Genomes and Genes
Experts and Doctors on arabidopsis in Chicago, Illinois, United States
Locale: Chicago, Illinois, United States
- D Agostino I, Deruère J, Kieber J. Characterization of the response of the Arabidopsis response regulator gene family to cytokinin. Plant Physiol. 2000;124:1706-17 pubmed..The expression of ARR5 in the apical meristems was confirmed by whole mount in situ analysis of seedlings and is consistent with a role for cytokinin in regulating cell division in vivo. ..
- Sangster T, Salathia N, Undurraga S, Milo R, Schellenberg K, Lindquist S, et al. HSP90 affects the expression of genetic variation and developmental stability in quantitative traits. Proc Natl Acad Sci U S A. 2008;105:2963-8 pubmed publisher..Thus, HSP90 may centrally influence canalization, assimilation, and the rapid evolutionary alteration of phenotype through the concealment and exposure of cryptic genetic variation. ..
- Halavaty A, Moffat K. Coiled-coil dimerization of the LOV2 domain of the blue-light photoreceptor phototropin 1 from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013;69:1316-21 pubmed publisher..The J? helix predominantly interacts with the ?-sheet and plays a role in coiled-coil formation and dimerization. ..
- Lee M, Lu H, Jung H, Greenberg J. A key role for the Arabidopsis WIN3 protein in disease resistance triggered by Pseudomonas syringae that secrete AvrRpt2. Mol Plant Microbe Interact. 2007;20:1192-200 pubmed..syringae carrying avrRpm1. Thus, WIN3 is a key element of the RPS2 defense response pathway and a basal and systemic defense component. ..
- Dobritsa A, Coerper D. The novel plant protein INAPERTURATE POLLEN1 marks distinct cellular domains and controls formation of apertures in the Arabidopsis pollen exine. Plant Cell. 2012;24:4452-64 pubmed publisher..The identification of INP1 opens up new avenues for studies of how formation of distinct cellular domains results in the production of different extracellular morphologies. ..
- Pattanayak G, Venkataramani S, Hortensteiner S, Kunz L, Christ B, Moulin M, et al. Accelerated cell death 2 suppresses mitochondrial oxidative bursts and modulates cell death in Arabidopsis. Plant J. 2012;69:589-600 pubmed publisher..Together, the data suggest that ACD2 localizes dynamically during infection to protect cells from pro-death mobile substrate molecules, some of which may originate in chloroplasts, but have major effects on mitochondria. ..
- Huang Y, Li H, Hutchison C, Laskey J, Kieber J. Biochemical and functional analysis of CTR1, a protein kinase that negatively regulates ethylene signaling in Arabidopsis. Plant J. 2003;33:221-33 pubmed..These results suggest that CTR1 interacts with ETR1 in vivo, and that this association is required to turn off the ethylene-signaling pathway. ..
- Wilhelmi L, Preuss D. Self-sterility in Arabidopsis due to defective pollen tube guidance. Science. 1996;274:1535-7 pubmed..The pop2 and pop3 mutations exhibited genetic redundancy: Self-sterility occurred only when male and female tissues were defective in both genes. This phenotype resembles that found in many self-incompatible species. ..
- Woeste K, Ye C, Kieber J. Two Arabidopsis mutants that overproduce ethylene are affected in the posttranscriptional regulation of 1-aminocyclopropane-1-carboxylic acid synthase. Plant Physiol. 1999;119:521-30 pubmed..Taken together, these data suggest that the eto1 and eto3 mutations elevate ethylene biosynthesis by affecting the posttranscriptional regulation of ACS. ..
- Dobritsa A, Lei Z, Nishikawa S, Urbanczyk Wochniak E, Huhman D, Preuss D, et al. LAP5 and LAP6 encode anther-specific proteins with similarity to chalcone synthase essential for pollen exine development in Arabidopsis. Plant Physiol. 2010;153:937-55 pubmed publisher..Finally, the genetic interaction between LAP5 and an anther gene involved in fatty acid hydroxylation (CYP703A2) demonstrated that they act synergistically in exine production. ..
