TY  - JOUR
AB  - Genome sequence assemblies form a durable and precise framework that supports nearly all areas of biological research, including evolutionary biology, taxonomy and conservation, pathogen population diversity, crop domestication and biochemistry. In the early days of plant genomics, resources were limited to a handful of tractable genomes, leading to a tension between focus on discovering mechanisms in experimental species such as Arabidopsis thaliana (Arabidopsis) and on trait analyses in crop species. This tension arose from difficulties in translating knowledge of gene function across the large evolutionary distances between Arabidopsis and diverse crop species without comparative genome support. For some time, these clashing interests influenced funding priorities in plant science that limited both the acquisition of knowledge of mechanisms in Arabidopsis and the timely development of the capacity of crop science to incorporate knowledge of genes and their mechanisms. In this review we show how advances in genomics analysis technologies are revealing a high degree of conservation of molecular mechanisms between evolutionarily distant plant species. This progress is bridging the model-species-to-crop barrier, resulting in ever-increasing unification of plant science that is now accelerating progress in understanding mechanisms underlying diverse traits in crops and improving their performance. We lay out some examples of important priorities and outcomes arising from these new opportunities.
AU  - Bevan, M.W.*
AU  - Messerer, M.
AU  - Gundlach, H.
AU  - Kamal, N.*
AU  - Hall, A.*
AU  - Spannagl, M.
AU  - Mayer, K.F.X.
C1  - 74160
C2  - 57354
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
TI  - Integrating Arabidopsis and crop species gene discovery for crop improvement.
JO  - Plant Cell
VL  - 37
IS  - 5
PB  - Oxford Univ Press Inc
PY  - 2025
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Arabidopsis (Arabidopsis thaliana) plants can produce photosynthetic tissue with active chloroplasts at temperatures as low as 4°C, and this process depends on the presence of the nuclear-encoded, chloroplast-localized RNA-binding protein CP29A. In this study, we demonstrate that CP29A undergoes phase separation in vitro and in vivo in a temperature-dependent manner, which is mediated by a prion-like domain (PLD) located between the two RNA recognition motif (RRM) domains of CP29A. The resulting droplets display liquid-like properties and are found near chloroplast nucleoids. The PLD is required to support chloroplast RNA splicing and translation in cold-treated tissue. Together, our findings suggest that plant chloroplast gene expression is compartmentalized by inducible condensation of CP29A at low temperatures, a mechanism that could play a crucial role in plant cold resistance.
AU  - Legen, J.*
AU  - Lenzen, B.*
AU  - Kachariya, N.
AU  - Feltgen, S.*
AU  - Gao, Y.*
AU  - Mergenthal, S.*
AU  - Weber, W.*
AU  - Klotzsch, E.*
AU  - Zoschke, R.*
AU  - Sattler, M.
AU  - Schmitz-Linneweber, C.*
C1  - 70660
C2  - 55700
TI  - A prion-like domain is required for phase separation and chloroplast RNA processing during cold acclimation in Arabidopsis.
JO  - Plant Cell
PY  - 2024
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Altering plant water use efficiency (WUE) is a promising approach for achieving sustainable crop production in changing climate scenarios. Here, we show that WUE can be tuned by alleles of a single gene discovered in elite maize (Zea mays) breeding material. Genetic dissection of a genomic region affecting WUE led to the identification of the gene ZmAbh4 as causative for the effect. CRISPR/Cas9-mediated ZmAbh4 inactivation increased WUE without growth reductions in well-watered conditions. ZmAbh4 encodes an enzyme that hydroxylates the phytohormone abscisic acid (ABA) and initiates its catabolism. Stomatal conductance is regulated by ABA and emerged as a major link between variation in WUE and discrimination against the heavy carbon isotope (Δ13C) during photosynthesis in the C4 crop maize. Changes in Δ13C persisted in kernel material, which offers an easy-to-screen proxy for WUE. Our results establish a direct physiological and genetic link between WUE and Δ13C through a single gene with potential applications in maize breeding.
AU  - Blankenagel, S.*
AU  - Eggels, S.*
AU  - Frey, M.*
AU  - Grill, E.*
AU  - Bauer, E.*
AU  - Dawid, C.*
AU  - Fernie, A.R.*
AU  - Haberer, G.
