Experts and Doctors on arabidopsis proteins in New York, United States


Locale: New York, United States
Topic: arabidopsis proteins

Top Publications

  1. Sanchez J, Duque P, Chua N. ABA activates ADPR cyclase and cADPR induces a subset of ABA-responsive genes in Arabidopsis. Plant J. 2004;38:381-95 pubmed
  2. Cotto Rios X, Jones M, Busino L, Pagano M, Huang T. APC/CCdh1-dependent proteolysis of USP1 regulates the response to UV-mediated DNA damage. J Cell Biol. 2011;194:177-86 pubmed publisher
    ..Thus, we propose a role for APC/C(Cdh1) in modulating the status of PCNA monoubiquitination and UV DNA repair before S phase entry. ..
  3. Chen Y, Hu L, Punta M, Bruni R, Hillerich B, Kloss B, et al. Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature. 2010;467:1074-80 pubmed publisher
  4. Klahre U, Chua N. The Arabidopsis actin-related protein 2 (AtARP2) promoter directs expression in xylem precursor cells and pollen. Plant Mol Biol. 1999;41:65-73 pubmed
    ..In addition, strong expression was observed in pollen grains. We discuss the potential role of an arp2/3 complex in plant development. ..
  5. Xu J, Chua N. Dehydration stress activates Arabidopsis MPK6 to signal DCP1 phosphorylation. EMBO J. 2012;31:1975-84 pubmed publisher
    ..Our results suggest that mRNA decapping through MPK6-DCP1-DCP5 pathway serves as a rapid response to dehydration stress in Arabidopsis. ..
  6. Lee J, Yi L, Li J, Schweitzer K, Borgmann M, Naumann M, et al. Crystal structure and versatile functional roles of the COP9 signalosome subunit 1. Proc Natl Acad Sci U S A. 2013;110:11845-50 pubmed publisher
    ..Therefore, the CSN complex uses multiple mechanisms to hinder NF-?B activation, a principle likely to hold true for its regulation of many other targets and pathways...
  7. Kim S, Yang J, Xu J, Jang I, Prigge M, Chua N. Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol. 2008;49:1634-44 pubmed publisher
    ..Genetic and molecular analyses show that CBP20 and 80 have overlapping function in the same developmental pathway as SE and HYL1. Our results identify new components in miRNA biogenesis. ..
  8. Short T. Overexpression of Arabidopsis phytochrome B inhibits phytochrome A function in the presence of sucrose. Plant Physiol. 1999;119:1497-506 pubmed
    ..It is possible that phyA and phyB interact with a common reaction partner but that either the energy state of the cell or a separate sugar-signaling mechanism modulates the phytochrome-signaling interactions. ..
  9. Xu J, Chua N. Arabidopsis decapping 5 is required for mRNA decapping, P-body formation, and translational repression during postembryonic development. Plant Cell. 2009;21:3270-9 pubmed publisher
    ..In vitro experiments using wheat germ extracts confirmed that DCP5 is a translational repressor. Our results showed that DCP5 is required for translational repression and P-body formation and plays an indirect role in mRNA decapping. ..

More Information


  1. Wang L, Schwer B, Englert M, Beier H, Shuman S. Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog. Nucleic Acids Res. 2006;34:517-27 pubmed
    ..The plant ligase, like yeast Trl1 but unlike T4 RNA ligase 1, requires a 2'-PO4 end for tRNA splicing in vivo. ..
  2. Banno H, Chua N. Characterization of the arabidopsis formin-like protein AFH1 and its interacting protein. Plant Cell Physiol. 2000;41:617-26 pubmed
    ..AFH1 may form a membrane anchored complex with FIP2, which might be involved in the organization of the actin cytoskeleton...
  3. Seo H, Watanabe E, Tokutomi S, Nagatani A, Chua N. Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. Genes Dev. 2004;18:617-22 pubmed
    ..Our results indicate that COP1 acts as an E3 ligase to regulate phyA signaling by targeting elimination of the phyA photoreceptor itself. ..
