User:Alexei Ilinykh/Sandbox 1 - Revision history

Alexei Ilinykh: /* Evolution of Tus and RTP systems */

2011-05-23T03:11:31Z

Evolution of Tus and RTP systems

←Older revision		Revision as of 03:11, 23 May 2011
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	== Evolution of Tus and RTP systems ==		== Evolution of Tus and RTP systems ==

-	[[Image:~~EColi_chromosome_map~~.jpg\|thumb\|"border"\|\|\|300x300px\|\|\| Basic representations of the phylogenetic trees of E. coli and B. subtilis.]]	+	[[Image:phylogenetic.jpg\|thumb\|"border"\|\|\|300x300px\|\|\| Basic representations of the phylogenetic trees of E. coli and B. subtilis.]]

	The study of Tus and the RTP systems reveal two systems which are key in the termination of replication in their hosts. However, while both systems induce termination, considerable differences in their structure and mechanisms of action strongly indicate that the systems evolved independently <ref>PMID:8857533</ref>.		The study of Tus and the RTP systems reveal two systems which are key in the termination of replication in their hosts. However, while both systems induce termination, considerable differences in their structure and mechanisms of action strongly indicate that the systems evolved independently <ref>PMID:8857533</ref>.

Alexei Ilinykh: /* Evolution of Tus and RTP systems */

2011-05-23T03:11:06Z

Evolution of Tus and RTP systems

←Older revision		Revision as of 03:11, 23 May 2011
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	== Evolution of Tus and RTP systems ==		== Evolution of Tus and RTP systems ==
		+
		+	[[Image:EColi_chromosome_map.jpg\|thumb\|"border"\|\|\|300x300px\|\|\| Basic representations of the phylogenetic trees of E. coli and B. subtilis.]]

	The study of Tus and the RTP systems reveal two systems which are key in the termination of replication in their hosts. However, while both systems induce termination, considerable differences in their structure and mechanisms of action strongly indicate that the systems evolved independently <ref>PMID:8857533</ref>.		The study of Tus and the RTP systems reveal two systems which are key in the termination of replication in their hosts. However, while both systems induce termination, considerable differences in their structure and mechanisms of action strongly indicate that the systems evolved independently <ref>PMID:8857533</ref>.

Alexei Ilinykh at 03:01, 23 May 2011

2011-05-23T03:01:07Z

←Older revision		Revision as of 03:01, 23 May 2011
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-	{{ Comparison of DNA Replication Termination in ''Bacillus subtilis'' and ''Escherichia coli'' }}	+	= Comparison of DNA Replication Termination in ''Bacillus subtilis'' and ''Escherichia coli'' =

	== Termination sites in ''B.subtilis'' and ''E. coli'' ==		== Termination sites in ''B.subtilis'' and ''E. coli'' ==

Alexei Ilinykh at 03:00, 23 May 2011

2011-05-23T03:00:40Z

←Older revision		Revision as of 03:00, 23 May 2011
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-	{{Comparison of DNA Replication Termination in ''Bacillus subtilis'' and ''Escherichia coli''}}	+	{{ Comparison of DNA Replication Termination in ''Bacillus subtilis'' and ''Escherichia coli'' }}

	== Termination sites in ''B.subtilis'' and ''E. coli'' ==		== Termination sites in ''B.subtilis'' and ''E. coli'' ==

Alexei Ilinykh at 03:00, 23 May 2011

2011-05-23T03:00:05Z

←Older revision		Revision as of 03:00, 23 May 2011
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-	= Comparison of DNA Replication Termination in ''Bacillus subtilis'' and ''Escherichia coli'' =	+	{{Comparison of DNA Replication Termination in ''Bacillus subtilis'' and ''Escherichia coli''}}

	== Termination sites in ''B.subtilis'' and ''E. coli'' ==		== Termination sites in ''B.subtilis'' and ''E. coli'' ==

