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.
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
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 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):
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).
Id: gene: YJU3; ORF: YK1094W
Swiss Port: http://www.expasy.ch/cgi-bin/niceprot.pl?P28321
Genbank Id: CAA81932
Null allele: viable
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
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
abhydrolase, alph/beta hydrolase fold
catalytic domain found in many enzymes
complete proteome peroxiase lysophospholipase chloroperoxidase synthase polymerase
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
40-50% positives with lisophospholipases of other organisms
Kyte Doolittle Plot
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
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
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.
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):
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
W.M. Gelbart, J.H. Miller, R.C. Lewontin. 1999. Modern Genetic
Analysis.W.H. Freeman and Company, New York, pp. 88-90.
October 1997. Link between aging and the nucleolus. Genes and Dev. 11(19):
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.
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
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.
SGD database. 2001.Stanford.
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.
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.
YPD database. 2001. Proteome,
Lisa's Home Page
Genomics Home Page
Davidson Home Page
Contact info: firstname.lastname@example.org