Genomes and Genes
Experts and Doctors on arabidopsis in Durham, North Carolina, United States
Locale: Durham, North Carolina, United States
- Shibata M, Breuer C, Kawamura A, Clark N, Rymen B, Braidwood L, et al. GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis. Development. 2018;145: pubmed publisher..This study therefore uncovers a core regulatory module that fine-tunes the extent of root hair growth by the orchestrated actions of opposing transcription factors. ..
- Streisfeld M, Rausher M. Genetic changes contributing to the parallel evolution of red floral pigmentation among Ipomoea species. New Phytol. 2009;183:751-63 pubmed publisher..Regulatory mutations thus appear to be preferentially targeted during evolutionary change between species. We discuss possible explanations for this apparent bias...
- Sozzani R, Cui H, Moreno Risueno M, Busch W, Van Norman J, Vernoux T, et al. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature. 2010;466:128-32 pubmed publisher..Taken together, we provide evidence for a direct link between developmental regulators, specific components of the cell-cycle machinery and organ patterning. ..
- Paquette A, Benfey P. Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT. Plant Physiol. 2005;138:636-40 pubmed
- Roudier F, Fernandez A, Fujita M, Himmelspach R, Borner G, Schindelman G, et al. COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. Plant Cell. 2005;17:1749-63 pubmed..Our observations suggest that COB, through its involvement in cellulose microfibril orientation, is an essential factor in highly anisotropic expansion during plant morphogenesis. ..
- DINNENY J, Long T, Wang J, Jung J, Mace D, Pointer S, et al. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science. 2008;320:942-5 pubmed publisher..By performing a similar analysis using iron deprivation, we identified common cell-type-specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions. ..
- Wang D, Pajerowska Mukhtar K, Culler A, Dong X. Salicylic acid inhibits pathogen growth in plants through repression of the auxin signaling pathway. Curr Biol. 2007;17:1784-90 pubmed..We demonstrate that this inhibitory effect on auxin signaling is a part of the SA-mediated disease-resistance mechanism. ..
- Song J, Durrant W, Wang S, Yan S, Tan E, Dong X. DNA repair proteins are directly involved in regulation of gene expression during plant immune response. Cell Host Microbe. 2011;9:115-24 pubmed publisher..Given that the SSN2-RAD51D complex is conserved in eukaryotes, their dual function in homologous recombination and transcription regulation of plant-defense genes suggests a general link between these two stress responses. ..
- Pajerowska Mukhtar K, Wang W, Tada Y, Oka N, Tucker C, Fonseca J, et al. The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition. Curr Biol. 2012;22:103-12 pubmed publisher..Through this unique regulatory mechanism, TBF1 can sense the metabolic changes upon pathogen invasion and trigger the specific transcriptional reprogramming through its target genes expression. ..
- Moreno Risueno M, Van Norman J, Moreno A, Zhang J, Ahnert S, Benfey P. Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science. 2010;329:1306-11 pubmed publisher..This molecular mechanism has characteristics that resemble molecular clock-driven activities in animal species. ..
- Hu J, Mitchum M, Barnaby N, Ayele B, Ogawa M, Nam E, et al. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. Plant Cell. 2008;20:320-36 pubmed publisher..The immediate upregulation of GA3ox1 and GA3ox4 after anthesis suggests that pollination and/or fertilization is a prerequisite for de novo GA biosynthesis in fruit, which in turn promotes initial elongation of the silique. ..
- Prasad K, Song B, Olson Manning C, Anderson J, Lee C, Schranz M, et al. A gain-of-function polymorphism controlling complex traits and fitness in nature. Science. 2012;337:1081-4 pubmed publisher..Ecological interactions in diverse environments likely contribute to the widespread polymorphism of this biochemical function. ..
