdev.org/cgi/content/full/14/1/81

Griffiths, Anthony, W.M. Gelbart, J.H. Miller, R.C. Lewontin. 1999. Modern Genetic
    Analysis.W.H. Freeman and Company, New York, pp. 88-90.

Guarente, Leonard. October 1997. Link between aging and the nucleolus. Genes and Dev. 11(19):
    2449-2455. http://www.genesdev.org/cgi/content/full/11/19/2449

Lee, S. K. , Johnson, R. E. , Yu, S. L. , Prakash, L. & Prakash, S. 1999. Requirement of Yeast
    SGS1 and SRS2 genes for replication and transcription. Science 286: 2339-2342.
    http://www.sciencemag.org/cgi/content/full/286/5448/2339?ijkey=bWVP.CI6.mh6A

Liu, Z., Macias, M. J., Bottomley, M. J., Stier, G., Linge, J. P., Nilges, M., Bork, P., Sattler, M. 1999. The Three-Dimensional Structure of the Hrdc Domain and Implications for the Werner
    and Bloom Syndrome Proteins. Structure (London) 7: 1557.

McVey, M. , Kaeberlein, M. , Tissenbaum, H. A. & Guarente, L. 2001. The short life span of
    Saccharomyces servisiae sgs1 and srs2 mutants is a composite of normal aging processes and
    mitotic arrest due to defective recombination. Genetics 157: 1531-1542.
    http://www.genetics.org/cgi/content/full/157/4/1531

SGD database. 2001.Stanford.
    http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=YJU3

Swiss-Port. 2001. http://www.expasy.ch/cgi-bin/niceport.pl?P35187

Watt, Paul M. and Ian D. Hickson. 1996. Failure to unwind causes cancer. Current Biology.
   6:265-267. http://journals.bmn.com/journals/list/browse?uid=JCUB.bb6308&rendertype=text

Watt PM, Louis EJ, Borts RH, Hickson ID. April 1995. Sgs1: a eukaryotic homolog of E. coli
    RecQ that interacts with topoisomerase II in vivo and is required for faithful chromosome
    segregation. Cell. 81(2): 253-60.

Yamagata K, Kato J, Shimamoto A, Goto M, Furuichi Y, Ikeda H. July 1998. Bloom's and
    Werner's syndrome genes suppress hyperrecombination in yeast sgs1 mutant: implication for
    genomic instability in human diseases. PNAS (U S A) 95(15):8733-8.
    http://www.pnas.org/cgi/content/full/95/15/8733

YPD database. 2001. Proteome, Inc.
    http://www.proteome.com/databases/YPD/reports/YJU3.html
 
 

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