Sandbox20: Difference between revisions

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[[Image:Theta Model of Replication.jpg | thumb | upright=1.7| right| Schematic representation of the replication termination fork and fork traps of the E. coli and B. subtilis chromosomes.]]

The replication of chromosomal DNA in most bacterial species occurs through a bidirectional mechanism, whereby two replication forks derived from the same origin of replication travel in opposite directions.<ref>PMID: 4562743</ref> This gives rise to the characteristic theta-shaped structure as the nascent DNA loop connecting the replication forks is generated. While the use of two [[1b77| replisomes]], one at each fork, accelerates replication, the phase of termination must be carefully coordinated. Specific sequences known as Ter sites lie just beyond the halfway point for each replisome. These halt the advance of replication forks in a direction-specific manner, and thereby form a ''replication fork trap''. As a result, each replisome can traverse only slightly more than half of the DNA before it is arrested. Together, the two sets of Ter sites define the terminus region where replication is terminated and the two forks fuse.

The replication of chromosomal DNA in most bacterial species occurs through a bidirectional mechanism, whereby two replication forks derived from the same origin of replication travel in opposite directions.<ref>PMID: 4562743</ref> This gives rise to the characteristic theta-shaped structure as the nascent DNA loop connecting the replication forks is generated. While the use of two [[1b77| replisomes]], one at each fork, accelerates replication, the phase of termination must be carefully coordinated. Specific sequences known as ''Ter sites'' lie just beyond the halfway point for each replisome. These halt the advance of replication forks in a direction-specific manner, and thereby form a ''replication fork trap''. As a result, each replisome can traverse only slightly more than half of the DNA before it is arrested. Together, the two sets of Ter sites define the terminus region where replication is terminated and the two forks fuse.

In E. coli, the replication fork trap is set in place by the binding of termination utilisation substance (Tus) to Ter sites; and in B. subtilis, the binding of replication termination protein (RTP) to Ter sites. The importance of these replication fork traps is still a matter of debate, as their inactivation does not interfere greatly with cell cycle progression<ref>PMID: 6442251</ref>, nor does it affect the well-being of daughter cells following cell division. However, the fact that Tus and RTP share no homology in sequence or structure yet both bind to ill-conserved Ter sites to elicit the same biological function suggests an evolutionary pressure towards a termination mechanism that involves replication fork traps.

It has been noted that the majority of genes in the B. subtilis genome have their promoters proximal to the origin of replication. Terminating replication before the replisome reaches the promoters may help the smooth running of transcriptional processes <ref>PMID:19019156 </ref> <ref>PMID: 2118869</ref>.

The function of the replication fork trap is enacted by the binding of termination proteins to Ter sites. In ''E. coli'', this is done by termination utilisation substance (''Tus''), and the functionally corresponding protein in ''B. subtilis'' is replication termination protein (''RTP''). The importance of these replication fork traps is still a matter of debate, as their inactivation does not interfere greatly with cell cycle progression<ref>PMID: 6442251</ref>, nor does it affect the well-being of daughter cells following cell division. However, the fact that the structurally and sequentially dissimilar Tus and RTP proteins both bind to ill-conserved Ter sites to elicit the same biological function suggests an evolutionary pressure towards a termination mechanism that involves replication fork traps. It has been noted that the majority of genes in the ''B. subtilis'' genome have their promoters proximal to the origin of replication. Terminating replication before the replisome reaches the promoters may help the smooth running of transcriptional processes <ref>PMID:19019156 </ref> <ref>PMID: 2118869</ref>.

During fork fusion, it is proposed that the fork arriving at the permissive face of the replication fork trap displaces the terminator protein and causes the disassembly of the replisome. A combination of helicase, toposiomerase, polymerase and ligase then fill the remaining gaps to make a chromosome dimer with the two full-length chromosomes joined. RecQ, topoisomerase III, single-strand binding protein (SSBP) and DNA polymerase I are said to play a role in this process <REF>PMID:18570879 </REF>. Finally, site-specific recombination takes place at the dif site to produce two identical monomeric chromosomes <ref>PMID:15554958 </ref>.

~~_____~~

The rate at which each replisome progresses may be altered by a number of factors, such as the presence of DNA-associated proteins. Although the location of their union is consequently not necessarily directly opposite the origin, it is not random either. Specific DNA termination sequences called ''Ter'' sites halt the advance of a replication fork from one direction only by recruiting specific protein factors. The position and orientation of these within the chromosome define a ''replication fork trap'', which allows either replisome to traverse only slightly more than half of the total DNA before being halted <ref>PMID: 19019156</ref>. Together, they define the restricted ''terminus region'' where replication is terminated.