- Brandstatter I, Kieber J. Two genes with similarity to bacterial response regulators are rapidly and specifically induced by cytokinin in Arabidopsis. Plant Cell. 1998;10:1009-19 pubmed..This homology, coupled with previously published work on the CKI1 histidine kinase homolog, suggests that these proteins may play a role in early cytokinin signaling. ..
- Liang H, Yao N, Song J, Luo S, Lu H, Greenberg J. Ceramides modulate programmed cell death in plants. Genes Dev. 2003;17:2636-41 pubmed..Strikingly, C2 ceramide induces, whereas its phosphorylated derivative partially blocks, plant PCD, supporting a role for ceramide phosphorylation in modulating cell death in plants. ..
- Brachi B, Morris G, Borevitz J. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol. 2011;12:232 pubmed publisher..Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context. ..
- Ingram P, Dettmer J, Helariutta Y, Malamy J. Arabidopsis Lateral Root Development 3 is essential for early phloem development and function, and hence for normal root system development. Plant J. 2011;68:455-67 pubmed publisher..Therefore, this study provides new insights into phloem-mediated resource allocation and its effects on plant root system architecture. ..
- Dobritsa A, Nishikawa S, Preuss D, Urbanczyk Wochniak E, Sumner L, Hammond A, et al. LAP3, a novel plant protein required for pollen development, is essential for proper exine formation. Sex Plant Reprod. 2009;22:167-77 pubmed publisher..The largest changes were seen in levels of a straight-chain hydrocarbon nonacosane and in naringenin chalcone, an obligate compound in the flavonoid biosynthesis pathway. ..
- Palanivelu R, Brass L, Edlund A, Preuss D. Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell. 2003;114:47-59 pubmed..Interestingly, wild-type tubes exhibit normal growth and guidance in pop2 pistils, perhaps by degrading excess GABA and sharpening the gradient leading to the micropyle. ..
- Mobley E, Kunkel B, Keith B. Identification, characterization and comparative analysis of a novel chorismate mutase gene in Arabidopsis thaliana. Gene. 1999;240:115-23 pubmed..Together, these data suggest that each isoform may play a distinct physiological role in coordinating chorismate mutase activity with developmental and environmental signals. ..
- Warpeha K, Upadhyay S, Yeh J, Adamiak J, Hawkins S, Lapik Y, et al. The GCR1, GPA1, PRN1, NF-Y signal chain mediates both blue light and abscisic acid responses in Arabidopsis. Plant Physiol. 2007;143:1590-600 pubmed..We also demonstrate that this mechanism is present in imbibed seeds wherein it affects germination rate. ..
- Updegraff E, Zhao F, Preuss D. The extracellular lipase EXL4 is required for efficient hydration of Arabidopsis pollen. Sex Plant Reprod. 2009;22:197-204 pubmed publisher..Our results indicate that changes in lipid composition at the pollen-stigma interface, possibly mediated by EXLs, are required for efficient pollination in species with dry stigmas. ..
- Jung H, Tschaplinski T, Wang L, Glazebrook J, Greenberg J. Priming in systemic plant immunity. Science. 2009;324:89-91 pubmed publisher..Furthermore, the predicted secreted protein AZI1 is also important for generating vascular sap that confers disease resistance. Thus, azelaic acid and AZI1 are components of plant systemic immunity involved in priming defenses. ..
- Warpeha K, Park Y, Williamson P. Susceptibility of intact germinating Arabidopsis thaliana to human fungal pathogens Cryptococcus neoformans and C. gattii. Appl Environ Microbiol. 2013;79:2979-88 pubmed publisher..In addition, an important role of laccase in plant as well as human virulence may suggest mechanisms for laccase retention and optimization during evolution of this fungal pathogen. ..
