New tangles in the auxin signaling web

F1000Prime Reports

Volumn 7, Issue , 2015, Pages

  Wright, R Clay ^a   Nemhauser, Jennifer L ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUXIN; AUXIN RESPONSE FACTOR; REPRESSOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; AUXIN RESPONSE ELEMENT; BINDING SITE; DIMERIZATION; DNA SEQUENCE; DNA STRUCTURE; GENOME; NONHUMAN; PLANT DEVELOPMENT; PLANT GROWTH; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; VASCULAR PLANT;

EMBRYOPHYTA;

EID: 84922384189     PISSN: None     EISSN: 20517599     Source Type: Journal    
DOI: 10.12703/P7-19     Document Type: Article

References (64)

1. De Smet I, Voss U, Lau S., Wilson M, Shao N, Timme R.E., Swarup R., Kerr I, Hodgman C, Bock R., Bennett M, Jürgens G, Beeckman T: Unraveling the evolution of auxin signaling. Plant Physiol 2011, 155:209-21.
2. Pickett FB, Wilson AK, Estelle M: The aux 1 Mutation of Arabidopsis Confers Both Auxin and Ethylene Resistance. Plant Physiol 1990, 94:1462-6.
3. Marchant A, Kargul J, May S.T., Muller P., Delbarre A, Perrot-Rechenmann C, Bennett MJ: AUX1 regulates root gravitropism in Arabidopsis by facilitating auxin uptake within root apical tissues. EMBO J 1999, 18:2066-73.
4. Friml J, Vieten A, Sauer M., Weijers D, Schwarz H, Hamann T., Offringa R, Jürgens G: Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis. Nature 2003, 426:147-53.
5. Petrásek J, Mravec J, Bouchard R., Blakeslee JJ, Abas M, Seifertová D, Wisniewska J, Tadele Z, Kubes M, Covanová M, Dhonukshe P, Skupa P, Benková E, Perry L, Krecek P, Lee OR, Fink GR, Geisler M, Murphy AS, Luschnig C, Zazímalová E, Friml J: PIN proteins perform a rate-limiting function in cellular auxin efflux. Science 2006, 312:914-8.
6. Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ: Composite structure of auxin response elements. Plant Cell 1995, 7:1611-23.
7. Ulmasov T, Hagen G, Guilfoyle TJ: ARF1, a transcription factor that binds to auxin response elements. Science 1997, 276:1865-8.
8. Ulmasov T, Murfett J, Hagen G., Guilfoyle TJ: Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell Online 1997, 9:1963-71.
9. Ruegger M, Dewey E, Gray W.M., Hobbie L., Turner J, Estelle M: The TIR1 protein of Arabidopsis functions in auxin response and is related to human SKP2 and yeast grr1p. Genes Dev 1998, 12:198-207.
10. Ulmasov T, Hagen G, Guilfoyle TJ: Dimerization and DNA binding of auxin response factors. Plant J Cell Mol Biol 1999, 19:309-19.
11. Ulmasov T, Hagen G, Guilfoyle TJ: Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci USA 1999, 96:5844-9.
12. Gray WM, Kepinski S, Rouse D., Leyser O, Estelle M: Auxin regulates SCF(TIR1)-dependent degradation of AUX/IAA proteins. Nature 2001,414:271-6.
13. Dharmasiri N, Dharmasiri S, Estelle M: The F-box protein TIR1 is an auxin receptor. Nature 2005, 435:441-5.
14. Kepinski S, Leyser O: The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 2005, 435:446-51.
15. Calderon-Villalobos LI, Tan X, Zheng N., Estelle M: Auxin perception-structural insights. Cold Spring Harb Perspect Biol 2010, 2: a005546.
16. Havens KA, Guseman JM, Jang S.S., Pierre-Jerome E, Bolten N, Klavins E., Nemhauser JL: A synthetic approach reveals extensive tunability of auxin signaling. Plant Physiol 2012, 160:135-42.
17. Calderón Villalobos LIA, Lee S, De Oliveira C, Ivetac A, Brandt W, Armitage L, Sheard LB, Tan X, Parry G, Mao H, Zheng N, Napier R, Kepinski S, Estelle M: A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin. Nat Chem Biol 2012, 8:477-85.
18. Vernoux T, Brunoud G, Farcot E., Morin V, Daele HV den, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J: The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol Syst Biol 2011, 7:508.
19. Shimizu-Mitao Y, Kakimoto T: Auxin Sensitivities of All Arabidopsis Aux/IAAs for Degradation in the Presence of Every TIR1/AFB. Plant Cell Physiol 2014, 55:1450-9.
20. Pierre-Jerome E, Moss BL, Nemhauser JL: Tuning the auxin transcriptional response. J Exp Bot 2013, 64:2557-63.