- Wang S, Durrant W, Song J, Spivey N, Dong X. Arabidopsis BRCA2 and RAD51 proteins are specifically involved in defense gene transcription during plant immune responses. Proc Natl Acad Sci U S A. 2010;107:22716-21 pubmed publisher..This study provides the molecular evidence showing that the BRCA2-RAD51 complex, known for its function in HR, also plays a direct and specific role in transcription regulation during plant immune responses. ..
- Muangprom A, Thomas S, Sun T, Osborn T. A novel dwarfing mutation in a green revolution gene from Brassica rapa. Plant Physiol. 2005;137:931-8 pubmed..This novel mutation confers nondeleterious dwarf phenotypes when transferred to Arabidopsis (Arabidopsis thaliana) and oilseed rape (Brassica napus), indicating its potential usefulness in other crop species. ..
- Wang D, Amornsiripanitch N, Dong X. A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog. 2006;2:e123 pubmed
- Zheng X, Spivey N, Zeng W, Liu P, Fu Z, Klessig D, et al. Coronatine promotes Pseudomonas syringae virulence in plants by activating a signaling cascade that inhibits salicylic acid accumulation. Cell Host Microbe. 2012;11:587-96 pubmed publisher..Thus, a signaling cascade by which coronatine confers its multiple virulence activities has been elucidated. ..
- Li X, Zhang Y, Clarke J, Li Y, Dong X. Identification and cloning of a negative regulator of systemic acquired resistance, SNI1, through a screen for suppressors of npr1-1. Cell. 1999;98:329-39 pubmed..Restoration of SAR in npr1-1 by the recessive sni1 mutation indicates that wild-type SNI1 may function as a negative regulator of SAR. We cloned the SNI1 gene and found that it encodes a leucine-rich nuclear protein. ..
- Colinas J, Schmidler S, Bohrer G, Iordanov B, Benfey P. Intergenic and genic sequence lengths have opposite relationships with respect to gene expression. PLoS ONE. 2008;3:e3670 pubmed publisher..These findings could shed light on the role and influence of noncoding sequences on gene expression. ..
- Silverstone A, Jung H, Dill A, Kawaide H, Kamiya Y, Sun T. Repressing a repressor: gibberellin-induced rapid reduction of the RGA protein in Arabidopsis. Plant Cell. 2001;13:1555-66 pubmed..The effect of rga on GA4 gene expression and the effect of GA on RGA protein level allow us to identify part of the mechanism by which GA homeostasis is achieved. ..
- Wang W, Barnaby J, Tada Y, Li H, Tör M, Caldelari D, et al. Timing of plant immune responses by a central circadian regulator. Nature. 2011;470:110-4 pubmed publisher..Temporal control of the defence genes by CCA1 differentiates their involvement in basal and R-gene-mediated defence. Our study has revealed a key functional link between the circadian clock and plant immunity. ..
- Fiorani F, Umbach A, Siedow J. The alternative oxidase of plant mitochondria is involved in the acclimation of shoot growth at low temperature. A study of Arabidopsis AOX1a transgenic plants. Plant Physiol. 2005;139:1795-805 pubmed
- Hughes R, Vrana J, Song J, Tucker C. Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and phytochrome B proteins. J Biol Chem. 2012;287:22165-72 pubmed publisher..We hypothesize that in plants, the phyB/CRY1 interaction may mediate cross-talk between the red/far-red- and blue/UV-sensing pathways, enabling fine-tuning of light responses to different spectral inputs. ..
- Fu Z, Yan S, Saleh A, Wang W, Ruble J, Oka N, et al. NPR3 and NPR4 are receptors for the immune signal salicylic acid in plants. Nature. 2012;486:228-32 pubmed publisher..Moreover, this mutant is defective in pathogen effector-triggered programmed cell death and immunity. Our study reveals the mechanism of SA perception in determining cell death and survival in response to pathogen challenge. ..
