TAL effector - Revision history

Michal Harel at 09:32, 12 December 2023

2023-12-12T09:32:31Z

← Older revision		Revision as of 09:32, 12 December 2023
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	[[4gjr]], [[4gjp]], [[4osm]], [[4osq]], [[4osr]], [[4oss]], [[4ost]], [[4osv]], [[4osw]], [[4osz]], [[4ot0]], [[4ot3]], [[4oto]] – XoTAL dHax3 (mutant) + DNA<br />		[[4gjr]], [[4gjp]], [[4osm]], [[4osq]], [[4osr]], [[4oss]], [[4ost]], [[4osv]], [[4osw]], [[4osz]], [[4ot0]], [[4ot3]], [[4oto]] – XoTAL dHax3 (mutant) + DNA<br />
	[[6jtq]], [[6jw0]], [[6jvz]], [[6jw4]], [[6jw3]], [[6jw2]], [[6jw5]], [[6jw1]] – XoTAL + DNA <br />		[[6jtq]], [[6jw0]], [[6jvz]], [[6jw4]], [[6jw3]], [[6jw2]], [[6jw5]], [[6jw1]] – XoTAL + DNA <br />
			[[6lew]] - TAL + DNA - ''Xanthomonas campestris''<br />

	==Reference==		==Reference==

Michal Harel at 08:59, 19 November 2020

2020-11-19T08:59:16Z

← Older revision		Revision as of 08:59, 19 November 2020
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	==3D structures of TAL effectors==		==3D structures of TAL effectors==
			Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}

	[[3ugm]] - XoTAL pthxo1 + DNA - ''Xanthomonas oryzae''<br />		[[3ugm]] - XoTAL pthxo1 + DNA - ''Xanthomonas oryzae''<br />
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	[[3v6t]], [[4osh]], [[4osi]], [[4osj]], [[4osk]], [[4osl]] – XoTAL dHax3 + DNA <br />		[[3v6t]], [[4osh]], [[4osi]], [[4osj]], [[4osk]], [[4osl]] – XoTAL dHax3 + DNA <br />
	[[4gjr]], [[4gjp]], [[4osm]], [[4osq]], [[4osr]], [[4oss]], [[4ost]], [[4osv]], [[4osw]], [[4osz]], [[4ot0]], [[4ot3]], [[4oto]] – XoTAL dHax3 (mutant) + DNA<br />		[[4gjr]], [[4gjp]], [[4osm]], [[4osq]], [[4osr]], [[4oss]], [[4ost]], [[4osv]], [[4osw]], [[4osz]], [[4ot0]], [[4ot3]], [[4oto]] – XoTAL dHax3 (mutant) + DNA<br />
			[[6jtq]], [[6jw0]], [[6jvz]], [[6jw4]], [[6jw3]], [[6jw2]], [[6jw5]], [[6jw1]] – XoTAL + DNA <br />

	==Reference==		==Reference==

Alexander Berchansky at 12:38, 15 June 2017

2017-06-15T12:38:11Z

← Older revision		Revision as of 12:38, 15 June 2017
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	<br>[[Image:overview.jpg\|left\|300px\|thumb\|Fig.1 Structure of the PthXo1 DNA binding region in complex with its target site. The coloring of individual repeats matches the schematic in XXX]]<br>		<br>[[Image:overview.jpg\|left\|300px\|thumb\|Fig.1 Structure of the PthXo1 DNA binding region in complex with its target site. The coloring of individual repeats matches the schematic in XXX]]<br>
			{{Clear}}
	==DNA binding module with marked RVD==		==DNA binding module with marked RVD==
	<br>[[Image:sanjana.png\|left\|400px\|thumb\|Fig.2]]<br>		<br>[[Image:sanjana.png\|left\|400px\|thumb\|Fig.2]]<br>
			{{Clear}}
	'''Figure 2''': Natural structure of TALEs derived from Xanthomonas sp. Each DNA-binding module consists of 34 amino acids, where the RVDs in the 12th and 13th amino acid positions of each repeat specify the DNA base being targeted according to the cipher NG = <scene name='Sandbox_Reserved_701/T_blau/1'>T</scene>, HD = <scene name='Sandbox_Reserved_701/C_schwarz/1'>C</scene>, NI = <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>, and NN = <scene name='Sandbox_Reserved_701/G_gelb/1'>G</scene> or <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>. The DNA-binding modules are flanked by nonrepetitive N and C termini, which carry the translocation, nuclear localization (NLS) and transcription activation (AD) domains. A cryptic signal within the N terminus specifies a thymine as the first base of the target site.<ref> PMID:022223736 </ref>		'''Figure 2''': Natural structure of TALEs derived from Xanthomonas sp. Each DNA-binding module consists of 34 amino acids, where the RVDs in the 12th and 13th amino acid positions of each repeat specify the DNA base being targeted according to the cipher NG = <scene name='Sandbox_Reserved_701/T_blau/1'>T</scene>, HD = <scene name='Sandbox_Reserved_701/C_schwarz/1'>C</scene>, NI = <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>, and NN = <scene name='Sandbox_Reserved_701/G_gelb/1'>G</scene> or <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>. The DNA-binding modules are flanked by nonrepetitive N and C termini, which carry the translocation, nuclear localization (NLS) and transcription activation (AD) domains. A cryptic signal within the N terminus specifies a thymine as the first base of the target site.<ref> PMID:022223736 </ref>

