A comprehensive analysis of microproteins reveals their potentially widespread mechanism of transcriptional regulation

Plant Physiology

Volumn 165, Issue 1, 2014, Pages 149-159

  Magnani, Enrico ^a,b   de Klein, Niek ^a   Nam, Hye In ^a   Kim, Jung Gun ^c   Pham, Kimberly ^a   Fiume, Elisa ^b   Mudgett, Mary Beth ^c   Rhee, Seung Yon ^a  

^a GEOPHYSICAL LABORATORY   (United States)

^b INSTITUT JEAN PIERRE BOURGIN   (France)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; TRANSCRIPTION FACTOR;

ANIMAL; ARABIDOPSIS; DISEASE RESISTANCE; FLOWER; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; IMMUNOLOGY; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; PLANT DISEASE; TIME;

ANIMALS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DISEASE RESISTANCE; EVOLUTION, MOLECULAR; FLOWERS; GENE EXPRESSION REGULATION, PLANT; PHYLOGENY; PLANT DISEASES; TIME FACTORS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84899795284     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.114.235903     Document Type: Article

References (55)

1. Alifragis P, Poortinga G, Parkhurst SM, Delidakis C (1997) A network of interacting transcriptional regulators involved in Drosophila neural fate specification revealed by the yeast two-hybrid system. Proc Natl Acad Sci USA 94: 13099-13104
2. Arabidopsis Interactome Mapping Consortium (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333: 601-607
3. Arata Y, Kouike H, Zhang Y, HermanMA, Okano H, Sawa H (2006) Wnt signaling and a Hox protein cooperatively regulate psa-3/Meis to determine daughter cell fate after asymmetric cell division in C. elegans. Dev Cell 11: 105-115
4. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al (2004) The Pfam protein families database. Nucleic Acids Res 32: D138-D141
5. Bentsink L, Jowett J, Hanhart CJ, Koornneef M (2006) Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Acad Sci USA 103: 17042-17047
6. Blanc G, Hokamp K, Wolfe KH (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137-144
7. Bürglin TR (1997) Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Nucleic Acids Res 25: 4173-4180
8. Campuzano S (2001) Emc, a negative HLH regulator with multiple functions in Drosophila development. Oncogene 20: 8299-8307
9. Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O'Donnell L, et al (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res 41: D816-D823
10. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743
11. Curtis MD, Grossniklaus U (2003) A gateway cloning vector set for highthroughput functional analysis of genes in planta. Plant Physiol 133: 462-469
12. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: 3
13. Dubos C, Le Gourrierec J, Baudry A, Huep G, Lanet E, Debeaujon I, Routaboul JM, Alboresi A, Weisshaar B, Lepiniec L (2008) MYBL2 is a new regulator of flavonoid biosynthesis in Arabidopsis thaliana. Plant J 55: 940-953
14. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797
15. Galstyan A, Cifuentes-Esquivel N, Bou-Torrent J, Martinez-Garcia JF (2011) The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors. Plant J 66: 258-267
16. Gatz C (2013) From pioneers to team players: TGA transcription factors provide a molecular link between different stress pathways. Mol Plant Microbe Interact 26: 151-159
17. Hackbusch J, Richter K, Müller J, Salamini F, Uhrig JF (2005) A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins. Proc Natl Acad Sci USA 102: 4908-4912
18. Haller K, Rambaldi I, Daniels E, Featherstone M (2004) Subcellular localization of multiple PREP2 isoforms is regulated by actin, tubulin, and nuclear export. J Biol Chem 279: 49384-49394
19. Hu W, dePamphilis CW, Ma H (2008) Phylogenetic analysis of the plantspecific zinc finger-homeobox and mini zinc finger gene families. J Integr Plant Biol 50: 1031-1045
20. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, et al (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40: D306-D312
21. Hyun Y, Lee I (2006) KIDARI, encoding a non-DNA Binding bHLH protein, represses light signal transduction in Arabidopsis thaliana. PlantMol Biol 61: 283-296
22. Jefferson RA (1989) The GUS reporter gene system. Nature 342: 837-838
23. Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, et al (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res 40: D841-D846
24. Kesarwani M, Yoo J, Dong X (2007) Genetic interactions of TGA transcription factors in the regulation of pathogenesis-related genes and disease resistance in Arabidopsis. Plant Physiol 144: 336-346
