Sandbox Reserved 933: Difference between revisions

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== Introduction ==

[[Image:Organ_identity.jpg|600px|left|thumb| Schematic presentation LEAFY regulatory roles in controlling floral organ identity (A) and the ABC model in ''Arabidopsis thaliana'' (B). ]]

'''''FLORICAULA/LEAFY'' (''FLO/LFY'')''' genes encode a plant specific transcription factor family that controlling floral fate of reproductive phase. <ref name="Weigel1992"> Detlef Weigel, John Alvarez, David R. Smyth, Martin F. Yanofsky, Elliot M. Meyerowitz, LEAFY controls floral meristem identity in Arabidopsis. Cell 69 :843-859, http://dx.doi.org/10.1016/0092-8674(92)90295-N.</ref> In the plant model system ''Arabidopsis thaliana '', ‘’LFY’’ also acts upstream of floral homeotic genes to modulate organ identity. <ref name= ''Irish2010'' > Irish, V. F. (2010), The flowering of Arabidopsis flower development. The Plant Journal, 61: 1014–1028. http://doi:10.1111/j.1365-313X.2009.04065.x

'''''FLORICAULA/LEAFY'' (''FLO/LFY'')''' genes encode a plant specific transcription factor family that controlling floral fate of reproductive phase. <ref name="Weigel1992"> Detlef Weigel, John Alvarez, David R. Smyth, Martin F. Yanofsky, Elliot M. Meyerowitz, LEAFY controls floral meristem identity in Arabidopsis. Cell 69 :843-859, http://dx.doi.org/10.1016/0092-8674(92)90295-N.</ref> In the plant model system ''Arabidopsis thaliana '', ‘’LFY’’ also acts upstream of floral homeotic genes to modulate organ identity. <ref name= ''Irish2010'' > Irish, V. F. (2010), The flowering of Arabidopsis flower development. The Plant Journal, 61: 1014–1028. http://doi:10.1111/j.1365-313X.2009.04065.x </ref> LFY activates the organ identity genes by binding to promoter regions of floral organ identity genes. LFY can directly bind to the promoter to '''''APELATA1'' (''AP1'')''', while co-regulators '''''UNUSUAL FLORAL ORGANS'' (''UFO'')''' <ref name= ''Chae2008'' >Chae, E., Tan, Q.K., Hill, T.A. & Irish, V.F. 2008. An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development. Development 135:1235-45 http:// doi: 10.1242/dev.015842</ref> and '''''WUSCHEL'' (''WUS'')'''<ref name= ''Siriwardana2012'' >Siriwardana, N. S. & Lamb, R. S. 2012. A conserved domain in the N-terminus is important for LEAFY dimerization and function in Arabidopsis thaliana. The Plant Journal 71: 736–749. http://doi/10.1111/j.1365-313X.2012.05026.x</ref> are required for increment of binding affinity to promoter regions of '''''APELATA3'' (''AP3'')''' and '''''AGAMOUS'' (''AG'')''', respectively. The exact mechanism how LFY binds to these promoters has yet to be well elucidated until the first structure report about <scene name='57/579703/Ap1-dimer/1'>LFY-pAP1</scene> and <scene name='57/579703/2vy2_assembly/1'>LFY-pAG</scene> (ref 5). Among land plants, FLO/LFY homologs share a highly conserved DNA binding region that a hypothesis claimed substitution in this domain might result in the functional divergence (ref 6). Recently, a new study (ref 7) provided new insights of structural basis of LEAFY evolution by changing DNA binding activity.

</ref> LFY activates the organ identity genes by binding to promoter regions of floral organ identity genes. LFY can directly bind to the promoter to '''''APELATA1'' (''AP1'')''', while co-regulators '''''UNUSUAL FLORAL ORGANS'' (''UFO'')''' (ref 3) and '''''WUSCHEL'' (''WUS'')''' (ref 4) are required for increment of binding affinity to promoter regions of '''''APELATA3'' (''AP3'')''' and '''''AGAMOUS'' (''AG'')''', respectively. The exact mechanism how LFY binds to these promoters has yet to be well elucidated until the first structure report about <scene name='57/579703/Ap1-dimer/1'>LFY-pAP1</scene> and <scene name='57/579703/2vy2_assembly/1'>LFY-pAG</scene> (ref 5). Among land plants, FLO/LFY homologs share a highly conserved DNA binding region that a hypothesis claimed substitution in this domain might result in the functional divergence (ref 6). Recently, a new study (ref 7) provided new insights of structural basis of LEAFY evolution by changing DNA binding activity.