  4. Ballesteros M, Bolle C, Lois L, Moore J, Vielle Calzada J, Grossniklaus U, et al. LAF1, a MYB transcription activator for phytochrome A signaling. Genes Dev. 2001;15:2613-25 pubmed
    ..This accumulation in speckles is abolished by a point mutation in a lysine residue (K258R), which might serve as a modification site by a small ubiquitin-like protein (SUMO). ..
  5. Nakajima K, Sena G, Nawy T, Benfey P. Intercellular movement of the putative transcription factor SHR in root patterning. Nature. 2001;413:307-11 pubmed
    ..These results support a model in which SHR protein acts both as a signal from the stele and as an activator of endodermal cell fate and SCR-mediated cell division. ..
  6. Lonien J, Schwender J. Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis. Plant Physiol. 2009;151:1617-34 pubmed publisher
    ..No such limited compensatory bypass could be observed in pkpbeta(1)pkpalpha. ..
  7. Ikeda Y, Banno H, Niu Q, Howell S, Chua N. The ENHANCER OF SHOOT REGENERATION 2 gene in Arabidopsis regulates CUP-SHAPED COTYLEDON 1 at the transcriptional level and controls cotyledon development. Plant Cell Physiol. 2006;47:1443-56 pubmed
    ..Phenotypes of induced ESR2 expression in a cuc1-1 mutant background were suppressed. Our results suggest that ESR2 plays a role in shoot regeneration through transcriptional regulation of CUC1. ..
  8. Li S, Yang Z, Du X, Liu R, Wilkinson A, Gozani O, et al. Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette. Structure. 2016;24:486-94 pubmed publisher
    ..Such recognition may contribute to epigenetic regulation of the initiation of DNA replication. ..
  9. Møller S, Kim Y, Kunkel T, Chua N. PP7 is a positive regulator of blue light signaling in Arabidopsis. Plant Cell. 2003;15:1111-9 pubmed
    ..Based on our findings and recent data regarding cryptochrome action, we propose that AtPP7 acts as a positive regulator of cryptochrome signaling in Arabidopsis. ..
  10. Di Laurenzio L, Wysocka Diller J, Malamy J, Pysh L, Helariutta Y, Freshour G, et al. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell. 1996;86:423-33 pubmed
    ..Tissue-specific expression is regulated at the transcriptional level. These results indicate a key role for SCR in regulating the radial organization of the root. ..
  11. Aliprantis A, Yang R, Weiss D, Godowski P, Zychlinsky A. The apoptotic signaling pathway activated by Toll-like receptor-2. EMBO J. 2000;19:3325-36 pubmed
    ..These results indicate that caspase activation is an innate immune response to microbial pathogens, culminating in apoptosis and cytokine production. ..
  12. Nero D, Katari M, Kelfer J, Tranchina D, Coruzzi G. In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana. BMC Bioinformatics. 2009;10:435 pubmed publisher
  13. Lois L, Lima C, Chua N. Small ubiquitin-like modifier modulates abscisic acid signaling in Arabidopsis. Plant Cell. 2003;15:1347-59 pubmed
    ..Reduction of AtSCE1a expression levels accentuates ABA-mediated growth inhibition. Our results suggest a role for SUMO in the modulation of the ABA signal transduction pathway. ..
  14. Kim D, Park M, Gwon G, Silkov A, Xu Z, Yang E, et al. An ankyrin repeat domain of AKR2 drives chloroplast targeting through coincident binding of two chloroplast lipids. Dev Cell. 2014;30:598-609 pubmed publisher
  15. Citovsky V, Kapelnikov A, Oliel S, Zakai N, Rojas M, Gilbertson R, et al. Protein interactions involved in nuclear import of the Agrobacterium VirE2 protein in vivo and in vitro. J Biol Chem. 2004;279:29528-33 pubmed
    ..Our results indicate that VIP1 functions as a molecular bridge between VirE2 and karyopherin alpha, allowing VirE2 to utilize the host cell nuclear import machinery even without being directly recognized by its components. ..