21. Peer WA: From perception to attenuation: auxin signalling and responses. Curr Opin Plant Biol 2013, 16:561-8.
22. Luschnig C, Vert G: The dynamics of plant plasma membrane proteins: PINs and beyond. Dev Camb Engl. 2014 Aug:141(15):2924-38.
23. Tivendale ND, Ross JJ, Cohen JD: The shifting paradigms of auxin biosynthesis. Trends Plant Sci 2014, 19:44-51.
24. Wang R, Estelle M: Diversity and specificity: auxin perception and signaling through the TIR1/AFB pathway. Curr Opin Plant Biol 2014, 21C:51-8.
25. Boer DR, Freire-Rios A, van den Berg WAM, Saaki T, Manfield IW, Kepinski S, López-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D, Coll M: Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors. Cell 2014, 156:577-89.
26. Korasick DA, Westfall CS, Lee S.G., Nanao MH, Dumas R, Hagen G, Guilfoyle T.J., Jez JM, Strader LC: Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression. Proc Natl Acad Sci 2014, 111: 5427-32.
27. Nanao MH, Vinos-Poyo T, Brunoud G., Thévenon E, Mazzoleni M., Mast D, Lainé S, Wang S, Hagen G, Li H, Guilfoyle TJ, Parcy F, Vernoux T, Dumas R: Structural basis for oligomerization of auxin transcriptional regulators. Nat Commun 2014, 5:3617.
28. Pierre-Jerome E, Jang SS, Havens K.A., Nemhauser JL, Klavins E: Recapitulation of the forward nuclear auxin response pathway in yeast. Proc Natl Acad Sci 2014, 111:9407-12.
29. Szemenyei H, Hannon M, Long JA: TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science 2008, 319:1384-6.
30. Parry G, Calderon-Villalobos LI, Prigge M., Peret B, Dharmasiri S, Itoh H., Lechner E, Gray WM, Bennett M, Estelle M: Complex regulation of the TIR1/AFB family of auxin receptors. Proc Natl Acad Sci 2009, 106:22540-5.
31. Overvoorde PJ, Okushima Y, Alonso J.M., Chan A., Chang C, Ecker JR, Hughes B, Liu A., Onodera C, Quach H, Smith A., Yu G, Theologis A: Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana. Plant Cell Online 2005, 17:3282-300.
32. Remington DL, Vision TJ, Guilfoyle T.J., Reed JW: Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol 2004, 135:1738-52.
33. Rademacher EH, Möller B, Lokerse A.S., Llavata-Peris CI, van den Berg W, Weijers D: A cellular expression map of the Arabidopsis AUXIN RESPONSE FACTOR gene family. Plant J 2011, 68:597-606.
34. Guilfoyle TJ, Hagen G: Getting a grasp on domain III/IV responsible for Auxin Response Factor-IAA protein interactions. Plant Sci 2012, 190:82-8.
35. Guilfoyle TJ, Ulmasov T, Hagen G: The ARF family of transcription factors and their role in plant hormone-responsive transcription. Cell Mol Life Sci CMLS 1998, 54:619-27.
36. Swaminathan K, Peterson K, Jack T: The plant B3 superfamily. Trends Plant Sci 2008, 13:647-55.
37. Tiwari SB, Hagen G, Guilfoyle T: The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 2003, 15:533-43.
38. Finet C, Berne-Dedieu A, Scutt C.P., Marlétaz F: Evolution of the ARF Gene Family in Land Plants: Old Domains, New Tricks. Mol Biol Evol 2013, 30:45-56.
39. Adams-Cioaba MA, Li Z, Tempel W., Guo Y, Bian C, Li Y., Lam R, Min J: Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins. FEBS Lett 2012, 586:859-65.
40. Weiste C, Dröge-Laser W: The Arabidopsis transcription factor bZIP11 activates auxin-mediated transcription by recruiting the histone acetylation machinery. Nat Commun 2014, 5:3883.
41. Nguyen HN, Kim JH, Jeong C.Y., Hong S-W, Lee H: Inhibition of histone deacetylation alters Arabidopsis root growth in response to auxin via PIN1 degradation. Plant Cell Rep 2013, 32:1625-36.
42. Anzola JM, Sieberer T, Ortbauer M., Butt H, Korbei B, Weinhofer I., Müllner AE, Luschnig C: Putative Arabidopsis Transcriptional Adaptor Protein (PROPORZ1) is required to modulate histone acetylation in response to auxin. Proc Natl Acad Sci 2010, 107: 10308-13.
43. Manzano C, Ramirez-Parra E, Casimiro I., Otero S, Desvoyes B, De Rybel B, Beeckman T, Casero P., Gutierrez C, C Del Pozo J: Auxin and epigenetic regulation of SKP2B, an F-box that represses lateral root formation. Plant Physiol 2012, 160:749-62.