AU  - Hammerl, R.*
AU  - Barbosa Medeiros, D.*
AU  - Ouzunova, M.*
AU  - Presterl, T.*
AU  - Ruß, V.*
AU  - Schäufele, R.*
AU  - Schlüter, U.*
AU  - Tardieu, F.*
AU  - Urbany, C.*
AU  - Urzinger, S.*
AU  - Weber, A.P.M.*
AU  - Schön, C.C.*
AU  - Avramova, V.*
C1  - 65661
C2  - 52873
SP  - 3860-3872
TI  - Natural alleles of the abscisic acid catabolism gene ZmAbh4 modulate water use efficiency and carbon isotope discrimination in maize.
JO  - Plant Cell
VL  - 34
IS  - 10
PY  - 2022
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Glucosylation modulates the biological activity of small molecules and frequently leads to their inactivation. The Arabidopsis thaliana glucosyltransferase UGT76B1 is involved in conjugating the stress hormone salicylic acid (SA) as well as isoleucic acid (ILA). Here, we show that UGT76B1 also glucosylates N-hydroxypipecolic acid (NHP), which is synthesized by FLAVIN-DEPENDENT MONOOXYGENASE 1 (FMO1) and activates systemic acquired resistance (SAR). Upon pathogen attack, Arabidopsis leaves generate two distinct NHP hexose conjugates, NHP-O-β-glucoside and NHP glucose ester, whereupon only NHP-O-β-glucoside formation requires a functional SA pathway. The ugt76b1 mutants specifically fail to generate the NHP-O-β-glucoside, and recombinant UGT76B1 synthesizes NHP-O-β-glucoside in vitro in competition with SA and ILA. The loss of UGT76B1 elevates the endogenous levels of NHP, SA, and ILA and establishes a constitutive SAR-like immune status. Introgression of the fmo1 mutant lacking NHP biosynthesis into the ugt76b1 background abolishes this SAR-like resistance. Moreover, overexpression of UGT76B1 in Arabidopsis shifts the NHP and SA pools toward O-β-glucoside formation and abrogates pathogen-induced SAR. Our results further indicate that NHP-triggered immunity is SA-dependent and relies on UGT76B1 as a common metabolic hub. Thereby, UGT76B1-mediated glucosylation controls the levels of active NHP, SA, and ILA in concert to balance the plant immune status.
AU  - Bauer, S.
AU  - Mekonnen, D.W.
AU  - Hartmann, M.*
AU  - Yildiz, I.*
AU  - Janowski, R.
AU  - Lange, B.
AU  - Geist, B.
AU  - Zeier, J.*
AU  - Schäffner, A.
C1  - 61750
C2  - 50443
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
SP  - 714-734
TI  - UGT76B1, a promiscuous hub of small molecule-based immune signaling, glucosylates N-hydroxypipecolic acid, and balances plant immunity.
JO  - Plant Cell
VL  - 33
IS  - 3
PB  - Oxford Univ Press Inc
PY  - 2021
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even 5-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
AU  - Mascher, M.*
AU  - Wicker, T.*
AU  - Jenkins, J.*
AU  - Plott, C.*
AU  - Lux, T.
AU  - Koh, C.S.*
AU  - Ens, J.*
AU  - Gundlach, H.
AU  - Boston, L.B.*
AU  - Tulpová, Z.*
AU  - Holden, S.*
AU  - Hernández-Pinzón, I.*
AU  - Scholz, U.*
AU  - Mayer, K.F.X.
AU  - Spannagl, M.
AU  - Pozniak, C.J.*
AU  - Sharpe, A.G.*
AU  - Šimková, H.*
AU  - Moscou, M.J.*
AU  - Grimwood, J.*
AU  - Schmutz, J.*
AU  - Stein, N.*
C1  - 61547
C2  - 50345
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
SP  - 1888-1906
TI  - Long-read sequence assembly: A technical evaluation in barley.
