Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA

Pathak, Prabhat Kumar; Zhang, Fei; Peng, Shuxia; Niu, Lifang; Chaturvedi, Juhi; Elliott, Justin; Xiang, Yan; Tadege, Million; Deng, Junpeng

doi:10.1107/S205979832100632X

Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA

Journal Article · 01 August 2021 · Acta Crystallogr. D

DOI:https://doi.org/10.1107/S205979832100632X· OSTI ID:1847112

Pathak, Prabhat Kumar; Zhang, Fei; Peng, Shuxia; Niu, Lifang; Chaturvedi, Juhi; Elliott, Justin; Xiang, Yan; Tadege, Million; Deng, Junpeng

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH); OTHER U.S. STATES

OSTI ID:: 1847112

Journal Information:: Acta Crystallogr. D, Vol. 77, Issue (8)

Country of Publication:: United States

Language:: ENGLISH

References (63)

Electrostatics of nanosystems: Application to microtubules and the ribosome Baker, N. A.; Sept, D.; Joseph, S. Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041 https://doi.org/10.1073/pnas.181342398	journal	August 2001
Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals Burglin, T. R. Nucleic Acids Research, Vol. 25, Issue 21 https://doi.org/10.1093/nar/25.21.4173	journal	November 1997
Homeodomain proteins: an update Bürglin, Thomas R.; Affolter, Markus Chromosoma, Vol. 125, Issue 3 https://doi.org/10.1007/s00412-015-0543-8	journal	October 2015
Transcriptional Control of a Plant Stem Cell Niche Busch, Wolfgang; Miotk, Andrej; Ariel, Federico D. Developmental Cell, Vol. 18, Issue 5 https://doi.org/10.1016/j.devcel.2010.03.012	journal	May 2010
The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis Causier, Barry; Ashworth, Mary; Guo, Wenjia Plant Physiology, Vol. 158, Issue 1 https://doi.org/10.1104/pp.111.186999	journal	November 2011
Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens Chaikuad, Apirat; Knapp, Stefan; von Delft, Frank Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 8 https://doi.org/10.1107/S1399004715007968	journal	July 2015
The role of WOX genes in flower development Costanzo, Enrico; Trehin, Christophe; Vandenbussche, Michiel Annals of Botany, Vol. 114, Issue 7 https://doi.org/10.1093/aob/mcu123	journal	June 2014
An improved protocol for rapid freezing of protein samples for long-term storage Deng, Junpeng; Davies, Douglas R.; Wisedchaisri, Goragot Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 1 https://doi.org/10.1107/S0907444903024491	journal	December 2003
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Dolinsky, T. J.; Czodrowski, P.; Li, H. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm276	journal	May 2007
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A. Nucleic Acids Research, Vol. 32, Issue Web Server, p. W665-W667 https://doi.org/10.1093/nar/gkh381	journal	July 2004
Stem Cell Regulation by Arabidopsis WOX Genes Dolzblasz, Alicja; Nardmann, Judith; Clerici, Elena Molecular Plant, Vol. 9, Issue 7 https://doi.org/10.1016/j.molp.2016.04.007	journal	July 2016
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties Fleming, Patrick J.; Fleming, Karen G. Biophysical Journal, Vol. 114, Issue 4 https://doi.org/10.1016/j.bpj.2018.01.002	journal	February 2018
Comparison of X-ray and NMR structures for the Antennapedia homeodomain–DNA complex Fraenkel, Ernest; Pabo, Carl O. Nature Structural & Molecular Biology, Vol. 5, Issue 8 https://doi.org/10.1038/1382	journal	August 1998
The genesis and evolution of homeobox gene clusters Garcia-Fernàndez, Jordi Nature Reviews Genetics, Vol. 6, Issue 12 https://doi.org/10.1038/nrg1723	journal	November 2005
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins Gouet, P. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg556	journal	July 2003
The WUS homeobox-containing (WOX) protein family van der Graaff, Eric; Laux, Thomas; Rensing, Stefan A. Genome Biology, Vol. 10, Issue 12 https://doi.org/10.1186/gb-2009-10-12-248	journal	January 2009
Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana Haecker, A. Development, Vol. 131, Issue 3 https://doi.org/10.1242/dev.00963	journal	January 2004
Transcriptional circuits in control of shoot stem cell homeostasis Han, Han; Liu, Xing; Zhou, Yun Current Opinion in Plant Biology, Vol. 53 https://doi.org/10.1016/j.pbi.2019.10.004	journal	February 2020
Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean Hao, Qingnan; Zhang, Ling; Yang, Yanyan Plants, Vol. 8, Issue 7 https://doi.org/10.3390/plants8070215	journal	July 2019
TDIF Peptide Signaling Regulates Vascular Stem Cell Proliferation via the WOX4 Homeobox Gene in Arabidopsis Hirakawa, Yuki; Kondo, Yuki; Fukuda, Hiroo The Plant Cell, Vol. 22, Issue 8 https://doi.org/10.1105/tpc.110.076083	journal	August 2010