44. Chapman EJ, Estelle M: Mechanism of auxin-regulated gene expression in plants. Annu Rev Genet 2009, 43:265-85.
45. Shin R, Burch AY, Huppert K.A., Tiwari SB, Murphy AS, Guilfoyle TJ, Schachtman DP: The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. Plant Cell 2007, 19: 2440-53.
46. Varaud E, Brioudes F, Szécsi J, Leroux J., Brown S, Perrot-Rechenmann C, Bendahmane M: AUXIN RESPONSE FACTOR8 regulates Arabidopsis petal growth by interacting with the bHLH transcription factor BIGPETALp. Plant Cell 2011, 23:973-83.
47. Oh E, Zhu J-Y, Bai M-Y, Arenhart RA, Sun Y, Wang Z-Y: Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. eLife 2014, 3.
48. Kim J, Harter K, Theologis A: Protein-protein interactions among the Aux/IAA proteins. Proc Natl Acad Sci 1997, 94:11786-91.
49. Rinaldi MA, Liu J, Enders T.A., Bartel B., Strader LC: A gain-of-function mutation in IAA16 confers reduced responses to auxin and abscisic acid and impedes plant growth and fertility. Plant Mol Biol 2012, 79:359-73.
50. Sullivan AM, Arsovski AA, Lempe J, Bubb K.L., Weirauch MT, Sabo PJ, Sandstrom R, Thurman R.E., Neph S., Reynolds AP, Stergachis AB, Vernot B, Johnson A.K., Haugen E., Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA: Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana. Cell Rep 2014, 8:2015-30.
51. Godoy M, Franco-Zorrilla JM, Pérez-Pérez J, Oliveros JC, Lorenzo O, Solano R: Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. Plant J Cell Mol Biol 2011, 66:700-11.
52. Nishimura K, Fukagawa T, Takisawa H., Kakimoto T, Kanemaki M: An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat Methods 2009, 6:917-22.
53. Deal RB, Henikoff S: The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc 2011, 6:56-68.
54. Zhang X, Yazaki J, Sundaresan A., Cokus S, Chan SW-L, Chen H, Henderson I.R., Shinn P., Pellegrini M, Jacobsen SE, Ecker JR.: Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis. Cell 2006, 126:1189-201.
55. Lewis DR, Olex AL, Lundy S.R., Turkett WH, Fetrow JS, Muday GK: A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis. Plant Cell Online 2013, 25:3329-46.
56. Rensing SA, Lang D, Zimmer A.D., Terry A., Salamov A, Shapiro H, Nishiyama T., Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T., Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, et al.: The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 2008, 319:64-9.
57. Prigge MJ, Lavy M, Ashton N.W., Estelle M: Physcomitrella patens Auxin-Resistant Mutants Affect Conserved Elements of an Auxin-Signaling Pathway. Curr Biol 2010, 20:1907-12.
58. Bowman JL, Floyd SK, Sakakibara K: Green Genes-Comparative Genomics of the Green Branch of Life. Cell 2007, 129:229-34.
59. Ishizaki K, Nonomura M, Kato H., Yamato KT, Kohchi T: Visualization of auxin-mediated transcriptional activation using a common auxin-responsive reporter system in the liverwort Marchantia polymorpha. J Plant Res 2012, 125:643-51.
60. Sugano SS, Shirakawa M, Takagi J., Matsuda Y, Shimada T, Hara-Nishimura I, Kohchi T: CRISPR/Cas9-Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L. Plant Cell Physiol 2014, 55:475-81.
61. Cove DJ, Perroud P-F, Charron AJ, McDaniel S.F., Khandelwal A., Quatrano RS: The Moss Physcomitrella patens: A Novel Model System for Plant Development and Genomic Studies. Cold Spring Harb Protoc 2009, 2009:pdb.emo1 15.
62. Ishizaki K, Johzuka-Hisatomi Y, Ishida S., Iida S, Kohchi T: Homologous recombination-mediated gene targeting in the liverwort Marchantia polymorpha L. Sci Rep 2013, 3:1532.
63. Tromas A, Paque S, Stierlé V, Quettier A-L, Muller P, Lechner E, Genschik P, Perrot-Rechenmann C: Auxin-binding protein 1 is a negative regulator of the SCF(TIR1/AFB) pathway. Nat Commun 2013, 4:2496.
64. Xu T, Dai N, Chen J., Nagawa S, Cao M, Li H., Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones AM, Friml J, Patterson SE, Bleecker AB, Yang Z: Cell Surface ABP1-TMK Auxin-Sensing Complex Activates ROP GTPase Signaling. Science 2014, 343:1025-8.