Sandbox Reserved 933: Difference between revisions

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</StructureSection>

== LEAFY Evolution <ref name="Sayou2014" /> ==

[[Image:LEAFY_Evolution.007.jpg|800px|Right|thumb| Figure 4. A summary of LEAFY evolution by substation ~~in three residues~~ on three different types of DNA binding motif. Position 312 and 345 are ~~mainly responsible for the difference between~~ type I ~~and~~ type II binding motif (AtLFY and PpLFY). In algae, LFY binds to the type III motif is largely because amino acid substitution disrupt the interface of dimer (TsLFY). In this figure, 3D structures were visualized by Pymol with assembly files of 2VY1 and 4BHK calculated by PISA. Lower 2D diagrams present how different LFY interact with three types of binding motifs. Information in the diagram were summarized from Hames et al. 2008, Sayou et al. 2014 and further visualized by keynote.]]

[[Image:LEAFY_Evolution.007.jpg|800px|Right|thumb| Figure 4. A summary of LEAFY evolution by substation on three different types of DNA binding motif. Position 312 and 345 are critical importance in determining type I or type II binding motif (AtLFY and PpLFY). In algae, LFY binds to the type III motif is largely because amino acid substitution disrupt the interface of dimer (TsLFY). In this figure, 3D structures were visualized by Pymol with assembly files of 2VY1 and 4BHK calculated by PISA. Lower 2D diagrams present how different LFY interact with three types of binding motifs. Information in the diagram were summarized from Hames et al. 2008, Sayou et al. 2014 and further visualized by keynote.]]

Different from other transcription factor families, LFY and its homologs retains as a single copy gene in almost all land plants. This brought a new entry point that how LFY evolved to control different developmental processes in other plant lineages. LFY homologs in mosses have been reported controlling cell division, through binding to a different motif rather than the one that was found in ''Arabidopsis''. Multiple alignment and a new method by systematic evolution of ligands by exponential enrichment (SELEX) of LFY and its homologs revealed that at specific position, few amino acids were substituted from angiosperms to algae to bind to specific motifs. Such motifs can be further categorized into three subgroups: Type I (angiosperm), type II (mosses) and type III (algae), which probably result in a diverged functionality. Crystal structure of DNA-protein complex composed of a moss LFY homolog from ''Physicomitrella patens'' and its binding sites further validated this hypothesis. In ''Arabidopsis'', site specific recognition of LFY is conducted by two residues located at a HTH motif. Interestingly, another residue 312D was found in the HTH motif mediating direct site specific recognition to a cytosine at the major groove.(figure 4, PpLFY) In contrast, 312 was occupied by a histidine and bond to a residue R345 from α7 in ''Arabidopsis'', and the DNA binding motif at the position is a guanine instead of a cytosine (figure 4, AtLFY). This structural difference finally result in a difference between type I and type II binding motif. Additionally, there are no difference in dimerization in binding type I and II motif, because three important residues mediating cooperative binding are not changed. In different from type I & II binding, LFY homologs in algea bind to the type III binding motif by a unique structure. Switching of His 387 to a Ser in the three critical cooperative binding site dramatically change the dimerization surface (figure 4, KsLFY). Here is a movie that showing how the LFY evolved. Surprisingly, a LFY homolog in hornwort, shares a promiscuous binding habit, that it can bind all three types of binding motifs. This phenomenon can be explained at structural. At 312 position, LFY homolog in ''N. aenigmaticus'' harbors a glutamine, which is identical to type algae LFY. However, 345C and 387H indicate the similar binding properties with type I and II. This finding give new insights about a single copy gene evolution, through a promiscuous intermediate. An interesting movie showing this progress very well: https://www.youtube.com/watch?v=Yvk3ond-WHk.

== Reference ==

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 </StructureSection>
 == LEAFY Evolution <ref name="Sayou2014" /> ==
-[[Image:LEAFY_Evolution.007.jpg|800px|Right|thumb| Figure 4. A summary of LEAFY evolution by substation in three residues on three different types of DNA binding motif. Position 312 and 345 are mainly responsible for the difference between type I and type II binding motif (AtLFY and PpLFY). In algae, LFY binds to the type III motif is largely because amino acid substitution disrupt the interface of dimer (TsLFY). In this figure, 3D structures were visualized by Pymol with assembly files of 2VY1 and 4BHK calculated by PISA. Lower 2D diagrams present how different LFY interact with three types of binding motifs. Information in the diagram were summarized from Hames et al. 2008, Sayou et al. 2014 and further visualized by keynote.]]
+[[Image:LEAFY_Evolution.007.jpg|800px|Right|thumb| Figure 4. A summary of LEAFY evolution by substation on three different types of DNA binding motif. Position 312 and 345 are critical importance in determining type I or type II binding motif (AtLFY and PpLFY). In algae, LFY binds to the type III motif is largely because amino acid substitution disrupt the interface of dimer (TsLFY). In this figure, 3D structures were visualized by Pymol with assembly files of 2VY1 and 4BHK calculated by PISA. Lower 2D diagrams present how different LFY interact with three types of binding motifs. Information in the diagram were summarized from Hames et al. 2008, Sayou et al. 2014 and further visualized by keynote.]]
 Different from other transcription factor families, LFY and its homologs retains as a single copy gene in almost all land plants. This brought a new entry point that how LFY evolved to control different developmental processes in other plant lineages. LFY homologs in mosses have been reported controlling cell division, through binding to a different motif rather than the one that was found in ''Arabidopsis''. Multiple alignment and a new method by systematic evolution of ligands by exponential enrichment (SELEX) of LFY and its homologs revealed that at specific position, few amino acids were substituted from angiosperms to algae to bind to specific motifs. Such motifs can be further categorized into three subgroups: Type I (angiosperm), type II (mosses) and type III (algae), which probably result in a diverged functionality. Crystal structure of DNA-protein complex composed of a moss LFY homolog from ''Physicomitrella patens'' and its binding sites further validated this hypothesis. In ''Arabidopsis'', site specific recognition of LFY is conducted by two residues located at a HTH motif. Interestingly, another residue 312D  was found in the HTH motif mediating direct site specific recognition to a cytosine at the major groove.(figure 4, PpLFY) In contrast, 312 was occupied by a histidine and bond to a residue R345 from α7 in ''Arabidopsis'', and the DNA binding motif at the position is a guanine instead of a cytosine (figure 4, AtLFY). This structural difference finally result in a difference between type I and type II binding motif. Additionally, there are no difference in dimerization in binding type I and II motif, because three important residues mediating cooperative binding are not changed. In different from type I & II binding, LFY homologs in algea bind to the type III binding motif by a unique structure. Switching of His 387 to a Ser in the three critical cooperative binding site dramatically change the dimerization surface (figure 4, KsLFY). Here is a movie that showing how the LFY evolved. Surprisingly, a LFY homolog in hornwort, shares a promiscuous binding habit, that it can bind all three types of binding motifs. This phenomenon can be explained at structural. At 312 position, LFY homolog in ''N. aenigmaticus'' harbors a glutamine, which is identical to type algae LFY. However, 345C and 387H indicate the similar binding properties with type I and II. This finding give new insights about a single copy gene evolution, through a promiscuous intermediate. An interesting movie showing this progress very well: https://www.youtube.com/watch?v=Yvk3ond-WHk.
 == Reference ==
 <references/>