User:Meng Han Liu/Sandbox 1
From Proteopedia
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==Introduction== | ==Introduction== | ||
| - | In prokaryotes such as [http://en.wikipedia.org/wiki/E.coli ''E. coli''] and [http://en.wikipedia.org/wiki/B._subtilis ''B. subtilis''], chromosomal DNA exists in a circular fashion whereby [[DNA Replication, Transcription and Translation#DNA replication|DNA replication]] takes place at a common [http://en.wikipedia.org/wiki/Origin_of_replication#Prokaryotic origin] (''oriC'') <ref>Duggin, I.G. and S.D. Bell, Termination Structures in the Escherichia coli Chromosome Replication Fork Trap. Journal of Molecular Biology, 2009. 387(3): p. 532-539</ref>. Two [http://en.wikipedia.org/wiki/Replication_fork replication forks] move bidirectionally from ''oriC'' to replicate DNA until they meet, and the forks fuse with one another to form two circular daughter chromosomes <ref>Wake, R.G. and G.F. King, A tale of two terminators: crystal structures sharpen the debate on DNA replication fork arrest mechanisms. Structure, 1997. 5: p. 1-5</ref>. The region where the two replication forks meet is defined as the “terminus region”, located roughly opposite of ''oriC'' <ref>Duggin, I.G., Wake, R. Gerry, Bell, Stephen D. Bell and Hill, Thomas M., The replication fork trap and termination of chromosome replication. Molecular Microbiology, 2008. 70(6): p. 1323-1333</ref>. Bacteria uses a [http://en.wikipedia.org/wiki/Circular_bacterial_chromosome#Termination “replication fork trap”] system for successful termination of replication and this requires two factors: | + | In prokaryotes such as [http://en.wikipedia.org/wiki/E.coli ''E. coli''] and [http://en.wikipedia.org/wiki/B._subtilis ''B. subtilis''], chromosomal DNA exists in a circular fashion whereby [[DNA Replication, Transcription and Translation#DNA replication|DNA replication]] takes place at a common [http://en.wikipedia.org/wiki/Origin_of_replication#Prokaryotic origin] (''oriC'') <ref>Duggin, I.G. and S.D. Bell, Termination Structures in the Escherichia coli Chromosome Replication Fork Trap. Journal of Molecular Biology, 2009. 387(3): p. 532-539</ref>. Two [http://en.wikipedia.org/wiki/Replication_fork replication forks] move bidirectionally from ''oriC'' to replicate DNA until they eventually meet, and the forks fuse with one another to form two circular daughter chromosomes <ref>Wake, R.G. and G.F. King, A tale of two terminators: crystal structures sharpen the debate on DNA replication fork arrest mechanisms. Structure, 1997. 5: p. 1-5</ref>. The region where the two replication forks meet is defined as the “terminus region”, located roughly opposite of ''oriC'' <ref>Duggin, I.G., Wake, R. Gerry, Bell, Stephen D. Bell and Hill, Thomas M., The replication fork trap and termination of chromosome replication. Molecular Microbiology, 2008. 70(6): p. 1323-1333</ref>. Bacteria uses a [http://en.wikipedia.org/wiki/Circular_bacterial_chromosome#Termination “replication fork trap”] system for successful termination of replication and this requires two factors: |
#DNA terminator (''Ter'') sites | #DNA terminator (''Ter'') sites | ||
#A specific terminator protein that can bind ''Ter'' | #A specific terminator protein that can bind ''Ter'' | ||
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''Ter'' is a short consensus DNA sequence (around 20 base pairs long) that enables binding of its cognate terminator protein in order to arrest or halt replication fork progression in a polar manner i.e. it blocks replication fork coming in one direction (the non-permissive side) but allows passage when replication fork approaches from the other direction (the permissive side) <ref>Kamada, K., et al., Structure of a replication-terminator protein complexed with DNA. Nature (London), 1996. 383(6601): p. 598-603</ref>. In both ''E. coli'' and ''B. subtilis'', multiple ''Ter'' sites are organized into two subgroups that flank the terminus region. Since replication fork arrest is unidirectional, ''Ter'' sites are distributed so that one subgroup only arrests the clockwise-moving fork while the other subgroup only arrests the anti-clockwise moving fork <ref>Duggin, I.G. and J.A. Wilce, Termination of replication in bacteria. eLS2005: John Wiley & Sons, Ltd</ref>. A suggestive reason for the presence of multiple ''Ter'' sites is to act as a safety measure to ensure termination of replication and fork fusion occur within the terminus region even if one of the replication forks managed to precede the innermost ''Ter'' sites. | ''Ter'' is a short consensus DNA sequence (around 20 base pairs long) that enables binding of its cognate terminator protein in order to arrest or halt replication fork progression in a polar manner i.e. it blocks replication fork coming in one direction (the non-permissive side) but allows passage when replication fork approaches from the other direction (the permissive side) <ref>Kamada, K., et al., Structure of a replication-terminator protein complexed with DNA. Nature (London), 1996. 383(6601): p. 598-603</ref>. In both ''E. coli'' and ''B. subtilis'', multiple ''Ter'' sites are organized into two subgroups that flank the terminus region. Since replication fork arrest is unidirectional, ''Ter'' sites are distributed so that one subgroup only arrests the clockwise-moving fork while the other subgroup only arrests the anti-clockwise moving fork <ref>Duggin, I.G. and J.A. Wilce, Termination of replication in bacteria. eLS2005: John Wiley & Sons, Ltd</ref>. A suggestive reason for the presence of multiple ''Ter'' sites is to act as a safety measure to ensure termination of replication and fork fusion occur within the terminus region even if one of the replication forks managed to precede the innermost ''Ter'' sites. | ||