Alexei Ilinykh at 02:56, 23 May 2011

2011-05-23T02:56:47Z

←Older revision		Revision as of 02:56, 23 May 2011
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-	= DNA Replication Termination =	+	= Comparison of DNA Replication Termination in ''Bacillus subtilis'' and ''Escherichia coli'' =

	== Termination sites in ''B.subtilis'' and ''E. coli'' ==		== Termination sites in ''B.subtilis'' and ''E. coli'' ==

Alexei Ilinykh at 02:52, 23 May 2011

2011-05-23T02:52:01Z

←Older revision		Revision as of 02:52, 23 May 2011
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		+	= DNA Replication Termination =
		+
	== Termination sites in ''B.subtilis'' and ''E. coli'' ==		== Termination sites in ''B.subtilis'' and ''E. coli'' ==
	[[Image:EColi_chromosome_map.jpg\|thumb\|"border"\|\|\|300x300px\|\|\|Chromosome map of the 4.6 Mb ''E.Coli'' genome indicating the location and orientation of Ter sites. The two groups of Ter sites are depicted in red and black respectively. An origin of replication (''OriC'') is also shown.]]		[[Image:EColi_chromosome_map.jpg\|thumb\|"border"\|\|\|300x300px\|\|\|Chromosome map of the 4.6 Mb ''E.Coli'' genome indicating the location and orientation of Ter sites. The two groups of Ter sites are depicted in red and black respectively. An origin of replication (''OriC'') is also shown.]]

Alexei Ilinykh: /* The Dif site: The real termination point? */

2011-05-23T02:27:25Z

The Dif site: The real termination point?

←Older revision		Revision as of 02:27, 23 May 2011
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	== The Dif site: The real termination point? ==		== The Dif site: The real termination point? ==
		+	[[Image:Difsite.jpg\|thumb\|"border"\|\|\|500x350px\|\|\|Chromosome map of the 4.2 Mb ''B. Subtilis'' genome indicating the location and orientation of Ter sites. The two groups of Ter sites are depicted in red and black respectively. An origin of replication (''OriC'') is also shown along with the dif site]]

	In bacteria, replication of DNA occurs by the way of two replication forks diverging away from the origin of replication, ''oriC'', before fusing and terminating at the terminus region. This system of replication is utilized in both ''E. Coli'' and ''B. Subtilis'' <ref>PMID: 10931283</ref>. These prokaryotes utilize two distinct termination systems, Tus and RTP respectively, to end replication. One interesting feature of replication in organisms with circular chromosomes, is the formation of chromosomal multimers. These multimers must be resolved through the use of Xer recombinases at a site called Dif. Without this, daughter cells cannot be segregated<ref>PMID: 21223577</ref>.		In bacteria, replication of DNA occurs by the way of two replication forks diverging away from the origin of replication, ''oriC'', before fusing and terminating at the terminus region. This system of replication is utilized in both ''E. Coli'' and ''B. Subtilis'' <ref>PMID: 10931283</ref>. These prokaryotes utilize two distinct termination systems, Tus and RTP respectively, to end replication. One interesting feature of replication in organisms with circular chromosomes, is the formation of chromosomal multimers. These multimers must be resolved through the use of Xer recombinases at a site called Dif. Without this, daughter cells cannot be segregated<ref>PMID: 21223577</ref>.
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	While the work performed in previous studies had studied bacteria, Duggin and Bell (2011) most recently performed a study on the Archaeon ''Sulfolobus solfataricus''. This Archea shares a degree of similiarity with the previously studied bacteria in possessing a circular chromosome with replication origins and also possessing dif sites. Importantly however, the paper showed that the dif site is not implicated in termination and furthermore exists outside fork fusion zones <ref>PMID: 21113132</ref>.		While the work performed in previous studies had studied bacteria, Duggin and Bell (2011) most recently performed a study on the Archaeon ''Sulfolobus solfataricus''. This Archea shares a degree of similiarity with the previously studied bacteria in possessing a circular chromosome with replication origins and also possessing dif sites. Importantly however, the paper showed that the dif site is not implicated in termination and furthermore exists outside fork fusion zones <ref>PMID: 21113132</ref>.
-
-	[[Image:difsite.jpg\|\|\|\|"middle"\|500x300px\|\|\|]]

	== References ==		== References ==
	<references/>		<references/>

Alexei Ilinykh: /* The Dif site: The real termination point? */

2011-05-23T02:26:10Z

The Dif site: The real termination point?