JO  - Plant Cell
VL  - 33
IS  - 6
PB  - Oxford Univ Press Inc
PY  - 2021
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is present in all photosynthetic organisms and is a key enzyme for photosynthesis-driven life on Earth. Its most prominent form is a hetero-oligomer in which small subunits (SSU) stabilize the core of the enzyme built from large subunits (LSU), yielding, after a chaperone-Assisted multistep assembly process, an LSU8SSU8 hexadecameric holoenzyme. Here we use Chlamydomonas reinhardtii and a combination of site-directed mutants to dissect the multistep biogenesis pathway of Rubisco in vivo. We identify assembly intermediates, in two of which LSU are associated with the RAF1 chaperone. Using genetic and biochemical approaches we further unravel a major regulation process during Rubisco biogenesis, in which LSU translation is controlled by its ability to assemble with the SSU, via the mechanism of control by epistasy of synthesis (CES). Altogether this leads us to propose a model whereby the last assembly intermediate, an LSU8-RAF1 complex, provides the platform for SSU binding to form the Rubisco enzyme, and when SSU is not available, converts to a key regulatory form that exerts negative feedback on the initiation of LSU translation.
AU  - Wietrzynski, W.
AU  - Traverso, E.*
AU  - Wollman, F.A.*
AU  - Wostrikoff, K.*
C1  - 62535
C2  - 50787
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
SP  - 1706-1727
TI  - The state of oligomerization of Rubisco controls the rate of synthesis of the Rubisco large subunit in Chlamydomonas reinhardtii.
JO  - Plant Cell
VL  - 33
IS  - 5
PB  - Oxford Univ Press Inc
PY  - 2021
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - How the membrane trafficking system spatially organizes intracellular activities and intercellular signaling networks in plants is not well understood. Transport Protein Particle (TRAPP) complexes play key roles in the selective delivery of membrane vesicles to various subcellular compartments in yeast and animals but remain to be fully characterized in plants. Here, we investigated TRAPP complexes in Arabidopsis (Arabidopsis thaliana) using immunoprecipitation followed by quantitative mass spectrometry analysis of AtTRS33, a conserved core component of all TRAPP complexes. We identified 14 AtTRS33-interacting proteins, including homologs of all 13 TRAPP components in mammals and a protein that has homologs only in multicellular photosynthetic organisms and is thus named TRAPP-Interacting Plant Protein (TRIPP). TRIPP specifically associates with the TRAPPII complex through binary interactions with two TRAPPII-specific subunits. TRIPP colocalized with a subset of TRS33 compartments and trans-Golgi network markers in a TRS33-dependent manner. Loss-of-function tripp mutants exhibited dwarfism, sterility, partial photomorphogenesis in the dark, reduced polarity of the auxin transporter PIN2, incomplete cross wall formation, and altered localization of a TRAPPII-specific component. Therefore, TRIPP is a plant-specific component of the TRAPPII complex with important functions in trafficking, plant growth, and development.
AU  - Garcia, V.J.*
AU  - Xu, S.*
AU  - Ravikumar, R.*
AU  - Wang, W.*
AU  - Elliott, L.*
AU  - Gonzalez, E.*
AU  - Fesenko, M.*
AU  - Altmann, M.
AU  - Brunschweiger, B.*
AU  - Falter-Braun, P.
AU  - Moore, I.*
AU  - Burlingame, A.*
AU  - Assaad, F.F.*
AU  - Wang, Z.*
C1  - 59730
C2  - 48998
CY  - 15501 Monona Drive, Rockville, Md 20855 Usa
SP  - 2424-2443
TI  - TRIPP is a plant-specific component of the Arabidopsis TRAPPII membrane trafficking complex with important roles in plant development.
JO  - Plant Cell
VL  - 32
IS  - 7
PB  - Amer Soc Plant Biologists
PY  - 2020
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - A systemic analysis identifies GROWTH-REGULATING FACTORS as DELLA-targeted transcription factors during cold stress in Arabidopsis.DELLA proteins are repressors of the gibberellin (GA) hormone signaling pathway that act mainly by regulating transcription factor activities in plants. GAs induce DELLA repressor protein degradation and thereby control a number of critical developmental processes as well as responses to stresses such as cold. The strong effect of cold temperatures on many physiological processes has rendered it difficult to assess, based on phenotypic criteria, the role of GA and DELLAs in plant growth during cold stress. Here, we uncover substantial differences in the GA transcriptomes between plants grown at ambient temperature (21 degrees C) and plants exposed to cold stress (4 degrees C) in Arabidopsis (Arabidopsis thaliana). We further identify over 250, to the largest extent previously unknown, DELLA-transcription factor interactions using the yeast two-hybrid system. By integrating both data sets, we reveal that most members of the nine-member GRF (GROWTH REGULATORY FACTOR) transcription factor family are DELLA interactors and, at the same time, that several GRF genes are targets of DELLA-modulated transcription after exposure to cold stress. We find that plants with altered GRF dosage are differentially sensitive to the manipulation of GA and hence DELLA levels, also after cold stress, and identify a subset of cold stress-responsive genes that qualify as targets of this DELLA-GRF regulatory module.