25. Kim YM, Woo JC, Song PS, Soh MS (2002) HFR1, a phytochrome A-signalling component, acts in a separate pathway from HY5, downstream of COP1 in Arabidopsis thaliana. Plant J 30: 711-719
26. Kim YS, Kim SG, Lee M, Lee I, Park HY, Seo PJ, Jung JH, Kwon EJ, Suh SW, Paek KH, et al (2008) HD-ZIP III activity is modulated by competitive inhibitors via a feedback loop in Arabidopsis shoot apical meristem development. Plant Cell 20: 920-933
27. Kimura S, Koenig D, Kang J, Yoong FY, Sinha N (2008) Natural variation in leaf morphology results from mutation of a novel KNOX gene. Curr Biol 18: 672-677
28. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, Kakutani T (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523
29. Koonin EV, Aravind L, Kondrashov AS (2000) The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576
30. Kummerfeld SK, Teichmann SA (2006) DBD: a transcription factor prediction database. Nucleic Acids Res 34: D74-D81
31. Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, et al (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci USA 107: 8063-8070
32. Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 28: 149-156
33. Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424: 147-151
34. Magnani E, Hake S (2008) KNOX lost the OX: the Arabidopsis KNATM gene defines a novel class of KNOX transcriptional regulators missing the homeodomain. Plant Cell 20: 875-887
35. McCourt RM, Delwiche CF, Karol KG (2004) Charophyte algae and land plant origins. Trends Ecol Evol 19: 661-666
36. Noro B, Culi J, McKay DJ, Zhang W, Mann RS (2006) Distinct functions of homeodomain-containing and homeodomain-less isoforms encoded by homothorax. Genes Dev 20: 1636-1650
37. Papp B, Pál C, Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197
38. Ren Z, Zheng Z, Chinnusamy V, Zhu J, Cui X, Iida K, Zhu JK (2010) RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis. Proc Natl Acad Sci USA 107: 5669-5674
39. Roig-Villanova I, Bou-Torrent J, Galstyan A, Carretero-Paulet L, Portolés S, Rodríguez-Concepción M, Martínez-García JF (2007) Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins. EMBO J 26: 4756-4767
40. Sambrook J, Russell DW (2006) Amplification of cDNA generated by reverse transcription of mRNA. CSH Protoc 2006 Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506
41. Seo PJ, Hong SY, Ryu JY, Jeong EY, Kim SG, Baldwin IT, Park CM (2012) Targeted inactivation of transcription factors by overexpression of their truncated forms in plants. Plant J 72: 162-172
42. Shearer HL, Cheng YT, Wang L, Liu J, Boyle P, Després C, Zhang Y, Li X, Fobert PR (2012) Arabidopsis clade I TGA transcription factors regulate plant defenses in an NPR1-independent fashion. Mol Plant Microbe Interact 25: 1459-1468
43. Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6: 791-802
44. Staudt AC, Wenkel S (2011) Regulation of protein function by "micro-Proteins. EMBO Rep 12: 35-42
45. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599
46. Ulmasov T, Hagen G, Guilfoyle TJ (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276: 1865-1868
47. Van Doren M, Ellis HM, Posakony JW (1991) The Drosophila extramacrochaetae protein antagonizes sequence-specific DNA binding by daughterless/achaete-scute protein complexes. Development 113: 245-255
48. Van Doren M, Powell PA, Pasternak D, Singson A, Posakony JW (1992) Spatial regulation of proneural gene activity: auto-and cross-activation of achaete is antagonized by extramacrochaetae. Genes Dev 6: 2592-2605
49. Wang H, Zhu Y, Fujioka S, Asami T, Li J, Li J (2009) Regulation of Arabidopsis brassinosteroid signaling by atypical basic helix-loop-helix proteins. Plant Cell 21: 3781-3791
50. Wenkel S, Emery J, Hou BH, Evans MM, Barton MK (2007) A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes. Plant Cell 19: 3379-3390
51. Xia K, Fu Z, Hou L, Han JD (2008) Impacts of protein-protein interaction domains on organism and network complexity. Genome Res 18: 1500-1508
52. Yang Y, Hwang CK, D'Souza UM, Lee SH, Junn E, Mouradian MM (2000) Three-amino acid extension loop homeodomain proteins Meis2 and TGIF differentially regulate transcription. J Biol Chem 275: 20734-20741
53. Zalewski CS, Floyd SK, Furumizu C, Sakakibara K, Stevenson DW, Bowman JL (2013) Evolution of the class IV HD-zip gene family in streptophytes. Mol Biol Evol 30: 2347-2365
54. Zdobnov EM, Apweiler R (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848
55. Zhang LY, Bai MY, Wu J, Zhu JY, Wang H, Zhang Z, Wang W, Sun Y, Zhao J, Sun X, et al (2009) Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis. Plant Cell 21: 3767-3780