Arabidopsis WUSCHEL Is a Bifunctional Transcription Factor That Acts as a Repressor in Stem Cell Regulation and as an Activator in Floral Patterning Ikeda, Miho; Mitsuda, Nobutaka; Ohme-Takagi, Masaru The Plant Cell, Vol. 21, Issue 11 https://doi.org/10.1105/tpc.109.069997	journal	November 2009
WUSCHEL: a master regulator in plant growth signaling Jha, Priyanka; Ochatt, Sergio J.; Kumar, Vijay Plant Cell Reports, Vol. 39, Issue 4 https://doi.org/10.1007/s00299-020-02511-5	journal	January 2020
WOX4 Promotes Procambial Development Ji, Jiabing; Strable, Josh; Shimizu, Rena Plant Physiology, Vol. 152, Issue 3 https://doi.org/10.1104/pp.109.149641	journal	December 2009
Analysis of the Transcription Factor WUSCHEL and Its Functional Homologue in Antirrhinum Reveals a Potential Mechanism for Their Roles in Meristem Maintenance Kieffer, Martin; Stern, Yaniv; Cook, Holly The Plant Cell, Vol. 18, Issue 3 https://doi.org/10.1105/tpc.105.039107	journal	February 2006
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Krissinel, E.; Henrick, K. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12 https://doi.org/10.1107/S0907444904026460	journal	November 2004
Structural basis for antagonism of human interleukin 18 by poxvirus interleukin 18-binding protein Krumm, B.; Meng, X.; Li, Y. Proceedings of the National Academy of Sciences, Vol. 105, Issue 52 https://doi.org/10.1073/pnas.0809086106	journal	December 2008
Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior LaRonde-LeBlanc, Nicole A.; Wolberger, Cynthia Genes & Development, Vol. 17, Issue 16 https://doi.org/10.1101/gad.1103303	journal	August 2003
The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis Laux, T.; Mayer, K. F.; Berger, J. Development, Vol. 122, Issue 1 https://doi.org/10.1242/dev.122.1.87	journal	January 1996
Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA Lee, John K.; Bosnakovski, Darko; Toso, Erik A. Cell Reports, Vol. 25, Issue 11 https://doi.org/10.1016/j.celrep.2018.11.060	journal	December 2018
Crystal Structure of the MATa1/MATα2 Homeodomain Heterodimer Bound to DNA Li, Thomas; Stark, Martha R.; Johnson, Alexer D. Science, Vol. 270, Issue 5234 https://doi.org/10.1126/science.270.5234.262	journal	October 1995
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Evolutionarily conserved repressive activity of WOX proteins mediates leaf blade outgrowth and floral organ development in plants Lin, H.; Niu, L.; McHale, N. A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 1 https://doi.org/10.1073/pnas.1215376110	journal	December 2012
STENOFOLIA acts as a repressor in regulating leaf blade outgrowth Lin, Hao; Niu, Lifang; Tadege, Million Plant Signaling & Behavior, Vol. 8, Issue 6 https://doi.org/10.4161/psb.24464	journal	June 2013
The STENOFOLIA gene from Medicago alters leaf width, flowering time and chlorophyll content in transgenic wheat Liu, Meiyan; Lei, Lei; Miao, Fang Plant Biotechnology Journal, Vol. 16, Issue 1 https://doi.org/10.1111/pbi.12759	journal	June 2017
A Molecular Link between Stem Cell Regulation and Floral Patterning in Arabidopsis Lohmann, Jan U.; Hong, Ray L.; Hobe, Martin Cell, Vol. 105, Issue 6 https://doi.org/10.1016/S0092-8674(01)00384-1	journal	June 2001
Structural Basis of Disease-Causing Mutations in Hepatocyte Nuclear Factor 1β ^, Lu, Peng; Rha, Geun Bae; Chi, Young-In Biochemistry, Vol. 46, Issue 43 https://doi.org/10.1021/bi7010527	journal	October 2007
Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression Martin-Arevalillo, Raquel; Nanao, Max H.; Larrieu, Antoine Proceedings of the National Academy of Sciences, Vol. 114, Issue 30 https://doi.org/10.1073/pnas.1703054114	journal	July 2017
Role of WUSCHEL in Regulating Stem Cell Fate in the Arabidopsis Shoot Meristem Mayer, Klaus F. X.; Schoof, Heiko; Haecker, Achim Cell, Vol. 95, Issue 6 https://doi.org/10.1016/S0092-8674(00)81703-1	journal	December 1998
Solving structures of protein complexes by molecular replacement with Phaser McCoy, Airlie J. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1 https://doi.org/10.1107/S0907444906045975	journal	December 2006
HEADLESS , a WUSCHEL homolog, uncovers novel aspects of shoot meristem regulation and leaf blade development in Medicago truncatula Meng, Yingying; Liu, Huan; Wang, Hui Journal of Experimental Botany, Vol. 70, Issue 1 https://doi.org/10.1093/jxb/ery346	journal	September 2018
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906019949	journal	July 2006
Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless Miyazono, Ken-ichi; Zhi, Yuehua; Takamura, Yuriko The EMBO Journal, Vol. 29, Issue 9 https://doi.org/10.1038/emboj.2010.53	journal	April 2010