AU  - Lantzouni, O.*
AU  - Alkofer, A.
AU  - Falter-Braun, P.
AU  - Schwechheimer, C.*
C1  - 59108
C2  - 48565
CY  - 15501 Monona Drive, Rockville, Md 20855 Usa
SP  - 1018-1034
TI  - Growth-regulating factors interact with DELLAs and regulate growth in cold stress.
JO  - Plant Cell
VL  - 32
IS  - 4
PB  - Amer Soc Plant Biologists
PY  - 2020
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Throughout the temperate zones, plants face combined drought and heat spells in increasing frequency and intensity. Here, we compared periodic (intermittent, i.e., high-frequency) versus chronic (continuous, i.e., high-intensity) drought-heat stress scenarios in gray poplar (Populus× canescens) plants for phenotypic and transcriptomic effects during stress and after recovery. Photosynthetic productivity after stress recovery exceeded the performance of poplar trees without stress experience. We analyzed the molecular basis of this stress-related memory phenotype and investigated gene expression responses across five major tree compartments including organs and wood tissues. For each of these tissue samples, transcriptomic changes induced by the two stress scenarios were highly similar during the stress phase but strikingly divergent after recovery. Characteristic molecular response patterns were found across tissues but involved different genes in each tissue. Only a small fraction of genes showed similar stress and recovery expression profiles across all tissues, including type 2C protein phosphatases, the LATE EMBRYOGENESIS ABUNDANT PROTEIN4-5 genes, and homologs of the Arabidopsis (Arabidopsis thaliana) transcription factor HOMEOBOX7. Analysis of the predicted transcription factor regulatory networks for these genes suggested that a complex interplay of common and tissue-specific components contributes to the coordination of post-recovery responses to stress in woody plants.
AU  - Georgii, E.
AU  - Kugler, K.G.
AU  - Pfeifer, M.
AU  - Vanzo, E.
AU  - Block, K.
AU  - Domagalska, M.A.*
AU  - Jud, W.
AU  - AbdElgawad, H.*
AU  - Asard, H.*
AU  - Reinhardt, R.*
AU  - Hansel, A.*
AU  - Spannagl, M.
AU  - Schäffner, A.
AU  - Palme, K.*
AU  - Mayer, K.F.X.
AU  - Schnitzler, J.-P.
C1  - 55421
C2  - 46264
CY  - 15501 Monona Drive, Rockville, Md 20855 Usa
SP  - 346-367
TI  - The systems architecture of molecular memory in poplar after abiotic stress.
JO  - Plant Cell
VL  - 31
IS  - 2
PB  - Amer Soc Plant Biologists
PY  - 2019
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - This study investigates the role of volatile organic compounds in systemic acquired resistance (SAR), a salicylic acid (SA)-associated, broad-spectrum immune response in systemic, healthy tissues of locally infected plants. Gas chromatography coupled to mass spectrometry analyses of SAR-related emissions of wild-type and non-SAR-signal-producing mutant plants associated SAR with monoterpene emissions. Headspace exposure of Arabidopsis thaliana to a mixture of the bicyclic monoterpenes α-pinene and β-pinene induced defense, accumulation of reactive oxygen species, and expression of SA- and SAR-related genes, including the SAR regulatory AZELAIC ACID INDUCED1 (AZI1) gene and three of its paralogs. Pinene-induced resistance was dependent on SA biosynthesis and signaling and on AZI1. A. thaliana geranylgeranyl reductase1 mutants with reduced monoterpene biosynthesis were SAR-defective but mounted normal local resistance and methyl salicylate-induced defense responses, suggesting that monoterpenes act in parallel with SA. The volatile emissions from SAR signal-emitting plants induced defense in neighboring plants and this was associated with the presence of α-pinene, β-pinene, and camphene in the emissions of the 'sender' plants. Our data suggest that monoterpenes, particularly pinenes, promote SAR, acting through ROS and AZI1, and likely function as infochemicals in plant-to-plant signaling, thus allowing defense signal propagation between neighboring plants.