  16. Reyes J, Chua N. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J. 2007;49:592-606 pubmed
    ..Our results suggest that ABA-induced accumulation of miR159 is a homeostatic mechanism to direct MYB33 and MYB101 transcript degradation to desensitize hormone signaling during seedling stress responses. ..
  17. Kiba T, Henriques R, Sakakibara H, Chua N. Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana. Plant Cell. 2007;19:2516-30 pubmed
    ..Together, our results show that ZTL targets PRR5 for degradation by 26S proteasomes in the circadian clock and in early photomorphogenesis. ..
  18. Jang I, Yang S, Yang J, Chua N. Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling. Genes Dev. 2007;21:2100-11 pubmed
  19. Morton B, Dar V, Wright S. Analysis of site frequency spectra from Arabidopsis with context-dependent corrections for ancestral misinference. Plant Physiol. 2009;149:616-24 pubmed publisher
  20. Shevell D, Kunkel T, Chua N. Cell wall alterations in the arabidopsis emb30 mutant. Plant Cell. 2000;12:2047-60 pubmed
    ..Together, these results suggest that emb30 mutations result in an abnormal cell wall, which in turn may account for the defects in cell adhesion and polar cell growth control observed in the mutants. ..
  21. Goldberg J. Decoding of sorting signals by coatomer through a GTPase switch in the COPI coat complex. Cell. 2000;100:671-9 pubmed
  22. Catala R, Ouyang J, Abreu I, Hu Y, Seo H, Zhang X, et al. The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell. 2007;19:2952-66 pubmed
    ..From these results, we conclude that SIZ1 regulates Arabidopsis growth and that this SUMO E3 ligase plays a role in drought stress response likely through the regulation of gene expression. ..
  23. Nogueira F, Madi S, Chitwood D, Juarez M, Timmermans M. Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev. 2007;21:750-5 pubmed
    ..Our findings indicate that tasiR-ARF, a ta-siRNA, and miR166 establish opposing domains along the adaxial-abaxial axis, thus revealing a novel mechanism of pattern formation. ..
  24. Stern M, Aihara H, Cho K, Kim G, Horiguchi G, Roccaro G, et al. Structurally related Arabidopsis ANGUSTIFOLIA is functionally distinct from the transcriptional corepressor CtBP. Dev Genes Evol. 2007;217:759-69 pubmed
    ..We therefore propose to categorize AN as a subfamily member within the CtBP/BARS/RIBEYE/AN superfamily. ..
  25. Ali N, Halfter U, Chua N. Cloning and biochemical characterization of a plant protein kinase that phosphorylates serine, threonine, and tyrosine. J Biol Chem. 1994;269:31626-9 pubmed
    ..Phosphoamino acid analysis of the autophosphorylated kinase shows that ADK1 phosphorylates serine, threonine, and tyrosine. Using poly (Glu/Tyr) as a substrate, we confirm that ADK1 is capable of phosphorylating tyrosine residues. ..
  26. Jang I, Yang J, Seo H, Chua N. HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling. Genes Dev. 2005;19:593-602 pubmed
    ..Taken together, our results show that HFR1 is ubiquitinated by COP1 E3 ligase and marked for post-translational degradation during photomorphogenesis. ..
  27. Mayer K, Shanklin J. A structural model of the plant acyl-acyl carrier protein thioesterase FatB comprises two helix/4-stranded sheet domains, the N-terminal domain containing residues that affect specificity and the C-terminal domain containing catalytic residues. J Biol Chem. 2005;280:3621-7 pubmed
    ..Together these data corroborate the structural model and show that the hot dog fold is common to enzymes from both prokaryotes and eukaryotes and that this fold supports at least three different catalytic mechanisms. ..
  28. Zeidler M, Zhou Q, Sarda X, Yau C, Chua N. The nuclear localization signal and the C-terminal region of FHY1 are required for transmission of phytochrome A signals. Plant J. 2004;40:355-65 pubmed
    ..Together with the results from global expression analysis, our findings point to an important role of FHY1 in phyA signaling through its nuclear translocation and induction of gene expression. ..