←Older revision		Revision as of 02:26, 23 May 2011
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	While the work performed in previous studies had studied bacteria, Duggin and Bell (2011) most recently performed a study on the Archaeon ''Sulfolobus solfataricus''. This Archea shares a degree of similiarity with the previously studied bacteria in possessing a circular chromosome with replication origins and also possessing dif sites. Importantly however, the paper showed that the dif site is not implicated in termination and furthermore exists outside fork fusion zones <ref>PMID: 21113132</ref>.		While the work performed in previous studies had studied bacteria, Duggin and Bell (2011) most recently performed a study on the Archaeon ''Sulfolobus solfataricus''. This Archea shares a degree of similiarity with the previously studied bacteria in possessing a circular chromosome with replication origins and also possessing dif sites. Importantly however, the paper showed that the dif site is not implicated in termination and furthermore exists outside fork fusion zones <ref>PMID: 21113132</ref>.

		+	[[Image:difsite.jpg\|\|\|\|"middle"\|500x300px\|\|\|]]

	== References ==		== References ==
	<references/>		<references/>

Alexei Ilinykh at 02:07, 23 May 2011

2011-05-23T02:07:02Z

←Older revision		Revision as of 02:07, 23 May 2011
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	However, this asymmetry is accomplished in distinct ways; Tus is an inherently asymmetric monomer, whereas RTP takes on an asymmetric conformation once bound to DNA. RTP also lacks any specific base locking mechanism, as seen by the flipping of C (6) in the Tus-ter complex. The fact that such different proteins can have similar functions whilst sharing some basic similarities in mechanism supports the idea of independent, convergent evolution of the systems in ''E. coli'' and ''B. subtilis'' <ref name = "strofrepterprowithdna" />.		However, this asymmetry is accomplished in distinct ways; Tus is an inherently asymmetric monomer, whereas RTP takes on an asymmetric conformation once bound to DNA. RTP also lacks any specific base locking mechanism, as seen by the flipping of C (6) in the Tus-ter complex. The fact that such different proteins can have similar functions whilst sharing some basic similarities in mechanism supports the idea of independent, convergent evolution of the systems in ''E. coli'' and ''B. subtilis'' <ref name = "strofrepterprowithdna" />.

		+	== Evolution of Tus and RTP systems ==

		+	The study of Tus and the RTP systems reveal two systems which are key in the termination of replication in their hosts. However, while both systems induce termination, considerable differences in their structure and mechanisms of action strongly indicate that the systems evolved independently <ref>PMID:8857533</ref>.
		+
		+	Studies of the Tus-ter system have revealed the evolutionary development of the Tus protein in ''E. Coli'' <ref>PMID: 11523786</ref>. Although it has not been conserved identically in other species, there are organisms in which Tus-like proteins with high sequence homology have been identified <ref>PMID: 16148308</ref>. A study by Rocklein and Kuempel (1992) specifically identified ''S. enterica'' serovar Typhimurium as carrying a termination protein very similar to Tus with 78% sequence homology <ref>PMID: 1495392</ref>. More recent work has identified Tus-ter systems in ''Y. pestis'' and ''K. pneumonia'' both with sequence homologies over 50% <ref>PMID: 11523786</ref>. Furthermore, there have been studies showing Tus-like genes which have been found in plasmids. Specifically two proteins R394 and rts-1 have been found by Koch in two IncT plasmids <ref>PMID: 11106794</ref>.
		+
		+	Likewise, the RTP system of ''B. subtilius'' has many homologues in other species. Griffiths ''et al.'', (1998) found RTP homologs in ''B.atrophaeus'', ''b. amyloliquefaciens'', ''B mojavensis'' and ''B. vallismortis''. The sequences of RTP across the species were similar, but had up to 17.2% (''B. atrophaeus'') different bases. Yet despite this, only five amino acids were changed <ref>PMID: 9642188</ref>. This contrasts with Tus evolution, which has shown much greater sequence differences.
		+
		+	The research on the development of RTP in Bacillus utilized phylogenetic trees mapping the different species <ref>PMID: 11058132</ref>. This allowed the study to conclude that the RTP gene arose only after they had diverged from a common ancestor known as ''B. licheniformis'' <ref>PMID: 9642188</ref>. A more recent study, mapped the entire genome of ''B. licheniformis'' confirming that no RTP like gene existed. Furthermore, no RTP gene has been found on ''B. Halodurans'', narrowing the window in which RTP likely arose <ref>PMID: 15461803</ref>.