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| + | ===DNA terminator proteins=== | ||
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| + | DNA terminator proteins are proteins that can recognize and bind ''Ter'' DNA to form a complex in order to achieve polar trapping of replication forks <ref>Duggin, I.G. and J.A. Wilce, Termination of replication in bacteria. eLS2005: John Wiley & Sons, Ltd</ref>. In ''E. coli'', this protein is called Tus (terminus utilization substance) whilst in ''B. sutilis'', it is called RTP (replication termination protein). Based on experimental data using mutated ''Ter'' sites and DNA terminator mutants suggests that both protein-DNA (terminator-''Ter'') and protein-protein (terminator-[http://en.wikipedia.org/wiki/Replisome replisome]) interactions are important for successful polar fork arrest <ref>Kaplan, D.L.a.B., D., Mechanisms of polar arrest of a replication fork. Molecular Microbiology, 2009. 72(2): p. 279-285</ref>. | ||
Revision as of 15:46, 19 May 2011
Contents |
Introduction
In prokaryotes such as E. coli and B. subtilis, chromosomal DNA exists in a circular fashion whereby DNA replication takes place at a common origin (oriC) [1]. Two replication forks move bidirectionally from oriC to replicate DNA until they eventually meet, and the forks fuse with one another to form two circular daughter chromosomes [2]. The region where the two replication forks meet is defined as the “terminus region”, located roughly opposite of oriC [3]. Bacteria uses a “replication fork trap” system for successful termination of replication and this requires two factors:
- DNA terminator (Ter) sites
- A specific terminator protein that can bind Ter
DNA terminator (Ter) sites
Ter is a short consensus DNA sequence (around 20 base pairs long) that enables binding of its cognate terminator protein in order to arrest or halt replication fork progression in a polar manner i.e. it blocks replication fork coming in one direction (the non-permissive side) but allows passage when replication fork approaches from the other direction (the permissive side) [4]. In both E. coli and B. subtilis, multiple Ter sites are organized into two subgroups that flank the terminus region. Since replication fork arrest is unidirectional, Ter sites are distributed so that one subgroup only arrests the clockwise-moving fork while the other subgroup only arrests the anti-clockwise moving fork [5]. A suggestive reason for the presence of multiple Ter sites is to act as a safety measure to ensure termination of replication and fork fusion occur within the terminus region even if one of the replication forks managed to precede the innermost Ter sites.
DNA terminator proteins
DNA terminator proteins are proteins that can recognize and bind Ter DNA to form a complex in order to achieve polar trapping of replication forks [6]. In E. coli, this protein is called Tus (terminus utilization substance) whilst in B. sutilis, it is called RTP (replication termination protein). Based on experimental data using mutated Ter sites and DNA terminator mutants suggests that both protein-DNA (terminator-Ter) and protein-protein (terminator-replisome) interactions are important for successful polar fork arrest [7].
RTP
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References
- ↑ Duggin, I.G. and S.D. Bell, Termination Structures in the Escherichia coli Chromosome Replication Fork Trap. Journal of Molecular Biology, 2009. 387(3): p. 532-539
- ↑ Wake, R.G. and G.F. King, A tale of two terminators: crystal structures sharpen the debate on DNA replication fork arrest mechanisms. Structure, 1997. 5: p. 1-5
- ↑ Duggin, I.G., Wake, R. Gerry, Bell, Stephen D. Bell and Hill, Thomas M., The replication fork trap and termination of chromosome replication. Molecular Microbiology, 2008. 70(6): p. 1323-1333
- ↑ Kamada, K., et al., Structure of a replication-terminator protein complexed with DNA. Nature (London), 1996. 383(6601): p. 598-603
- ↑ Duggin, I.G. and J.A. Wilce, Termination of replication in bacteria. eLS2005: John Wiley & Sons, Ltd
- ↑ Duggin, I.G. and J.A. Wilce, Termination of replication in bacteria. eLS2005: John Wiley & Sons, Ltd
- ↑ Kaplan, D.L.a.B., D., Mechanisms of polar arrest of a replication fork. Molecular Microbiology, 2009. 72(2): p. 279-285