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The general structure of LEAFY DNA binding domain consists 2 <scene name='57/579703/Beta-strand/1'>β strands</scene> at the beginning followed by 7 <scene name='57/579703/Alpha-helices_color/2'> α helices</scene>. A <scene name='57/579703/Alpha-helices_color/3'>helix-turn-helix</scene> (HTH) motif can be found between α2 and α3 helices, which is recruited to the <scene name='57/579703/Major_groove/2'>major groove </scene>of the binding DNA. There are two amino acid at this motif, <scene name='57/579703/Major_groove_asn291/1'>Asn 291</scene> on α2 and <scene name='57/579703/Major_groove_asn291/2'>Lys 307</scene> on α3 directly mediate site specific recognition with <scene name='57/579703/Major_groove_detail/1'>two guanines</scene> at the DNA strand. These two recognition sites were further validated by electrophoresis mobility shift assay (EMSA): mutation at either Asn 291 or Lys 307 dramatically decrease binding affinity to pAP1. In the minor groove, site specific recognition is conducted by <scene name='57/579703/Arg_237/1'>Arg 237</scene>, which is at the beginning of this structure. ''Arabidopsis'' intermediate mutant ''lfy-4'' (P240L) and ''lfy-5'' (T244M) were located near this site and validate the function ''in planta''. The detail site specific recognition is summaries at right figure produced by PyMol.

=== DNA binding required cooperative dimerization ===

Transcription factors tent to form homodimer or heterodimer to increase the binding specificity and affinity. Experimental evidence indicates a potential LFY dimer on the binding site. Crystal structure proved that LFY can form dimers at both <scene name='57/579703/Ap1-dimer/2'>pAP1</scene> and <scene name='57/579703/2vy2_assembly/2'>pAG</scene> sites. The binding affinity of LFY protein dimer binds increased by 90-fold compared to the first LFY monomer in EMSA assay. Detailed structure revealed that the contact of two dimerized protein is mediated by <scene name='57/579703/Ap1-dimer/8'>three residues</scene> located at on helix (<scene name='57/579703/Ap1-dimer/3'>α7</scene>) and one loop (<scene name='57/579703/Ap1-dimer/4'>loop12</scene>) at the other protein. Hydrogen bonds can be formed between <scene name='57/579703/Ap1-dimer/7'>Asn 290</scene> and <scene name='57/579703/Ap1-dimer/5'>His 387</scene>/<scene name='57/579703/Ap1-dimer/6'>Arg 390</scene> are essential for this dimeriation. The detailed interaction is shown in the right figure produced by Pymol. Mutation in any of these three amino acids abolished the binding in EMSA assay. Recently, another experiment showing that despite these three residues, the entire N-terminal consensus is critical important for stabilizing the homodimerization, where strong physical interaction can be found by GST-pull down, Y2H and BiFC experiment at in vitro, in vivo and in planta level.

Transcription factors tent to form homodimer or heterodimer to increase the binding specificity and affinity. Experimental evidence indicates a potential LFY dimer on the binding site. Crystal structure proved that LFY can form dimers at both <scene name='57/579703/Ap1-dimer/2'>pAP1</scene> and <scene name='57/579703/2vy2_assembly/2'>pAG</scene> sites. The binding affinity of LFY protein dimer binds increased by 90-fold compared to the first LFY monomer in EMSA assay. Detailed structure revealed that the contact of two dimerized protein is mediated by <scene name='57/579703/Ap1-dimer/8'>three residues</scene> located at on helix (<scene name='57/579703/Ap1-dimer/3'>α7</scene>) and one loop (<scene name='57/579703/Ap1-dimer/4'>loop12</scene>) at the other protein. Hydrogen bonds can be formed between <scene name='57/579703/Ap1-dimer/7'>Asn 290</scene> and <scene name='57/579703/Ap1-dimer/5'>His 387</scene>/<scene name='57/579703/Ap1-dimer/6'>Arg 390</scene> are essential for this dimeriation. The detailed interaction is shown in the right figure produced by Pymol. Mutation in any of these three amino acids abolished the binding in EMSA assay. Recently, another experiment showing that despite these three residues, the entire N-terminal consensus is critical important for stabilizing the homodimerization, where strong physical interaction can be found by GST-pull down, Y2H and BiFC experiment at ''in vitro'', ''in vivo'' and ''in planta'' level.