  29. Tian G, Mohanty A, Chary S, Li S, Paap B, Drakakaki G, et al. High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta. Plant Physiol. 2004;135:25-38 pubmed
  30. Møller S, Kunkel T, Chua N. A plastidic ABC protein involved in intercompartmental communication of light signaling. Genes Dev. 2001;15:90-103 pubmed
  31. Kim A, Yano H, Cho H, Meyer D, Monks B, Margolis B, et al. Akt1 regulates a JNK scaffold during excitotoxic apoptosis. Neuron. 2002;35:697-709 pubmed
    ..Overexpression of Akt1 mutants that bind JIP1 reduced excitotoxic apoptosis. These results suggest that Akt1 binding to JIP1 acts as a regulatory gate preventing JNK activation, which is released under conditions of excitotoxic injury. ..
  32. Lin S, Martin R, Mongrand S, Vandenabeele S, Chen K, Jang I, et al. RING1 E3 ligase localizes to plasma membrane lipid rafts to trigger FB1-induced programmed cell death in Arabidopsis. Plant J. 2008;56:550-61 pubmed publisher
    ..Our results suggest that RING1 acts as a signal from the plasma membrane lipid rafts to trigger the FB1-induced plant programmed cell death pathway. ..
  33. Takahashi T, Gasch A, Nishizawa N, Chua N. The DIMINUTO gene of Arabidopsis is involved in regulating cell elongation. Genes Dev. 1995;9:97-107 pubmed
    ..Our results suggest that the DIM gene product plays a critical role in the general process of plant cell elongation. ..
  34. Goll M, Kirpekar F, Maggert K, Yoder J, Hsieh C, Zhang X, et al. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science. 2006;311:395-8 pubmed
    ..Indirect sequence recognition is also a feature of eukaryotic DNA methyltransferases, which may have arisen from a Dnmt2-like RNA methyltransferase. ..
  35. Duque P, Chua N. IMB1, a bromodomain protein induced during seed imbibition, regulates ABA- and phyA-mediated responses of germination in Arabidopsis. Plant J. 2003;35:787-99 pubmed
    ..In imbibed seeds, IMB1 modulates the transcription of a battery of genes, providing clues on its mode of action. ..
  36. Foster R, Chua N. An Arabidopsis mutant with deregulated ABA gene expression: implications for negative regulator function. Plant J. 1999;17:363-72 pubmed
    ..Genetic analyses indicate that the ade1 mutant is a monogenic recessive trait. A role for negative regulator function in ABA signalling is discussed. ..
  37. Fang Y, Hearn S, Spector D. Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis. Mol Biol Cell. 2004;15:2664-73 pubmed
  38. Gutierrez R, Stokes T, Thum K, Xu X, Obertello M, Katari M, et al. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A. 2008;105:4939-44 pubmed publisher
    ..Phase response curve analysis shows that distinct N-metabolites can advance or delay the CCA1 phase. Regulation of CCA1 by organic N signals may represent a novel input mechanism for N-nutrients to affect plant circadian clock function. ..
  39. Guo M, Thomas J, Collins G, Timmermans M. Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis. Plant Cell. 2008;20:48-58 pubmed publisher
    ..This regulatory mechanism may be conserved in simple leafed species of monocot and dicot lineages and constitutes a potential key determinant in the evolution of compound leaves. ..
  40. Roudier F, Schindelman G, DeSalle R, Benfey P. The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. Plant Physiol. 2002;130:538-48 pubmed
    ..Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface. ..
  41. Yan K, Yan S, Farooq A, Han A, Zeng L, Zhou M. Structure and conserved RNA binding of the PAZ domain. Nature. 2003;426:468-74 pubmed
    ..Furthermore, we show that PAZ domains from different human Argonaute proteins also bind RNA, establishing a conserved function for this domain. ..
  42. Jang I, Henriques R, Seo H, Nagatani A, Chua N. Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus. Plant Cell. 2010;22:2370-83 pubmed publisher
    ..Our results identify COP1 as an E3 ligase for phyB and other stable phytochromes and uncover the mechanism by which PIFs negatively regulate phyB levels. ..