AU  - Riedlmeier, M.
AU  - Ghirardo, A.
AU  - Wenig, M.
AU  - Knappe, C.
AU  - Koch, K.
AU  - Georgii, E.
AU  - Dey, S.
AU  - Parker, J.E.*
AU  - Schnitzler, J.-P.
AU  - Vlot, A.C.
C1  - 51195
C2  - 43104
CY  - Rockville
SP  - 1440-1459
TI  - Monoterpenes support systemic acquired resistance within and between plants.
JO  - Plant Cell
VL  - 29
IS  - 6
PB  - Amer Soc Plant Biologists
PY  - 2017
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Plant growth and development are highly regulated processes that are coordinated by hormones including the brassinosteroids (BRs), a group of steroids with structural similarity to steroid hormones of mammals. Although it is well understood how BRs are produced and how their signals are transduced, BR targets, which directly confer the hormone's growth-promoting effects, have remained largely elusive. Here, we show that BRs regulate the biosynthesis of gibberellins (GAs), another class of growth-promoting hormones, in Arabidopsis thaliana. We reveal that Arabidopsis mutants deficient in BR signaling are severely impaired in the production of bioactive GA, which is correlated with defective GA biosynthetic gene expression. Expression of the key GA biosynthesis gene GA20ox1 in the BR signaling mutant bri1-301 rescues many of its developmental defects. We provide evidence that supports a model in which the BR-regulated transcription factor BES1 binds to a regulatory element in promoters of GA biosynthesis genes in a BR-induced manner to control their expression. In summary, our study underscores a role of BRs as master regulators of GA biosynthesis and shows that this function is of major relevance for the growth and development of vascular plants.
AU  - Unterholzner, S.J.*
AU  - Rozhon, W.*
AU  - Papacek, M.*
AU  - Ciomas, J.*
AU  - Lange, T.*
AU  - Kugler, K.G.
AU  - Mayer, K.F.X.
AU  - Sieberer, T.*
AU  - Poppenberger, B.*
C1  - 46536
C2  - 37720
SP  - 2261-2272
TI  - Brassinosteroids are master regulators of gibberellin biosynthesis in arabidopsis.
JO  - Plant Cell
VL  - 27
IS  - 8
PY  - 2015
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Arabidopsis thaliana tortifolía2 carries a point mutation in α-tubulin 4 and shows aberrant cortical microtubule dynamics. The microtubule defect of tortifolia2 leads to overbranching and right-handed helical growth in the single-celled leaf trichomes. Here, we use tortifolia2 to further our understanding of microtubules in plant cell differentiation. Trichomes at the branching stage show an apical ring of cortical microtubules, and our analyses support that this ring is involved in marking the prospective branch site. tortifolia2 showed ectopic microtubule bundles at this stage, consistent with a function for microtubules in selecting new branch sites. Overbranching of tortifolia2 required the C-terminal binding protein/brefeldin A-ADP ribosylated substrate protein ANGUSTIFOLIA1, and our results indicate that the angustifolia1 mutant is hypersensitive to alterations in microtubule dynamics. To analyze whether actin and microtubules cooperate in the trichome cell expansion process, we generated double mutants of tortifolia2 with distorted1, a mutant that is defective in the actin-related ARP2/3 complex. The double mutant trichomes showed a complete loss of growth anisotropy, suggesting a genetic interaction of actin and microtubules. Green fluorescent protein labeling of F-actin or microtubules in tortifolia2 distorted1 double mutants indicated that F-actin enhances microtubule dynamics and enables reorientation. Together, our results suggest actin-dependent and -independent functions of cortical microtubules in trichome differentiation.
AU  - Sambade, A.*
AU  - Findlay, K.*
AU  - Schäffner, A.
AU  - Lloyd, C.W.*
AU  - Buschmann, H.*
C1  - 31207
C2  - 34202
CY  - Rockville
SP  - 1629-1644 
TI  - Actin-dependent and -independent functions of cortical microtubules in the differentiation of Arabidopsis leaf trichomes.