- Heidel A, Dong X. Fitness benefits of systemic acquired resistance during Hyaloperonospora parasitica infection in Arabidopsis thaliana. Genetics. 2006;173:1621-8 pubmed..The mutants with constitutive SAR all failed to show a fitness benefit in comparison to wild type under a H. parasitica pathogen treatment, suggesting that SAR is induced to prevent an excessive fitness cost. ..
- Smertenko A, Chang H, Sonobe S, Fenyk S, Weingartner M, Bögre L, et al. Control of the AtMAP65-1 interaction with microtubules through the cell cycle. J Cell Sci. 2006;119:3227-37 pubmed..We conclude that normal metaphase spindle organisation and the transition to anaphase is dependent on inactivation of AtMAP65-1. ..
- Tang R, Han S, Zheng H, Cook C, Choi C, Woerner T, et al. Coupling diurnal cytosolic Ca2+ oscillations to the CAS-IP3 pathway in Arabidopsis. Science. 2007;315:1423-6 pubmed..The phase and period of oscillations are likely determined by stomatal conductance. Thus, the internal concentration of Ca2+ in plant cells is constantly being actively revised. ..
- Song H, Golovkin M, Reddy A, Endow S. In vitro motility of AtKCBP, a calmodulin-binding kinesin protein of Arabidopsis. Proc Natl Acad Sci U S A. 1997;94:322-7 pubmed
- He Z, Fujiki M, Kohorn B. A cell wall-associated, receptor-like protein kinase. J Biol Chem. 1996;271:19789-93 pubmed..We suggest that Wak1 is a good candidate for a physical continuum between the cell wall and the cytoplasm, and since the kinase is cytoplasmic, it also has the potential to mediate signals to the cytoplasm from the cell wall. ..
- Li C, Guan Z, Liu D, Raetz C. Pathway for lipid A biosynthesis in Arabidopsis thaliana resembling that of Escherichia coli. Proc Natl Acad Sci U S A. 2011;108:11387-92 pubmed publisher..Although the structure of the lipid A end product generated by plants is still unknown, our work demonstrates that plants synthesize lipid A precursors using the same enzymatic pathway present in E. coli. ..
- Clarke J, Aarts N, Feys B, Dong X, Parker J. Constitutive disease resistance requires EDS1 in the Arabidopsis mutants cpr1 and cpr6 and is partially EDS1-dependent in cpr5. Plant J. 2001;26:409-20 pubmed..The data allow us to place EDS1 as a necessary downstream component of cpr1- and cpr6-mediated responses, but suggest a more complex relationship between EDS1 and cpr5 in plant defense. ..
- Stevenson Paulik J, Odom A, York J. Molecular and biochemical characterization of two plant inositol polyphosphate 6-/3-/5-kinases. J Biol Chem. 2002;277:42711-8 pubmed
- Stevenson Paulik J, Bastidas R, Chiou S, Frye R, York J. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc Natl Acad Sci U S A. 2005;102:12612-7 pubmed..Our results define a commercially viable strategy for the genetic engineering of phytate-free grain and provide insights into the role of inositol polyphosphate kinases in phosphate signaling biology. ..
- Sun T, Kamiya Y. The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin biosynthesis. Plant Cell. 1994;6:1509-18 pubmed..Subcellular localization of the GA1 protein was studied using 35S-labeled GA1 protein and isolated pea chloroplasts. The results showed that the GA1 protein is imported into and processed in pea chloroplasts in vitro. ..
- Bowling S, Clarke J, Liu Y, Klessig D, Dong X. The cpr5 mutant of Arabidopsis expresses both NPR1-dependent and NPR1-independent resistance. Plant Cell. 1997;9:1573-84 pubmed..Identification of this mutation indicates that these pathways are connected in early signal transduction steps and that they have overlapping functions in providing resistance. ..
- Anderson C, Wagner T, Perret M, He Z, He D, Kohorn B. WAKs: cell wall-associated kinases linking the cytoplasm to the extracellular matrix. Plant Mol Biol. 2001;47:197-206 pubmed..How WAKs are involved in signaling from the pectin extracellular matrix in coordination with GRPs will be key to our understanding of the cell wall's role in cell growth. ..