	== The Dif site: The real termination point? ==		== The Dif site: The real termination point? ==
Line 107:		Line 115:
	While the work performed in previous studies had studied bacteria, Duggin and Bell (2011) most recently performed a study on the Archaeon ''Sulfolobus solfataricus''. This Archea shares a degree of similiarity with the previously studied bacteria in possessing a circular chromosome with replication origins and also possessing dif sites. Importantly however, the paper showed that the dif site is not implicated in termination and furthermore exists outside fork fusion zones <ref>PMID: 21113132</ref>.		While the work performed in previous studies had studied bacteria, Duggin and Bell (2011) most recently performed a study on the Archaeon ''Sulfolobus solfataricus''. This Archea shares a degree of similiarity with the previously studied bacteria in possessing a circular chromosome with replication origins and also possessing dif sites. Importantly however, the paper showed that the dif site is not implicated in termination and furthermore exists outside fork fusion zones <ref>PMID: 21113132</ref>.

-	== Evolution of Tus and RTP systems ==
-
-	The study of Tus and the RTP systems reveal two systems which are key in the termination of replication in their hosts. However, while both systems induce termination, considerable differences in their structure and mechanisms of action strongly indicate that the systems evolved independently <ref>PMID:8857533</ref>.
-
-	Studies of the Tus-ter system have revealed the evolutionary development of the Tus protein in ''E. Coli'' <ref>PMID: 11523786</ref>. Although it has not been conserved identically in other species, there are organisms in which Tus-like proteins with high sequence homology have been identified <ref>PMID: 16148308</ref>. A study by Rocklein and Kuempel (1992) specifically identified ''S. enterica'' serovar Typhimurium as carrying a termination protein very similar to Tus with 78% sequence homology <ref>PMID: 1495392</ref>. More recent work has identified Tus-ter systems in ''Y. pestis'' and ''K. pneumonia'' both with sequence homologies over 50% <ref>PMID: 11523786</ref>. Furthermore, there have been studies showing Tus-like genes which have been found in plasmids. Specifically two proteins R394 and rts-1 have been found by Koch in two IncT plasmids <ref>PMID: 11106794</ref>.
-
-	Likewise, the RTP system of ''B. subtilius'' has many homologues in other species. Griffiths ''et al.'', (1998) found RTP homologs in ''B.atrophaeus'', ''b. amyloliquefaciens'', ''B mojavensis'' and ''B. vallismortis''. The sequences of RTP across the species were similar, but had up to 17.2% (''B. atrophaeus'') different bases. Yet despite this, only five amino acids were changed <ref>PMID: 9642188</ref>. This contrasts with Tus evolution, which has shown much greater sequence differences.
-
-	The research on the development of RTP in Bacillus utilized phylogenetic trees mapping the different species <ref>PMID: 11058132</ref>. This allowed the study to conclude that the RTP gene arose only after they had diverged from a common ancestor known as ''B. licheniformis'' <ref>PMID: 9642188</ref>. A more recent study, mapped the entire genome of ''B. licheniformis'' confirming that no RTP like gene existed. Furthermore, no RTP gene has been found on ''B. Halodurans'', narrowing the window in which RTP likely arose <ref>PMID: 15461803</ref>.

	== References ==		== References ==
	<references/>		<references/>