JO  - Plant Cell
VL  - 26
IS  - 4
PB  - Amer Soc Plant Biologists
PY  - 2014
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Aldoximes are known as floral and vegetative plant volatiles but also as biosynthetic intermediates for other plant defense compounds. While the cytochrome P450 monooxygenases (CYP) from the CYP79 family forming aldoximes as biosynthetic intermediates have been intensively studied, little is known about the enzymology of volatile aldoxime formation. We characterized two P450 enzymes, CYP79D6v3 and CYP79D7v2, which are involved in herbivore-induced aldoxime formation in western balsam poplar (Populus trichocarpa). Heterologous expression in Saccharomyces cerevisiae revealed that both enzymes produce a mixture of different aldoximes. Knockdown lines of CYP79D6/7 in gray poplar (Populus × canescens) exhibited a decreased emission of aldoximes, nitriles, and alcohols, emphasizing that the CYP79s catalyze the first step in the formation of a complex volatile blend. Aldoxime emission was found to be restricted to herbivore-damaged leaves and is closely correlated with CYP79D6 and CYP79D7 gene expression. The semi-volatile phenylacetaldoxime decreased survival and weight gain of gypsy moth (Lymantria dispar) caterpillars, suggesting that aldoximes may be involved in direct defense. The wide distribution of volatile aldoximes throughout the plant kingdom and the presence of CYP79 genes in all sequenced genomes of angiosperms suggest that volatile formation mediated by CYP79s is a general phenomenon in the plant kingdom.
AU  - Irmisch, S.*
AU  - Andrea, C.M.*
AU  - Boeckler, G.A.*
AU  - Schmidt, A.*
AU  - Reichelt, M.*
AU  - Schneider, B.*
AU  - Block, K.
AU  - Schnitzler, J.-P.
AU  - Gershenzon, J.*
AU  - Unsicker, S.B.*
AU  - Köllner, T.G.*
C1  - 28241
C2  - 33025
SP  - 4737-4754
TI  - Two herbivore-induced cytochrome P450 enzymes CYP79D6 and CYP79D7 catalyze the formation of volatile aldoximes involved in poplar defense.
JO  - Plant Cell
VL  - 25
IS  - 11
PB  - Amer. Soc. Plant Biologists
PY  - 2013
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (∼8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.
AU  - Martis, M.M.
AU  - Zhou, R.*
AU  - Haseneyer, G.*
AU  - Schmutzer, T.*
AU  - Vrana, J.*
AU  - Kubaláková, M.*
AU  - König, S.*
AU  - Kugler, K.G.
AU  - Scholz, U.*
AU  - Hackauf, B.*
AU  - Korzun, V.*
AU  - Schön, C.C.*
AU  - Dolezel, J.*
AU  - Bauer, E.*
AU  - Mayer, K.F.X.
AU  - Stein, N.*
C1  - 27958
C2  - 32877
SP  - 3685-3698
TI  - Reticulate evolution of the rye genome.
JO  - Plant Cell
VL  - 25
IS  - 10
PB  - Amer. Soc. Plant Biologists
PY  - 2013
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - The water status of plant leaves depends on the efficiency of the water supply, from the vasculature to inner tissues. This process is under hormonal and environmental regulation and involves aquaporin water channels. In Arabidopsis thaliana, the rosette hydraulic conductivity (K-ros) is higher in darkness than it is during the day. Knockout plants showed that three plasma membrane intrinsic proteins (PIPs) sharing expression in veins (PIP1;2, PIP2;1, and PIP2;6) contribute to rosette water transport, and PIP2;1 can fully account for K-ros responsiveness to darkness. Directed expression of PIP2;1 in veins of a pip2;1 mutant was sufficient to restore K-ros. In addition, a positive correlation, in both wild-type and PIP2;1-overexpressing plants, was found between K-ros and the osmotic water permeability of protoplasts from the veins but not from the mesophyll. Thus, living cells in veins form a major hydraulic resistance in leaves. Quantitative proteomic analyses showed that light-dependent regulation of K-ros is linked to diphosphorylation of PIP2;1 at Ser-280 and Ser-283. Expression in pip2;1 of phosphomimetic and phosphorylation- deficient forms of PIP2;1 demonstrated that phosphorylation at these two sites is necessary for K-ros enhancement under darkness. These findings establish how regulation of a single aquaporin isoform in leaf veins critically determines leaf hydraulics.
AU  - Prado, K.*
AU  - Boursiac, Y.*
AU  - Tournaire-Roux, C.*
AU  - Monneuse, J.M.*
AU  - Postaire, O.*
AU  - Da Ines, O.
AU  - Schäffner, A.