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	<br>[[Image:Mak_An.png\|right\|400px\|thumb\|Fig.3]]<br>		<br>[[Image:Mak_An.png\|right\|400px\|thumb\|Fig.3]]<br>
			{{Clear}}
	'''Figure 3''': Domain organization of PthXo1 and structure of a single TAL effector repeat		'''Figure 3''': Domain organization of PthXo1 and structure of a single TAL effector repeat
	TAL effectors contain N-terminal signals for bacterial type III secretion, tandem repeats that specify the target nucleotide sequence, nuclear localization signals, and a C-terminal region that is required for transcriptional activation. PthXo1 contains 23.5 canonical repeats (color coded to match Figure 3) that contact the DNA target found in the promoter of the rice Os8N3 gene (17). Blue bases correspond to positions in the target where the match between protein and DNA differs from the optimal match specified by the recognition code (3,4). Arrows indicate the start and end of the crystallized protein construct. In the structure, repeats 22 to 23.5 are poorly ordered, as are the C-termini of the two N-terminal cryptic repeats. The sequence and structure of a representative repeat (#14) is shown; RVD residues (HD) that recognize cytosine are red.<ref> PMID:22222791 </ref>		TAL effectors contain N-terminal signals for bacterial type III secretion, tandem repeats that specify the target nucleotide sequence, nuclear localization signals, and a C-terminal region that is required for transcriptional activation. PthXo1 contains 23.5 canonical repeats (color coded to match Figure 3) that contact the DNA target found in the promoter of the rice Os8N3 gene (17). Blue bases correspond to positions in the target where the match between protein and DNA differs from the optimal match specified by the recognition code (3,4). Arrows indicate the start and end of the crystallized protein construct. In the structure, repeats 22 to 23.5 are poorly ordered, as are the C-termini of the two N-terminal cryptic repeats. The sequence and structure of a representative repeat (#14) is shown; RVD residues (HD) that recognize cytosine are red.<ref> PMID:22222791 </ref>

	<br>[[Image:nihms396484f3.jpg\|left\|400px\|thumb\|Fig.4]]<br>		<br>[[Image:nihms396484f3.jpg\|left\|400px\|thumb\|Fig.4]]<br>
			{{Clear}}
	'''Figure 4''': All of the repeats in the DNA-bound PthXo1 structure form highly similar two-helix bundles (Figure 1c). The helices span positions 3 to 11 and 14 to 33, locating the RVD in a loop between them. A proline located at position 27, creates a kink in the second helix that appears to be critical for the sequential packing and association of tandem repeats with the DNA double helix. The packing of consecutive helices within and between individual repeats is left-handed, in contrast to the right-handed packing of helices found in TPR proteins (10). The modular architecture of the TAL effector repeats is reminiscent of the mitochondrial transcription terminator [http://www.proteopedia.org/wiki/index.php/3n6s mTERF] (11) and the [http://www.proteopedia.org/wiki/index.php/TRAP RNA-binding attenuation protein TRAP] (12).		'''Figure 4''': All of the repeats in the DNA-bound PthXo1 structure form highly similar two-helix bundles (Figure 1c). The helices span positions 3 to 11 and 14 to 33, locating the RVD in a loop between them. A proline located at position 27, creates a kink in the second helix that appears to be critical for the sequential packing and association of tandem repeats with the DNA double helix. The packing of consecutive helices within and between individual repeats is left-handed, in contrast to the right-handed packing of helices found in TPR proteins (10). The modular architecture of the TAL effector repeats is reminiscent of the mitochondrial transcription terminator [http://www.proteopedia.org/wiki/index.php/3n6s mTERF] (11) and the [http://www.proteopedia.org/wiki/index.php/TRAP RNA-binding attenuation protein TRAP] (12).