A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes Mukherjee, K.; Brocchieri, L.; Burglin, T. R. Molecular Biology and Evolution, Vol. 26, Issue 12 https://doi.org/10.1093/molbev/msp201	journal	September 2009
Members of TALE and WUS subfamilies of homeodomain proteins with potentially important functions in development form dimers within each subfamily in rice Nagasaki, Hiroshi; Matsuoka, Makoto; Sato, Yutaka Genes & Genetic Systems, Vol. 80, Issue 4 https://doi.org/10.1266/ggs.80.261	journal	January 2005
Roles of the Middle Domain–Specific WUSCHEL-RELATED HOMEOBOX Genes in Early Development of Leaves in Arabidopsis Nakata, Miyuki; Matsumoto, Noritaka; Tsugeki, Ryuji The Plant Cell, Vol. 24, Issue 2 https://doi.org/10.1105/tpc.111.092858	journal	February 2012
Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites Noyes, Marcus B.; Christensen, Ryan G.; Wakabayashi, Atsuya Cell, Vol. 133, Issue 7 https://doi.org/10.1016/j.cell.2008.05.023	journal	June 2008
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape O’Malley, Ronan C.; Huang, Shao-shan Carol; Song, Liang Cell, Vol. 165, Issue 5 https://doi.org/10.1016/j.cell.2016.04.038	journal	May 2016
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion Painter, Jay; Merritt, Ethan A. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4 https://doi.org/10.1107/S0907444906005270	journal	March 2006
Structure of a DNA-bound Ultrabithorax–Extradenticle homeodomain complex Passner, Jonathan M.; Ryoo, Hyung Don; Shen, Leyi Nature, Vol. 397, Issue 6721 https://doi.org/10.1038/17833	journal	February 1999
Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers Sarkar, Ananda K.; Luijten, Marijn; Miyashima, Shunsuke Nature, Vol. 446, Issue 7137 https://doi.org/10.1038/nature05703	journal	April 2007
Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL Sloan, Jeremy; Hakenjos, Jana P.; Gebert, Michael Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16024-y	journal	May 2020
Shoot meristem maintenance is controlled by a GRAS -gene mediated signal from differentiating cells Stuurman, Jeroen; Jäggi, Fabienne; Kuhlemeier, Cris Genes & Development, Vol. 16, Issue 17 https://doi.org/10.1101/gad.230702	journal	September 2002
Control of dicot leaf blade expansion by a WOX gene, STF Tadege, Million; Lin, Hao; Niu, Lifang Plant Signaling & Behavior, Vol. 6, Issue 11 https://doi.org/10.4161/psb.6.11.17761	journal	November 2011
Differential Recruitment of WOX Transcription Factors for Lateral Development and Organ Fusion in Petunia and Arabidopsis Vandenbussche, Michiel; Horstman, Anneke; Zethof, Jan The Plant Cell, Vol. 21, Issue 8 https://doi.org/10.1105/tpc.109.065862	journal	August 2009
HEADLESS Regulates Auxin Response and Compound Leaf Morphogenesis in Medicago truncatula Wang, Hongfeng; Xu, Yiteng; Hong, Limei Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01024	journal	August 2019
Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions Wolberger, Cynthia; Vershon, Andrew K.; Liu, Beishan Cell, Vol. 67, Issue 3 https://doi.org/10.1016/0092-8674(91)90526-5	journal	November 1991
Large-scale phylogenomic analysis suggests three ancient superclades of the WUSCHEL-RELATED HOMEOBOX transcription factor family in plants Wu, Cheng-Chiang; Li, Fay-Wei; Kramer, Elena M. PLOS ONE, Vol. 14, Issue 10 https://doi.org/10.1371/journal.pone.0223521	journal	October 2019
WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex Yadav, Ram Kishor; Perales, Mariano; Gruel, Jérémy Genes & Development, Vol. 25, Issue 19 https://doi.org/10.1101/gad.17258511	journal	October 2011
STENOFOLIA Recruits TOPLESS to Repress ASYMMETRIC LEAVES2 at the Leaf Margin and Promote Leaf Blade Outgrowth in Medicago truncatula Zhang, Fei; Wang, Yewei; Li, Guifen The Plant Cell, Vol. 26, Issue 2 https://doi.org/10.1105/tpc.113.121947	journal	February 2014
An L1 box binding protein, GbML1, interacts with GbMYB25 to control cotton fibre development Zhang, Fei; Zuo, Kaijing; Zhang, Jieqiong Journal of Experimental Botany, Vol. 61, Issue 13 https://doi.org/10.1093/jxb/erq173	journal	July 2010
Structural Basis for Sequence Specific DNA Binding and Protein Dimerization of HOXA13 Zhang, Yonghong; Larsen, Christine A.; Stadler, H. Scott PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0023069	journal	August 2011
Control of plant stem cell function by conserved interacting transcriptional regulators Zhou, Yun; Liu, Xing; Engstrom, Eric M. Nature, Vol. 517, Issue 7534 https://doi.org/10.1038/nature13853	journal	October 2014

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