  43. Ishikawa M, Kiba T, Chua N. The Arabidopsis SPA1 gene is required for circadian clock function and photoperiodic flowering. Plant J. 2006;46:736-46 pubmed
    ..Our results indicate that SPA1 not only negatively controls phyA-mediated signaling in seedlings, but also regulates circadian rhythms and flowering time in plants. ..
  44. Johnson L, Du J, Hale C, Bischof S, Feng S, Chodavarapu R, et al. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2014;507:124-128 pubmed publisher
  45. Zhong X, Du J, Hale C, Gallego Bartolome J, Feng S, Vashisht A, et al. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell. 2014;157:1050-60 pubmed publisher
    ..These data suggest a model in which DRM2 is guided to target loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent RNA transcripts. ..
  46. Chung P, Park B, Wang H, Liu J, Jang I, Chua N. Light-Inducible MiR163 Targets PXMT1 Transcripts to Promote Seed Germination and Primary Root Elongation in Arabidopsis. Plant Physiol. 2016;170:1772-82 pubmed publisher
    ..Together, our results indicate that miR163 targets PXMT1 mRNA to promote seed germination and modulate root architecture during early development of Arabidopsis seedlings. ..
  47. Li Y, Mao Y, Rosal R, Dinnen R, Williams A, Brandt Rauf P, et al. Selective induction of apoptosis through the FADD/caspase-8 pathway by a p53 c-terminal peptide in human pre-malignant and malignant cells. Int J Cancer. 2005;115:55-64 pubmed
    ..p53p-Ant is a novel anticancer agent with unique selectivity for human cancer cells and could be useful as a prototype for the development of new anti-cancer agents. ..
  48. Jang I, Chung P, Hemmes H, Jung C, Chua N. Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus. Plant Cell. 2011;23:459-70 pubmed publisher
    ..The presence of activating and repressive histone marks suggests a mechanism for the rapid and reversible regulation of phyA by dark and light. ..
  49. Chitwood D, Nogueira F, Howell M, Montgomery T, Carrington J, Timmermans M. Pattern formation via small RNA mobility. Genes Dev. 2009;23:549-54 pubmed publisher
    ..Our observations have important ramifications for the function of small RNAs and suggest they can serve as mobile, instructive signals during development. ..
  50. Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell. 2012;24:4333-45 pubmed publisher
    ..RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of intron-containing lincRNAs. ..
  51. Soyano T, Thitamadee S, Machida Y, Chua N. ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis. Plant Cell. 2008;20:3359-73 pubmed publisher
    ..Moreover, VND genes and their downstream targets were downregulated in ASL20-SRDX plants. Therefore, ASL20 appears to be involved in a positive feedback loop for VND7 expression that regulates TE differentiation-related genes. ..
  52. Lodha M, Marco C, Timmermans M. The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes Dev. 2013;27:596-601 pubmed publisher
    ..Combined with recent studies in mammals, our findings reveal a conserved paradigm to epigenetically regulate homeobox gene expression during development. ..
  53. Xin Z, Wang A, Yang G, Gao P, Zheng Z. The Arabidopsis A4 subfamily of lectin receptor kinases negatively regulates abscisic acid response in seed germination. Plant Physiol. 2009;149:434-44 pubmed publisher
    ..1 and LecRKA4.2 regulate some of the ABA-responsive genes. Taken together, our results demonstrate that the A4 subfamily of LecRKs has a redundant function in the negative regulation of ABA response in seed germination. ..
  54. Lopez Molina L, Mongrand S, Kinoshita N, Chua N. AFP is a novel negative regulator of ABA signaling that promotes ABI5 protein degradation. Genes Dev. 2003;17:410-8 pubmed
    ..Our results suggest that AFP attenuates ABA signals by targeting ABI5 for ubiquitin-mediated degradation in nuclear bodies. ..
  55. Rotolo J, Zhang J, Donepudi M, Lee H, Fuks Z, Kolesnick R. Caspase-dependent and -independent activation of acid sphingomyelinase signaling. J Biol Chem. 2005;280:26425-34 pubmed
  56. Kidner C, Martienssen R. The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev Biol. 2005;280:504-17 pubmed
    ..CLF is over expressed in ago1, showing that the RNAi pathway regulates polycomb-type epigenetic modifiers. ..