- Jones Rhoades M, Borevitz J, Preuss D. Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins. PLoS Genet. 2007;3:1848-61 pubmed..The coexpression of highly similar proteins suggests a high degree of functional redundancy among embryo sac genes. ..
- Dean J, Delaney S. Metabolism of salicylic acid in wild-type, ugt74f1 and ugt74f2 glucosyltransferase mutants of Arabidopsis thaliana. Physiol Plant. 2008;132:417-25 pubmed publisher..The SAG formation was a result of the UGT74F1 activity. This work demonstrates that changes in the activity of either SAGT enzyme can have a dramatic effect on the metabolism of exogenously supplied SA in Arabidopsis. ..
- Lapik Y, Kaufman L. The Arabidopsis cupin domain protein AtPirin1 interacts with the G protein alpha-subunit GPA1 and regulates seed germination and early seedling development. Plant Cell. 2003;15:1578-90 pubmed..These data indicate that AtPirin1 likely functions immediately downstream of GPA1 in regulating seed germination and early seedling development. ..
- Mayfield J, Fiebig A, Johnstone S, Preuss D. Gene families from the Arabidopsis thaliana pollen coat proteome. Science. 2001;292:2482-5 pubmed..Analysis of the syntenic region in Brassica oleracea revealed even greater divergence, but a similar clustering of the genes. Such allelic flexibility may promote speciation in plants. ..
- Warpeha K, Gibbons J, Carol A, Slusser J, Tree R, Durham W, et al. Adequate phenylalanine synthesis mediated by G protein is critical for protection from UV radiation damage in young etiolated Arabidopsis thaliana seedlings. Plant Cell Environ. 2008;31:1756-70 pubmed publisher..Phe-derived pigments do not collect in the epidermal cells of pd1 mutants when seedlings are treated with UV, particularly at the cotyledon tip. Addition of Phe to the growth media restores a wt phenotype to pd1 mutants. ..
- Barrett L, Bell T, Dwyer G, Bergelson J. Cheating, trade-offs and the evolution of aggressiveness in a natural pathogen population. Ecol Lett. 2011;14:1149-57 pubmed publisher..These results suggest that niche differentiation can contribute to the maintenance of virulence polymorphisms, and that both within-host and between-host growth rates modulate cheating and cooperation in P. syringae populations. ..
- Zhang X, Cal A, Borevitz J. Genetic architecture of regulatory variation in Arabidopsis thaliana. Genome Res. 2011;21:725-33 pubmed publisher..Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL. ..
- Dobritsa A, Shrestha J, Morant M, Pinot F, Matsuno M, Swanson R, et al. CYP704B1 is a long-chain fatty acid omega-hydroxylase essential for sporopollenin synthesis in pollen of Arabidopsis. Plant Physiol. 2009;151:574-89 pubmed publisher..This implies that each of the three genes is required to provide an indispensable subset of fatty acid-derived components within the sporopollenin biosynthesis framework. ..
- von Besser K, Frank A, Johnson M, Preuss D. Arabidopsis HAP2 (GCS1) is a sperm-specific gene required for pollen tube guidance and fertilization. Development. 2006;133:4761-9 pubmed..Moreover, our findings suggest that sperm, long considered to be passive cargo, are involved in directing the pollen tube to its target. ..
- Austin J. High-pressure freezing and freeze substitution of Arabidopsis for electron microscopy. Methods Mol Biol. 2014;1062:473-86 pubmed publisher..This chapter will describe these modifications for the preparation of plant tissues for routine electron microscopic studies, immunocytochemistry, and 3D tomographic electron imaging. ..
- Greenberg J, Silverman F, Liang H. Uncoupling salicylic acid-dependent cell death and defense-related responses from disease resistance in the Arabidopsis mutant acd5. Genetics. 2000;156:341-50 pubmed..We propose that acd5 plants mimic P. syringae-infected wild-type plants and that both SA and ethylene are normally involved in regulating cell death during some susceptible pathogen infections. ..