Michal Harel at 09:29, 6 September 2016

2016-09-06T09:29:06Z

← Older revision		Revision as of 09:29, 6 September 2016
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	[[3v6p]] - XoTAL dHax3 <br />		[[3v6p]] - XoTAL dHax3 <br />
	[[4gg4]] – XoTAL dHax3 + DNA + RNA<br />		[[4gg4]] – XoTAL dHax3 + DNA + RNA<br />
	[[3v6t]] – XoTAL dHax3 + DNA <br />		[[3v6t]], [[4osh]], [[4osi]], [[4osj]], [[4osk]], [[4osl]] – XoTAL dHax3 + DNA <br />
	[[4gjr]], [[4gjp]] – XoTAL dHax3 (mutant) + DNA<br />		[[4gjr]], [[4gjp]], [[4osm]], [[4osq]], [[4osr]], [[4oss]], [[4ost]], [[4osv]], [[4osw]], [[4osz]], [[4ot0]], [[4ot3]], [[4oto]] – XoTAL dHax3 (mutant) + DNA<br />

	==Reference==		==Reference==

Michal Harel at 09:19, 6 September 2016

2016-09-06T09:19:00Z

← Older revision		Revision as of 09:19, 6 September 2016
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	<StructureSection load='3ugm' size='350' side='right' caption='Structure of TAL effector PthXo1 bound to its target DNA [[3ugm]]' scene=''>		<StructureSection load='3ugm' size='350' side='right' caption='Structure of TAL effector PthXo1 bound to its target DNA [[3ugm]]' scene=''>
	'''Transcription activator-like effector PthXo1''' (TALE PthXo1) TALEs are proteins originally derived from the plant pathogene Xanthomonas spp. The gene encoding for the effector are Pthxo1 and Pxo_00227. Originally they were detected in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2432079/ Xanthomonas Oryzae] but the TALE PthXo1 genes were transformed into [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3100984/ Escherichia Coli] to express the DNA-binding protein.		==Function==
			'''Transcription activator-like effector PthXo1''' (TALE PthXo1) TALEs are proteins originally derived from the plant pathogene ''Xanthomonas'' spp. The gene encoding for the effector are Pthxo1 and Pxo_00227. Originally they were detected in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2432079/ Xanthomonas Oryzae] but the TALE PthXo1 genes were transformed into [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3100984/ Escherichia Coli] to express the DNA-binding protein.

	{{ABSTRACT_PUBMED_022223736}} <ref> PMID:022223736 </ref>		{{ABSTRACT_PUBMED_022223736}} <ref> PMID:022223736 </ref>
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	<br>[[Image:overview.jpg\|left\|300px\|thumb\|Fig.1 Structure of the PthXo1 DNA binding region in complex with its target site. The coloring of individual repeats matches the schematic in XXX]]<br>		<br>[[Image:overview.jpg\|left\|300px\|thumb\|Fig.1 Structure of the PthXo1 DNA binding region in complex with its target site. The coloring of individual repeats matches the schematic in XXX]]<br>

	===DNA binding module with marked RVD===		==DNA binding module with marked RVD==
	<br>[[Image:sanjana.png\|left\|400px\|thumb\|Fig.2]]<br>		<br>[[Image:sanjana.png\|left\|400px\|thumb\|Fig.2]]<br>
	'''Figure 2''': Natural structure of TALEs derived from Xanthomonas sp. Each DNA-binding module consists of 34 amino acids, where the RVDs in the 12th and 13th amino acid positions of each repeat specify the DNA base being targeted according to the cipher NG = <scene name='Sandbox_Reserved_701/T_blau/1'>T</scene>, HD = <scene name='Sandbox_Reserved_701/C_schwarz/1'>C</scene>, NI = <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>, and NN = <scene name='Sandbox_Reserved_701/G_gelb/1'>G</scene> or <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>. The DNA-binding modules are flanked by nonrepetitive N and C termini, which carry the translocation, nuclear localization (NLS) and transcription activation (AD) domains. A cryptic signal within the N terminus specifies a thymine as the first base of the target site.<ref> PMID:022223736 </ref>		'''Figure 2''': Natural structure of TALEs derived from Xanthomonas sp. Each DNA-binding module consists of 34 amino acids, where the RVDs in the 12th and 13th amino acid positions of each repeat specify the DNA base being targeted according to the cipher NG = <scene name='Sandbox_Reserved_701/T_blau/1'>T</scene>, HD = <scene name='Sandbox_Reserved_701/C_schwarz/1'>C</scene>, NI = <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>, and NN = <scene name='Sandbox_Reserved_701/G_gelb/1'>G</scene> or <scene name='Sandbox_Reserved_701/A_gruen/1'>A</scene>. The DNA-binding modules are flanked by nonrepetitive N and C termini, which carry the translocation, nuclear localization (NLS) and transcription activation (AD) domains. A cryptic signal within the N terminus specifies a thymine as the first base of the target site.<ref> PMID:022223736 </ref>