  57. Zhang X, Garreton V, Chua N. The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation. Genes Dev. 2005;19:1532-43 pubmed
    ..Our results indicate that AIP2 negatively regulates ABA signaling by targeting ABI3 for post-translational destruction. ..
  58. Lim J, Helariutta Y, Specht C, Jung J, Sims L, Bruce W, et al. Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems. Plant Cell. 2000;12:1307-18 pubmed
    ..Analysis of the dynamic expression pattern of ZmSCR as well as other markers indicates the involvement of positional information as a primary determinant in regeneration of the root radial pattern. ..
  59. Zhou Q, Hare P, Yang S, Zeidler M, Huang L, Chua N. FHL is required for full phytochrome A signaling and shares overlapping functions with FHY1. Plant J. 2005;43:356-70 pubmed
    ..These findings reiterate the prevalence of partial degeneracy in plant signaling networks that regulate responses crucial to survival. ..
  60. Bolle C, Koncz C, Chua N. PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction. Genes Dev. 2000;14:1269-78 pubmed
    ..The results indicate that the truncated PAT1 protein acts in a dominant-negative fashion to inhibit phyA signaling. ..
  61. Qi Y, He X, Wang X, Kohany O, Jurka J, Hannon G. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature. 2006;443:1008-12 pubmed
    ..Second, AGO4 catalytic activity can be crucial for the generation of secondary siRNAs that reinforce its repressive effects. ..
  62. Lopez Molina L, Mongrand S, Chua N. A postgermination developmental arrest checkpoint is mediated by abscisic acid and requires the ABI5 transcription factor in Arabidopsis. Proc Natl Acad Sci U S A. 2001;98:4782-7 pubmed
    ..As expected for a key player in ABA-triggered processes, ABI5 protein accumulation, phosphorylation, stability, and activity are highly regulated by ABA during germination and early seedling growth. ..
  63. Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014;21:64-72 pubmed publisher
    ..The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA. ..
  64. Hausmann S, Koiwa H, Krishnamurthy S, Hampsey M, Shuman S. Different strategies for carboxyl-terminal domain (CTD) recognition by serine 5-specific CTD phosphatases. J Biol Chem. 2005;280:37681-8 pubmed
    ..We surmise that the reading of the CTD code does not obey uniform rules with respect to the location and phasing of specificity determinants. Thus, CTD code, like the CTD structure, is plastic. ..
  65. Bommert P, Nagasawa N, Jackson D. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet. 2013;45:334-7 pubmed publisher
    ..These findings indicate that modulation of fundamental stem cell proliferation control pathways has the potential to enhance crop yields...
  66. Ronemus M, Vaughn M, Martienssen R. MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell. 2006;18:1559-74 pubmed
    ..These results indicate that a subset of endogenous mRNA targets of RNA interference may be regulated through a mechanism of second-strand RNA synthesis and degradation initiated by or in addition to miRNA-mediated cleavage. ..
  67. Kinoshita N, Wang H, Kasahara H, Liu J, Macpherson C, Machida Y, et al. IAA-Ala Resistant3, an evolutionarily conserved target of miR167, mediates Arabidopsis root architecture changes during high osmotic stress. Plant Cell. 2012;24:3590-602 pubmed publisher
    ..Sequence comparison revealed the miR167 target site on IAR3 mRNA is conserved in evolutionarily distant plant species. Finally, we showed that IAR3 is required for drought tolerance. ..
  68. Aeschbacher R, Hauser M, Feldmann K, Benfey P. The SABRE gene is required for normal cell expansion in Arabidopsis. Genes Dev. 1995;9:330-40 pubmed
    ..This suggested that one of the roles of SABRE is to counter the action of ethylene in promoting radial expansion in plant cells. ..
  69. Gou J, Felippes F, Liu C, Weigel D, Wang J. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell. 2011;23:1512-22 pubmed publisher
    ..Our results reveal a direct link between the transition to flowering and secondary metabolism and provide a potential target for manipulation of anthocyanin and flavonol content in plants. ..