- Iyer Pascuzzi A, Benfey P. Fluorescence-activated cell sorting in plant developmental biology. Methods Mol Biol. 2010;655:313-9 pubmed publisher..In addition to gene expression, downstream applications of FACS include proteomic and metabolite analysis. This is a powerful method to examine biological functions of specific cell types and tissues with a systems biology approach. ..
- Kesarwani M, Yoo J, Dong X. Genetic interactions of TGA transcription factors in the regulation of pathogenesis-related genes and disease resistance in Arabidopsis. Plant Physiol. 2007;144:336-46 pubmed..TGA2's repressor activity overlaps with SNI1 because the tga2-2 sni1-1 double mutant shows a synergistic effect on PR gene expression. ..
- Li F, Rushworth C, Beck J, Windham M. Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage. Database (Oxford). 2017;2017: pubmed publisher..The BMW facilitates the accurate identification of Boechera samples and the investigation of reticulate evolution among the ±83 sexual diploid taxa in the genus, thereby greatly enhancing Boechera 's potential as a model system...
- Mosher R, Durrant W, Wang D, Song J, Dong X. A comprehensive structure-function analysis of Arabidopsis SNI1 defines essential regions and transcriptional repressor activity. Plant Cell. 2006;18:1750-65 pubmed publisher..The structural similarity of SNI1 to Armadillo repeat proteins implies that SNI1 may form a scaffold for interaction with proteins that modulate transcription...
- Gallagher K, Benfey P. Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement. Plant J. 2009;57:785-97 pubmed publisher..Finally, we provide evidence that movement requires both cytoplasmic and nuclear localization, strongly suggesting a mechanistic link between nuclear transport and cell-to-cell movement. ..
- Dixon D, van Lith M, Edwards R, Benham A. Cloning and initial characterization of the Arabidopsis thaliana endoplasmic reticulum oxidoreductins. Antioxid Redox Signal. 2003;5:389-96 pubmed..The ability to use a genetically tractable multicellular organism in combination with biochemical approaches should further our understanding of redox networks and Ero function in both plants and animals. ..
- Casson S, Topping J, Lindsey K. MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis. Plant J. 2009;57:857-69 pubmed publisher..These results demonstrate a requirement for the MDF-dependent pathway in regulating PIN/PLT- and WUS/CLV-mediated meristem activity. ..
- Sellars J, Landrum M, Congreve A, Dixon D, Mosely J, Beeby A, et al. Fluorescence quenched quinone methide based activity probes--a cautionary tale. Org Biomol Chem. 2010;8:1610-8 pubmed publisher..However, the relatively slow fragmentation of the carbamate linkage in such a strategy may cause problems of loss of signal or a decoupling of enzyme activity and labelling. ..
- Tsukagoshi H, Busch W, Benfey P. Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root. Cell. 2010;143:606-16 pubmed publisher..This pathway functions independently of auxin and cytokinin plant hormonal signaling. Comparison to ROS-regulated growth control in animals suggests that a similar mechanism is used in plants and animals. ..
- Anderson J, Lee C, Mitchell Olds T. Life-history QTLS and natural selection on flowering time in Boechera stricta, a perennial relative of Arabidopsis. Evolution. 2011;65:771-87 pubmed publisher..Additionally, we detected flowering-related QTLs in the field that were absent across the full range of laboratory conditions, thus emphasizing the need to conduct experiments in natural environments...
- Yan S, Wang W, Marques J, Mohan R, Saleh A, Durrant W, et al. Salicylic acid activates DNA damage responses to potentiate plant immunity. Mol Cell. 2013;52:602-10 pubmed publisher..Our study suggests that activation of DNA damage responses is an intrinsic component of the plant immune responses. ..