The significance of the fork trap is a matter of debate as its inactivation has no clear consequences <ref>PMID: 6442251</ref>, and fork fusion itself is in fact not essential, as the genome can be stably linearized <ref>PMID:17218953</ref>. It may be that prevention of one replication body from synthesizing the entire chromosome is necessary to prevent conflicts with transcription processes. The majority of genes within the B. subtilis genome are oriented such that their promoters are proximal to the origin of replication, suggesting a possible evolutionary pressure towards co-directionality of DNA replication and transcription <ref>PMID: 2118869</ref>. The importance, however, is underlined by the apparent independent evolution of terminator proteins Tus and RTP in E. coli and B. subtilis respectively

==The Role of the Terminus Region==

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@@ Line 6: / Line 6: @@
 [[Image:Theta Model of Replication.jpg | thumb | upright=1.7| right| Schematic representation of the replication termination fork and fork traps of the E. coli and B. subtilis chromosomes.]]
-The replication of chromosomal DNA in most bacterial species occurs through a bidirectional mechanism, whereby two replication forks derived from the same origin of replication travel in opposite directions.<ref>PMID: 4562743</ref> This gives rise to the characteristic theta-shaped structure as the nascent DNA loop connecting the replication forks is generated. While the use of two [[1b77| replisomes]], one at each fork, accelerates replication, the phase of termination must be carefully coordinated. Specific sequences known as Ter sites lie just beyond the halfway point for each replisome. These halt the advance of replication forks in a direction-specific manner, and thereby form a ''replication fork trap''. As a result, each replisome can traverse only slightly more than half of the DNA before it is arrested. Together, the two sets of Ter sites define the terminus region where replication is terminated and the two forks fuse.
+The replication of chromosomal DNA in most bacterial species occurs through a bidirectional mechanism, whereby two replication forks derived from the same origin of replication travel in opposite directions.<ref>PMID: 4562743</ref> This gives rise to the characteristic theta-shaped structure as the nascent DNA loop connecting the replication forks is generated. While the use of two [[1b77| replisomes]], one at each fork, accelerates replication, the phase of termination must be carefully coordinated. Specific sequences known as ''Ter sites'' lie just beyond the halfway point for each replisome. These halt the advance of replication forks in a direction-specific manner, and thereby form a ''replication fork trap''. As a result, each replisome can traverse only slightly more than half of the DNA before it is arrested. Together, the two sets of Ter sites define the terminus region where replication is terminated and the two forks fuse.
-In E. coli, the replication fork trap is set in place by the binding of termination utilisation substance (Tus) to Ter sites; and in B. subtilis, the binding of replication termination protein (RTP) to Ter sites. The importance of these replication fork traps is still a matter of debate, as their inactivation does not interfere greatly with cell cycle progression<ref>PMID: 6442251</ref>, nor does it affect the well-being of daughter cells following cell division. However, the fact that Tus and RTP share no homology in sequence or structure yet both bind to ill-conserved Ter sites to elicit the same biological function suggests an evolutionary pressure towards a termination mechanism that involves replication fork traps.
-It has been noted that the majority of genes in the B. subtilis genome have their promoters proximal to the origin of replication. Terminating replication before the replisome reaches the promoters may help the smooth running of transcriptional processes <ref>PMID:19019156 </ref> <ref>PMID: 2118869</ref>.
+The function of the replication fork trap is enacted by the binding of termination proteins to Ter sites. In ''E. coli'', this is done by termination utilisation substance (''Tus''), and the functionally corresponding protein in ''B. subtilis'' is replication termination protein (''RTP''). The importance of these replication fork traps is still a matter of debate, as their inactivation does not interfere greatly with cell cycle progression<ref>PMID: 6442251</ref>, nor does it affect the well-being of daughter cells following cell division. However, the fact that the structurally and sequentially dissimilar Tus and RTP proteins both bind to ill-conserved Ter sites to elicit the same biological function suggests an evolutionary pressure towards a termination mechanism that involves replication fork traps. It has been noted that the majority of genes in the ''B. subtilis'' genome have their promoters proximal to the origin of replication. Terminating replication before the replisome reaches the promoters may help the smooth running of transcriptional processes <ref>PMID:19019156 </ref> <ref>PMID: 2118869</ref>.
 During fork fusion, it is proposed that the fork arriving at the permissive face of the replication fork trap displaces the terminator protein and causes the disassembly of the replisome. A combination of helicase, toposiomerase, polymerase and ligase then fill the remaining gaps to make a chromosome dimer with the two full-length chromosomes joined. RecQ, topoisomerase III, single-strand binding protein (SSBP) and DNA polymerase I are said to play a role in this process <REF>PMID:18570879 </REF>. Finally, site-specific recombination takes place at the dif site to produce two identical monomeric chromosomes <ref>PMID:15554958 </ref>.
-_____
-The rate at which each replisome progresses may be altered by a number of factors, such as the presence of DNA-associated proteins. Although the location of their union is consequently not necessarily directly opposite the origin, it is not random either. Specific DNA termination sequences called ''Ter'' sites halt the advance of a replication fork from one direction only by recruiting specific protein factors. The position and orientation of these within the chromosome define a ''replication fork trap'', which allows either replisome to traverse only slightly more than half of the total DNA before being halted <ref>PMID: 19019156</ref>. Together, they define the restricted ''terminus region'' where replication is terminated.
-The significance of the fork trap is a matter of debate as its inactivation has no clear consequences <ref>PMID: 6442251</ref>, and fork fusion itself is in fact not essential, as the genome can be stably linearized <ref>PMID:17218953</ref>. It may be that prevention of one replication body from synthesizing the entire chromosome is necessary to prevent conflicts with transcription processes. The majority of genes within the B. subtilis genome are oriented such that their promoters are proximal to the origin of replication, suggesting a possible evolutionary pressure towards co-directionality of DNA replication and transcription  <ref>PMID: 2118869</ref>. The importance, however, is underlined by the apparent independent evolution of terminator proteins Tus and RTP in E. coli and B. subtilis respectively
 ==The Role of the Terminus Region==