  70. Banno H, Ikeda Y, Niu Q, Chua N. Overexpression of Arabidopsis ESR1 induces initiation of shoot regeneration. Plant Cell. 2001;13:2609-18 pubmed
    ..Our results suggest that ESR1 may regulate the induction of shoot regeneration after the acquisition of competence for organogenesis. ..
  71. Hemmes H, Henriques R, Jang I, Kim S, Chua N. Circadian clock regulates dynamic chromatin modifications associated with Arabidopsis CCA1/LHY and TOC1 transcriptional rhythms. Plant Cell Physiol. 2012;53:2016-29 pubmed publisher
    ..Analysis of clock-compromised CCA1-overexpressing lines provided evidence that light/dark photoperiods signal the establishment of these chromatin changes which are gated by the clock. ..
  72. Wang H, Zhang X, Liu J, Kiba T, Woo J, Ojo T, et al. Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J. 2011;67:292-304 pubmed publisher
  73. Zhang X, Yuan Y, Pei Y, Lin S, Tuschl T, Patel D, et al. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 2006;20:3255-68 pubmed
    ..These findings provide insight on the molecular arms race between host antiviral RNA silencing and virus counterdefense...
  74. Chen Y, Li F, Wurtzel E. Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiol. 2010;153:66-79 pubmed publisher
    ..Therefore, plant carotenogenesis evolved by recruitment of genes from noncarotenogenic bacteria. ..
  75. Rosas U, Cibrián Jaramillo A, Ristova D, Banta J, Gifford M, Fan A, et al. Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proc Natl Acad Sci U S A. 2013;110:15133-8 pubmed publisher
    ..This finding supports a role for plasticity responses in phenotypic evolution in natural environments. ..
  76. Liou M, Liou H. The ubiquitin-homology protein, DAP-1, associates with tumor necrosis factor receptor (p60) death domain and induces apoptosis. J Biol Chem. 1999;274:10145-53 pubmed
    ..Collectively, these observations highly suggest a role for DAP-1 in mediating TNF-induced cell death signaling pathways, presumably through the recruitment of FADD death effector. ..
  77. Yang S, Jang I, Henriques R, Chua N. FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the Arabidopsis transcription factors LAF1 and HFR1 to transmit phytochrome A signals for inhibition of hypocotyl elongation. Plant Cell. 2009;21:1341-59 pubmed publisher
    ..These results suggest that, in addition to assisting phyA nuclear accumulation, FHY1 and FHL are required to assemble photoreceptor/transcription factor complexes for phyA signaling. ..
  78. Seo H, Yang J, Ishikawa M, Bolle C, Ballesteros M, Chua N. LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1. Nature. 2003;423:995-9 pubmed
    ..After the activation of phyA, SPA1 stimulates the E3 activity of residual nuclear COP1 to ubiquitinate LAF1, thereby desensitizing phyA signals. ..
  79. Shevell D, Leu W, Gillmor C, Xia G, Feldmann K, Chua N. EMB30 is essential for normal cell division, cell expansion, and cell adhesion in Arabidopsis and encodes a protein that has similarity to Sec7. Cell. 1994;77:1051-62 pubmed
    ..Molecular data and microscopy studies of emb30 seedlings presented here indicate that EMB30 affects cell division, elongation, and adhesion and functions in seedling and adult plants as well as during embryogenic pattern formation. ..
  80. Zeidler M, Bolle C, Chua N. The phytochrome A specific signaling component PAT3 is a positive regulator of Arabidopsis photomorphogenesis. Plant Cell Physiol. 2001;42:1193-200 pubmed
    ..The protein can activate transcription in yeast when fused to the GAL4 DNA-binding domain. Our results show that PAT3 is a positive regulator of phytochrome A signal transduction. ..
  81. Fang Y, Spector D. Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr Biol. 2007;17:818-23 pubmed
    ..On the basis of these data, we propose that D-bodies are crucial for orchestrating pri-miRNA processing and/or storage/assembly of miRNA-processing complexes in the nuclei of plant cells. ..
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