- Silverstone A, Ciampaglio C, Sun T. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell. 1998;10:155-69 pubmed..Because the rga mutation abolished the high level of expression of the GA biosynthetic gene GA4 in the ga1-3 mutant background, we conclude that RGA may also play a role in controlling GA biosynthesis. ..
- Spoel S, Mou Z, Tada Y, Spivey N, Genschik P, Dong X. Proteasome-mediated turnover of the transcription coactivator NPR1 plays dual roles in regulating plant immunity. Cell. 2009;137:860-72 pubmed publisher..These in vivo data demonstrate dual roles for coactivator turnover in both preventing and stimulating gene transcription to regulate plant immunity. ..
- Qiu J, Wilson H, Rajagopalan K. Structure-based alteration of substrate specificity and catalytic activity of sulfite oxidase from sulfite oxidation to nitrate reduction. Biochemistry. 2012;51:1134-47 pubmed publisher..The crystal structures of the Mo domains of the double and triple mutants were determined to 2.4 and 2.1 Å resolution, respectively. ..
- Gamble R, Qu X, Schaller G. Mutational analysis of the ethylene receptor ETR1. Role of the histidine kinase domain in dominant ethylene insensitivity. Plant Physiol. 2002;128:1428-38 pubmed..A truncated version of etr1-1 that lacks the His kinase domain also conferred ethylene insensitivity. Possible mechanisms by which a truncated version of etr1-1 could exert dominance are discussed. ..
- ..The current challenge is to integrate these details into a systematic view of metal content, speciation, localization and use within organisms and ecosystems. ..
- Wathugala D, Hemsley P, Moffat C, Cremelie P, Knight M, Knight H. The Mediator subunit SFR6/MED16 controls defence gene expression mediated by salicylic acid and jasmonate responsive pathways. New Phytol. 2012;195:217-30 pubmed publisher..It is not, however, a universal regulator of stress gene transcription and is likely to mediate transcriptional activation of specific regulons only...
- Hrabak E, Chan C, Gribskov M, Harper J, Choi J, Halford N, et al. The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol. 2003;132:666-80 pubmed..The PlantsP database provides a resource of continuously updated information on protein kinases from Arabidopsis and other plants. ..
- Petricka J, Benfey P. Root layers: complex regulation of developmental patterning. Curr Opin Genet Dev. 2008;18:354-61 pubmed publisher..As a result, future research advances in this field will require tissue-specific information at both the single gene and global level...
- Lee J, Colinas J, Wang J, Mace D, Ohler U, Benfey P. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc Natl Acad Sci U S A. 2006;103:6055-60 pubmed..This study provides a systematic overview of regulation of TF expression at a cellular level. ..
- Zentella R, Zhang Z, Park M, Thomas S, Endo A, Murase K, et al. Global analysis of della direct targets in early gibberellin signaling in Arabidopsis. Plant Cell. 2007;19:3037-57 pubmed..In addition, one of the putative DELLA targets, XERICO, promotes accumulation of abscisic acid (ABA) that antagonizes GA effects. Therefore, DELLA may restrict GA-promoted processes by modulating both GA and ABA pathways. ..
- Deeks M, Rodrigues C, Dimmock S, Ketelaar T, Maciver S, Malhó R, et al. Arabidopsis CAP1 - a key regulator of actin organisation and development. J Cell Sci. 2007;120:2609-18 pubmed..Surprisingly, cap1 plants show disruption in plant signalling pathways required for co-ordinated organ expansion suggesting that plant CAP has evolved to attain plant-specific signalling functions. ..
- Cui H, Benfey P. Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root. Plant J. 2009;58:1016-27 pubmed publisher..Together, these results suggest that epigenetic regulation is probably the common basis for SCR and GA activity in cortex cell proliferation. ..
- Breakfield N, Corcoran D, Petricka J, Shen J, Sae Seaw J, Rubio Somoza I, et al. High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res. 2012;22:163-76 pubmed publisher..Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming that novel miRNAs predicted by PIPmiR have functional relevance. ..