	===Tertiary structure of the RVD===		==Tertiary structure of the RVD==

	<br>[[Image:Mak_An.png\|right\|400px\|thumb\|Fig.3]]<br>		<br>[[Image:Mak_An.png\|right\|400px\|thumb\|Fig.3]]<br>
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	Sequence-specific contacts of PthXo1 to the DNA are made exclusively by the second residue in each RVD to the corresponding base on the sense strand. In contrast, the side chain at the first position of each RVD contacts the backbone carbonyl oxygen of position 8 in each repeat, constraining the RVD-containing loop (Figure 3). Additional, nonspecific contacts to the DNA are made by a lysine and glutamine found at positions 16 and 17.		Sequence-specific contacts of PthXo1 to the DNA are made exclusively by the second residue in each RVD to the corresponding base on the sense strand. In contrast, the side chain at the first position of each RVD contacts the backbone carbonyl oxygen of position 8 in each repeat, constraining the RVD-containing loop (Figure 3). Additional, nonspecific contacts to the DNA are made by a lysine and glutamine found at positions 16 and 17.

	===Interaction between RVDs and DNA===		==Interaction between RVDs and DNA==

	‘HD’ RVDs:		‘HD’ RVDs:

Jaime Prilusky at 17:16, 9 February 2014

2014-02-09T17:16:21Z

Show changes

Jaime Prilusky: Sandbox Reserved 701 moved to TAL effector: requested by Editor

2014-02-09T17:10:14Z

Sandbox Reserved 701 moved to TAL effector: requested by Editor

← Older revision	Revision as of 17:10, 9 February 2014
(No difference)

Michal Harel at 12:02, 9 February 2014

2014-02-09T12:02:02Z

← Older revision		Revision as of 12:02, 9 February 2014
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	~~==3D structures of related TAL effectors==~~

	<br>[[Image:overview.jpg\|left\|300px\|thumb\|Fig.1 Structure of the PthXo1 DNA binding region in complex with its target site. The coloring of individual repeats matches the schematic in XXX]]<br>		<br>[[Image:overview.jpg\|left\|300px\|thumb\|Fig.1 Structure of the PthXo1 DNA binding region in complex with its target site. The coloring of individual repeats matches the schematic in XXX]]<br>

	[[4gg4]] – ~~TAL effector~~ dHax3 ~~bound to specific~~ DNA-RNA ~~hybrid~~<br />		==3D structures of TAL effectors==
	[[4gjr]] – ~~TAL effector~~ dHax3 ~~bound to methylated dsDNA~~<br />
			[[3ugm]] - XoTAL pthxo1 + DNA - ''Xanthomonas oryzae''<br />
			[[3v6p]] - XoTAL dHax3 <br />
			[[4gg4]] – XoTAL dHax3 + DNA + RNA<br />
			[[3v6t]] – XoTAL dHax3 + DNA <br />
			[[4gjr]], [[4gjp]] – XoTAL dHax3 (mutant) + DNA<br />

Philipp Warmer at 12:44, 3 January 2013

2013-01-03T12:44:25Z

← Older revision		Revision as of 12:44, 3 January 2013
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			===Interaction between RVDs and DNA===


	~~===Interaction between RVDs and DNA===~~

	‘HD’ RVDs:		‘HD’ RVDs:

Philipp Warmer at 12:43, 3 January 2013

2013-01-03T12:43:59Z

← Older revision		Revision as of 12:43, 3 January 2013
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	Sequence-specific contacts of PthXo1 to the DNA are made exclusively by the second residue in each RVD to the corresponding base on the sense strand. In contrast, the side chain at the first position of each RVD contacts the backbone carbonyl oxygen of position 8 in each repeat, constraining the RVD-containing loop (Figure 3). Additional, nonspecific contacts to the DNA are made by a lysine and glutamine found at positions 16 and 17.		Sequence-specific contacts of PthXo1 to the DNA are made exclusively by the second residue in each RVD to the corresponding base on the sense strand. In contrast, the side chain at the first position of each RVD contacts the backbone carbonyl oxygen of position 8 in each repeat, constraining the RVD-containing loop (Figure 3). Additional, nonspecific contacts to the DNA are made by a lysine and glutamine found at positions 16 and 17.







	===Interaction between RVDs and DNA===		===Interaction between RVDs and DNA===