</StructureSection>

== LEAFY Evolution ==

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@@ Line 8: / Line 8: @@
 == Introduction ==
 [[Image:Organ_identity.jpg|600px|left|thumb| Schematic presentation LEAFY regulatory roles in controlling floral organ identity (A) and the ABC model in ''Arabidopsis thaliana'' (B). ]]
-'''''FLORICAULA/LEAFY'' (''FLO/LFY'')''' genes encode a plant specific transcription factor family that controlling floral fate of reproductive phase. <ref name="Weigel1992"> Detlef Weigel, John Alvarez, David R. Smyth, Martin F. Yanofsky, Elliot M. Meyerowitz, LEAFY controls floral meristem identity in Arabidopsis. Cell 69 :843-859, http://dx.doi.org/10.1016/0092-8674(92)90295-N.</ref> In the plant model system ''Arabidopsis thaliana '', ‘’LFY’’ also acts upstream of floral homeotic genes to modulate organ identity. <ref name= ''Irish2010'' > Irish, V. F. (2010), The flowering of Arabidopsis flower development. The Plant Journal, 61: 1014–1028.  http://doi:10.1111/j.1365-313X.2009.04065.x
+'''''FLORICAULA/LEAFY'' (''FLO/LFY'')''' genes encode a plant specific transcription factor family that controlling floral fate of reproductive phase. <ref name="Weigel1992"> Detlef Weigel, John Alvarez, David R. Smyth, Martin F. Yanofsky, Elliot M. Meyerowitz, LEAFY controls floral meristem identity in Arabidopsis. Cell 69 :843-859, http://dx.doi.org/10.1016/0092-8674(92)90295-N.</ref> In the plant model system ''Arabidopsis thaliana '', ‘’LFY’’ also acts upstream of floral homeotic genes to modulate organ identity. <ref name= ''Irish2010'' > Irish, V. F. (2010), The flowering of Arabidopsis flower development. The Plant Journal, 61: 1014–1028.  http://doi:10.1111/j.1365-313X.2009.04065.x </ref>   LFY activates the organ identity genes by binding to promoter regions of floral organ identity genes. LFY can directly bind to the promoter to '''''APELATA1'' (''AP1'')''', while co-regulators '''''UNUSUAL FLORAL ORGANS'' (''UFO'')''' <ref name= ''Chae2008'' >Chae, E., Tan, Q.K., Hill, T.A. & Irish, V.F. 2008. An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development. Development 135:1235-45  http:// doi: 10.1242/dev.015842</ref> and '''''WUSCHEL'' (''WUS'')'''<ref name= ''Siriwardana2012'' >Siriwardana, N. S. & Lamb, R. S. 2012. A conserved domain in the N-terminus is important for LEAFY dimerization and function in Arabidopsis thaliana. The Plant Journal 71: 736–749. http://doi/10.1111/j.1365-313X.2012.05026.x</ref> are required for increment of binding affinity to promoter regions of '''''APELATA3'' (''AP3'')''' and '''''AGAMOUS'' (''AG'')''', respectively. The exact mechanism how LFY binds to these promoters has yet to be well elucidated until the first structure report about <scene name='57/579703/Ap1-dimer/1'>LFY-pAP1</scene> and <scene name='57/579703/2vy2_assembly/1'>LFY-pAG</scene> (ref 5). Among land plants, FLO/LFY homologs share a highly conserved DNA binding region that a hypothesis claimed substitution in this domain might result in the functional divergence (ref 6). Recently, a new study (ref 7) provided new insights of structural basis of LEAFY evolution by changing DNA binding activity.
-</ref>   LFY activates the organ identity genes by binding to promoter regions of floral organ identity genes. LFY can directly bind to the promoter to '''''APELATA1'' (''AP1'')''', while co-regulators '''''UNUSUAL FLORAL ORGANS'' (''UFO'')''' (ref 3) and '''''WUSCHEL'' (''WUS'')''' (ref 4) are required for increment of binding affinity to promoter regions of '''''APELATA3'' (''AP3'')''' and '''''AGAMOUS'' (''AG'')''', respectively. The exact mechanism how LFY binds to these promoters has yet to be well elucidated until the first structure report about <scene name='57/579703/Ap1-dimer/1'>LFY-pAP1</scene> and <scene name='57/579703/2vy2_assembly/1'>LFY-pAG</scene> (ref 5). Among land plants, FLO/LFY homologs share a highly conserved DNA binding region that a hypothesis claimed substitution in this domain might result in the functional divergence (ref 6). Recently, a new study (ref 7) provided new insights of structural basis of LEAFY evolution by changing DNA binding activity.
@@ Line 19: / Line 18: @@