- Mach J, Castillo A, Hoogstraten R, Greenberg J. The Arabidopsis-accelerated cell death gene ACD2 encodes red chlorophyll catabolite reductase and suppresses the spread of disease symptoms. Proc Natl Acad Sci U S A. 2001;98:771-6 pubmed..We suggest that economically important plants overexpressing ACD2 might also show increased tolerance to pathogens and might be useful for increasing crop yields. ..
- Korves T, Bergelson J. A developmental response to pathogen infection in Arabidopsis. Plant Physiol. 2003;133:339-47 pubmed..We propose that these changes in flowering time and branch architecture constitute a general developmental response to pathogen infection that may affect tolerance of and/or resistance to disease...
- Zhang X, Shiu S, Shiu S, Cal A, Borevitz J. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet. 2008;4:e1000032 pubmed publisher..Our results demonstrated extensive genetic and epigenetic polymorphisms between Arabidopsis accessions and suggested a possible relationship between natural CG methylation variation and gene expression variation. ..
- Vinatzer B, Jelenska J, Greenberg J. Bioinformatics correctly identifies many type III secretion substrates in the plant pathogen Pseudomonas syringae and the biocontrol isolate P. fluorescens SBW25. Mol Plant Microbe Interact. 2005;18:877-88 pubmed..Finally, using the reduced AvrRpt2(101-255) reporter, we confirmed seven predicted effectors from P. syringae pv. tomato DC3000, four from P. syringae pv. syringae B728a, and two from P. fluorescens SBW25. ..
- Yao N, Eisfelder B, Marvin J, Greenberg J. The mitochondrion--an organelle commonly involved in programmed cell death in Arabidopsis thaliana. Plant J. 2004;40:596-610 pubmed..However, unlike in animal cells, in plant cells, mitochondrial cytochrome c release is not an obligatory step in PCD control. ..
- Barchiesi J, Hedin N, Iglesias A, Gomez Casati D, Ballicora M, Busi M. Identification of a novel starch synthase III from the picoalgae Ostreococcus tauri. Biochimie. 2017;133:37-44 pubmed publisher..Results show that these residues are important for OsttaSSIII-C activity, suggesting a strong similarity between the active site of the O. tauri SSIII-C isoform and other bacterial glycogen synthases. ..
- Mayfield J, Preuss D. Rapid initiation of Arabidopsis pollination requires the oleosin-domain protein GRP17. Nat Cell Biol. 2000;2:128-30 pubmed
- Huang Y, Li H, Gupta R, Morris P, Luan S, Kieber J. ATMPK4, an Arabidopsis homolog of mitogen-activated protein kinase, is activated in vitro by AtMEK1 through threonine phosphorylation. Plant Physiol. 2000;122:1301-10 pubmed..Surprisingly, in contrast to the animal enzymes, AtMEK1 may not be a dual-specificity kinase but, rather, the required Tyr phosphorylation on ATMPK4 may result from autophosphorylation. ..
- Jakob K, Goss E, Araki H, Van T, Kreitman M, Bergelson J. Pseudomonas viridiflava and P. syringae--natural pathogens of Arabidopsis thaliana. Mol Plant Microbe Interact. 2002;15:1195-203 pubmed publisher..viridiflava isolates. We believe that these pathogens will provide a powerful system for exploring coevolution in natural plant-pathogen interactions...
- Little D, Rao H, Oliva S, Daniel Vedele F, Krapp A, Malamy J. The putative high-affinity nitrate transporter NRT2.1 represses lateral root initiation in response to nutritional cues. Proc Natl Acad Sci U S A. 2005;102:13693-8 pubmed..We propose that Arabidopsis NRT2.1 acts either as a nitrate sensor or signal transducer to coordinate the development of the root system with nutritional cues. ..
- Song J, Lu H, Greenberg J. Divergent roles in Arabidopsis thaliana development and defense of two homologous genes, aberrant growth and death2 and AGD2-LIKE DEFENSE RESPONSE PROTEIN1, encoding novel aminotransferases. Plant Cell. 2004;16:353-66 pubmed publisher..We suggest that AGD2 synthesizes an important amino acid-derived molecule that promotes development and suppresses defenses, whereas ALD1 generates a related amino acid-derived molecule important for activating defense signaling...
