Team:KULeuven/Literature

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==Interesting Reads==
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== Interesting Reads ==
===UmuD===
===UmuD===
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Most bacteria, including Escherichia coli, have a coordinated inducible
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'''N-terminal degradation tags (needed for T7, Lon protease based) UmuD'''<br>
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response to DNA damage known as the SOS response to combat damage to their
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Genes & Dev. 1998 Dec;12:3889-3899.
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genomes. The SOS response is triggered by the blockage of normal replication,
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Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues
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possibly caused by a lesion on the DNA. This event leads to the expression of
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required for proteolysis.
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at least 40 SOS regulated genes, among which are the proteins of interest: a
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Martín Gonzales, Ekaterina G. Frank, Arthur S. Levine and Roger Woodgate
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specialized DNA polymerase called DNA Pol V or UmuDC. The umuDC gene
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PMID: 9869642
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products have at least three roles in the cell, which are temporally regulated.
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UmuD2C appears to have a role in delaying the cell cycle and DNA replication,
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allowing time for accurate DNA repair processes to occur. After approximately
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20 minutes of UmuD 2 existing as a full-length protein, it self-cleaves to form
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UmuD’ 2 . The new UmuD’ 2 C complex, together with several other proteins, is
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capable of low fidelity translesion replication. Additionally, UmuD2 and UmuD’
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2 interact physically with several of the replicative DNA polymerase subunits and
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UmuD’ 2 C is capable of inhibiting homologous recombination while UmuD2C is
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not.
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'''Regulation of UmuD cleavage: role of the amino-terminal tail'''<br>
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J.Mol.Biol. 1998 Oct;282(4):721-730.
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Regulation of UmuD cleavage: role of the amino-terminal tail.
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John P McDonalda, Erinn E Maurya, Arthur S Levinea and Roger Woodgate
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PMID: 9743621
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'''N-terminal degradation tags (needed for T7, Lon protease based)UmuD''' <br>
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===LVA tag===
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http://www.genesdev.org/cgi/content/full/12/24/3889
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One obvious test of this hypothesis is an ability of these sequences to impart instability on an otherwise stable protein. To test this hypothesis, we constructed a plasmid (pKSD-PRP) expressing a chimeric gene encoding the first 40 amino acids of UmuD fused to a 7-amino-acid linker joined to the entire Streptoalloteichus hindustanus Ble protein.
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The S. hindustanus ble gene encodes a small, stable protein that provides resistance to the antibiotics of the phleomycin family.
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Furthermore, subsequent experimentation demonstrated that residues 1-29 of UmuD are sufficient to impart Lon recognition and degradation of the PRP similar to that seen with the 40-amino-acid fusion.
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The amino-terminal 40 amino acids of UmuD are sufficient to target the PRP for degradation by Lon in vivo.
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In contrast, the UmuD-PRP fusion is unstable in the lon+ background and displays a half-life of ~9 min.
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'''Regulation of UmuD cleavage: role of the amino-terminal tail''' <br>
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http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45S4955-4N&_user=877992&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000047079&_version=1&_urlVersion=0&_userid=877992&md5=5cf7322e67183cefdf18521b41317a32
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By constructing chimeric UmuD proteins, we determined that the amino-terminal tail of the UmuD proteins proximal to the Cys24-Gly25 cleavage site is mainly responsible for the difference in UmuDStand UmuDEc cleavage rates.
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suggesting that most of the enhanced cleavage properties can be attributed to the N-terminal tail (residues 1 to 29) of UmuDSt.
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This region contains the cleavage site and not the active catalytic site of the protein, which leads us to conclude that UmuDSt is, in fact, cleaved more efficiently because it is a better substrate than UmuDEc.
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'''UmuD'''
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http://bayesweb.wadsworth.org/binding_sites/umuD.html
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'''Amino Acid Sequence of UmuD'''
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http://www.expasy.ch/cgi-bin/get-entries?AC=P04153
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>P0AG12|UMUD_ECO57 Protein umuD - Escherichia coli O157:H7.
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MLFIKPADLREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNQLLIQHPSATYFVKASGDS
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MIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITIS
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SEDTLDVFGVVIHVVKAMR
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>P0AG11|UMUD_ECOLI Protein umuD - Escherichia coli (strain K12).
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MLFIKPADLREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNQLLIQHPSATYFVKASGDS
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MIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITIS
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SEDTLDVFGVVIHVVKAMR
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http://ecoliwiki.net/colipedia/index.php/umuD:Gene_Product(s)
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http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11057
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'''Nucleotide Sequence'''
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>gi|49175990:1229990-1230409 Escherichia coli str. K-12 substr. MG1655, complete genome
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ATGTTGTTTATCAAGCCTGCGGATCTCCGCGAAATTGTGACTTTTCCGCTATTTAGCGATCTTGTTCAGT
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GTGGCTTTCCTTCACCGGCAGCAGATTACGTTGAACAGCGCATCGATCTGAATCAACTGTTGATCCAGCA
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TCCCAGCGCGACTTACTTCGTCAAAGCAAGTGGTGATTCTATGATTGATGGTGGAATTAGTGACGGTGAT
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TTACTGATTGTCGATAGCGCTATTACCGCCAGCCATGGTGATATTGTCATCGCTGCTGTTGACGGCGAGT
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TTACGGTGAAAAAATTGCAACTACGCCCGACGGTACAGCTTATTCCCATGAACAGCGCGTACTCGCCCAT
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TACCATCAGTAGTGAAGATACGCTGGATGTCTTTGGTGTGGTGATCCACGTCGTTAAGGCGATGCGCTGA
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We will probably need the first 90 nucleotides or so.
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===GFP===
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'''Fast degrading GFP'''<br>
'''Fast degrading GFP'''<br>
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http://aem.asm.org/cgi/content/full/64/6/2240?view=long&pmid=9603842
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Appl Environ Microbiol. 1998 Jun;64(6):2240-6.
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New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria.
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Andersen JB, Sternberg C, Poulsen LK, Bjorn SP, Givskov M, Molin S.
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PMID: 9603842

Latest revision as of 15:51, 3 October 2008

  dock/undock dropdown  

Interesting Reads

UmuD

N-terminal degradation tags (needed for T7, Lon protease based) UmuD

Genes & Dev. 1998 Dec;12:3889-3899.
Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues
required for proteolysis.
Martín Gonzales, Ekaterina G. Frank, Arthur S. Levine and Roger Woodgate
PMID: 9869642

Regulation of UmuD cleavage: role of the amino-terminal tail

J.Mol.Biol. 1998 Oct;282(4):721-730.
Regulation of UmuD cleavage: role of the amino-terminal tail.
John P McDonalda, Erinn E Maurya, Arthur S Levinea and Roger Woodgate
PMID: 9743621

LVA tag

Fast degrading GFP

Appl Environ Microbiol. 1998 Jun;64(6):2240-6.
New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria.
Andersen JB, Sternberg C, Poulsen LK, Bjorn SP, Givskov M, Molin S.
PMID: 9603842
Retrieved from "http://2008.igem.org/Team:KULeuven/Literature"