 The general structure of LEAFY DNA binding domain consists 2 <scene name='57/579703/Beta-strand/1'>β strands</scene> at the beginning followed by 7 <scene name='57/579703/Alpha-helices_color/2'> α helices</scene>. A <scene name='57/579703/Alpha-helices_color/3'>helix-turn-helix</scene> (HTH) motif can be found between α2 and  α3 helices, which is recruited to the <scene name='57/579703/Major_groove/2'>major groove </scene>of the binding DNA. There are two amino acid at this motif, <scene name='57/579703/Major_groove_asn291/1'>Asn 291</scene> on α2 and <scene name='57/579703/Major_groove_asn291/2'>Lys 307</scene> on α3 directly mediate site specific recognition with <scene name='57/579703/Major_groove_detail/1'>two guanines</scene> at the DNA strand. These two recognition sites were further validated by electrophoresis mobility shift assay (EMSA): mutation at either Asn 291 or Lys 307 dramatically decrease binding affinity to pAP1. In the minor groove, site specific recognition is conducted by <scene name='57/579703/Arg_237/1'>Arg 237</scene>, which is at the beginning of this structure. ''Arabidopsis'' intermediate mutant ''lfy-4'' (P240L) and ''lfy-5'' (T244M) were located near this site and validate the function ''in planta''. The detail site specific recognition is summaries at right figure produced by PyMol.
 === DNA binding required cooperative dimerization ===
-Transcription factors tent to form homodimer or heterodimer to increase the binding specificity and affinity. Experimental evidence indicates a potential LFY dimer on the binding site. Crystal structure proved that LFY can form dimers at both <scene name='57/579703/Ap1-dimer/2'>pAP1</scene> and <scene name='57/579703/2vy2_assembly/2'>pAG</scene> sites. The binding affinity of LFY protein dimer binds increased by 90-fold compared to the first LFY monomer in EMSA assay. Detailed structure revealed that the contact of two dimerized protein is mediated by <scene name='57/579703/Ap1-dimer/8'>three residues</scene> located at on helix (<scene name='57/579703/Ap1-dimer/3'>α7</scene>) and one loop (<scene name='57/579703/Ap1-dimer/4'>loop12</scene>) at the other protein. Hydrogen bonds can be formed between <scene name='57/579703/Ap1-dimer/7'>Asn 290</scene> and <scene name='57/579703/Ap1-dimer/5'>His 387</scene>/<scene name='57/579703/Ap1-dimer/6'>Arg 390</scene> are essential for this dimeriation. The detailed interaction is shown in the right figure produced by Pymol. Mutation in any of these three amino acids abolished the binding in EMSA assay. Recently, another experiment showing that despite these three residues, the entire N-terminal consensus is critical important for stabilizing the homodimerization, where strong physical interaction can be found by GST-pull down, Y2H and BiFC experiment at in vitro, in vivo and in planta level.
+Transcription factors tent to form homodimer or heterodimer to increase the binding specificity and affinity. Experimental evidence indicates a potential LFY dimer on the binding site. Crystal structure proved that LFY can form dimers at both <scene name='57/579703/Ap1-dimer/2'>pAP1</scene> and <scene name='57/579703/2vy2_assembly/2'>pAG</scene> sites. The binding affinity of LFY protein dimer binds increased by 90-fold compared to the first LFY monomer in EMSA assay. Detailed structure revealed that the contact of two dimerized protein is mediated by <scene name='57/579703/Ap1-dimer/8'>three residues</scene> located at on helix (<scene name='57/579703/Ap1-dimer/3'>α7</scene>) and one loop (<scene name='57/579703/Ap1-dimer/4'>loop12</scene>) at the other protein. Hydrogen bonds can be formed between <scene name='57/579703/Ap1-dimer/7'>Asn 290</scene> and <scene name='57/579703/Ap1-dimer/5'>His 387</scene>/<scene name='57/579703/Ap1-dimer/6'>Arg 390</scene> are essential for this dimeriation. The detailed interaction is shown in the right figure produced by Pymol. Mutation in any of these three amino acids abolished the binding in EMSA assay. Recently, another experiment showing that despite these three residues, the entire N-terminal consensus is critical important for stabilizing the homodimerization, where strong physical interaction can be found by GST-pull down, Y2H and BiFC experiment at ''in vitro'', ''in vivo'' and ''in planta'' level.
 </StructureSection>
 == LEAFY Evolution ==