- Fiebig A, Kimport R, Preuss D. Comparisons of pollen coat genes across Brassicaceae species reveal rapid evolution by repeat expansion and diversification. Proc Natl Acad Sci U S A. 2004;101:3286-91 pubmed..We tested cross-species interactions, showing that the ability of A. arenosa stigmas to hydrate pollen correlated with GRP divergence and identifying A. arenosa as a model for future studies of pollen recognition...
- Johnson M, von Besser K, Zhou Q, Smith E, Aux G, Patton D, et al. Arabidopsis hapless mutations define essential gametophytic functions. Genetics. 2004;168:971-82 pubmed..We also identified genomic DNA flanking the insertion element for eleven hap mutants and showed that hap1 disrupts AtMago, a gene whose ortholog is important for Drosophila cell polarity. ..
- Horton M, Hancock A, Huang Y, Toomajian C, Atwell S, Auton A, et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet. 2012;44:212-6 pubmed publisher..We have made the seeds we used to produce this Regional Mapping (RegMap) panel publicly available. This panel comprises one of the largest genomic mapping resources currently available for global natural isolates of a non-human species. ..
- Lee M, Jelenska J, Greenberg J. Arabidopsis proteins important for modulating defense responses to Pseudomonas syringae that secrete HopW1-1. Plant J. 2008;54:452-65 pubmed publisher..Thus, the WIN proteins have different roles in modulating plant defense. ..
- Jakob K, Kniskern J, Bergelson J. The role of pectate lyase and the jasmonic acid defense response in Pseudomonas viridiflava virulence. Mol Plant Microbe Interact. 2007;20:146-58 pubmed..viridiflava virulence on A. thaliana and found that pectate lyase activity is correlated with virulence, whereas the removal of pectate lyase or HrpL significantly reduced virulence. ..
- Zhong R, Thompson J, Ottesen E, Lamppa G. A forward genetic screen to explore chloroplast protein import in vivo identifies Moco sulfurase, pivotal for ABA and IAA biosynthesis and purine turnover. Plant J. 2010;63:44-59 pubmed publisher..These enzyme activities were not detected in aci2-1. ABA, IAA and/or purine turnover may play previously unrecognized roles in the regulation of chloroplast protein import in response to developmental, metabolic and environmental cues. ..
- Zhang X, Borevitz J. Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics. 2009;182:943-54 pubmed publisher..Our findings demonstrate a method of global functional characterization of allele-specific expression and highlight that chromatin structure is intertwined with evolution of cis- and trans-regulatory variation. ..
- Yao N, Greenberg J. Arabidopsis ACCELERATED CELL DEATH2 modulates programmed cell death. Plant Cell. 2006;18:397-411 pubmed
- Korves T, Bergelson J. A novel cost of R gene resistance in the presence of disease. Am Nat. 2004;163:489-504 pubmed..A spatially variable model suggests that a trade-off between net benefits and net costs with attack may help explain the persistence of individuals lacking R gene resistance to disease. ..
- Song J, Lu H, McDowell J, Greenberg J. A key role for ALD1 in activation of local and systemic defenses in Arabidopsis. Plant J. 2004;40:200-12 pubmed..Finally, ALD1 and PAD4 can mutually affect each other's expression in a constitutive defense mutant, suggesting that these two genes can act in a signal amplification loop...
- Karasov T, Barrett L, Hershberg R, Bergelson J. Similar levels of gene content variation observed for Pseudomonas syringae populations extracted from single and multiple host species. PLoS ONE. 2017;12:e0184195 pubmed publisher..Overall, our results demonstrate that while variation in the presence of specific genes can affect the success of a pathogen within its host, the majority of gene content variation is not strongly associated with patterns of host use. ..