AU  - Hem, S.*
AU  - Santoni, V.*
AU  - Maurel, C.*
C1  - 24694
C2  - 31634
SP  - 1029-1039
TI  - Regulation of Arabidopsis leaf hydraulics involves light-dependent phosphorylation of aquaporins in veins.
JO  - Plant Cell
VL  - 25
IS  - 3
PB  - Amer. Soc. Plant Biologists
PY  - 2013
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.
AU  - Laurie, J.D.*
AU  - Ali, S.*
AU  - Linning, R.*
AU  - Mannhaupt, G.
AU  - Wong, P.
AU  - Güldener, U.
AU  - Münsterkötter, M.
AU  - Moore, R.*
AU  - Kahmann, R.*
AU  - Bakkeren, G.*
AU  - Schirawski, J.*
C1  - 8241
C2  - 30028
SP  - 1733-1745
TI  - Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements.
JO  - Plant Cell
VL  - 24
IS  - 5
PB  - Amer. Soc. Plant Biologists
PY  - 2012
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - The Arabidopsis information portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.
AU  - International Arabidopsis Informatics Consortium (Mayer, K.F.X.)
C1  - 11717
C2  - 30767
SP  - 2248-2256
TI  - Taking the next step: Building an Arabidopsis information portal.
JO  - Plant Cell
VL  - 24
IS  - 6
PB  - Amer. Soc. Plant Biologists
PY  - 2012
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
AU  - Mayer, K.F.X.
AU  - Martis, M.M.
AU  - Hedley, P.E.*
AU  - Šimková, H.*
AU  - Liu, H.*
AU  - Morris, J.A.*
AU  - Steuernagel, B.*
AU  - Taudien, S.*
AU  - Roessner, S.K.
AU  - Gundlach, H.
AU  - Kubaláková, M.*
AU  - Suchánková, P.*
AU  - Murat, F.*
AU  - Felder, M.*
AU  - Nussbaumer, T.
AU  - Graner, A.*
AU  - Salse, J.*
AU  - Endo, T.*
AU  - Sakai, H.*
AU  - Tanaka, T.*
AU  - Itoh, T.*
AU  - Sato, K.*
AU  - Platzer, M.*
AU  - Matsumoto, T.*
AU  - Scholz, U.*
AU  - Dolezel, J.*
AU  - Waugh, R.*
AU  - Stein, N.*
C1  - 6559
C2  - 29071
SP  - 1249-1263
TI  - Unlocking the barley genome by chromosomal and comparative genomics.
JO  - Plant Cell
VL  - 23
IS  - 4
PB  - American Soc. of Plant Biologists
PY  - 2011
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Plants coordinate and tightly regulate pathogen defense by the mostly antagonistic salicylate (SA)- and jasmonate (JA)-mediated signaling pathways. Here, we show that the previously uncharacterized glucosyltransferase UGT76B1 is a novel player in this SA-JA signaling crosstalk. UGT76B1 was selected as the top stress-induced isoform among all 122 members of the Arabidopsis thaliana UGT family. Loss of UGT76B1 function leads to enhanced resistance to the biotrophic pathogen Pseudomonas syringae and accelerated senescence but increased susceptibility toward necrotrophic Alternaria brassicicola. This is accompanied by constitutively elevated SA levels and SA-related marker gene expression, whereas JA-dependent markers are repressed. Conversely, UGT76B1 overexpression has the opposite effect. Thus, UGT76B1 attenuates SA-dependent plant defense in the absence of infection, promotes the JA response, and delays senescence. The ugt76b1 phenotypes were SA dependent, whereas UGT76B1 overexpression indicated that this gene possibly also has a direct effect on the JA pathway. Nontargeted metabolomic analysis of UGT76B1 knockout and overexpression lines using ultra-high-resolution mass spectrometry and activity assays with the recombinant enzyme led to the ab initio identification of isoleucic acid (2-hydroxy-3-methyl-pentanoic acid) as a substrate of UGT76B1. Exogenously applied isoleucic acid increased resistance against P. syringae infection. These findings indicate a novel link between amino acid-related molecules and plant defense that is mediated by small-molecule glucosylation. 22080599
AU  - von Saint Paul, V.
AU  - Zhang, W.
AU  - Kanawati, B.
AU  - Geist, B.
AU  - Faus-Kessler, T.
AU  - Schmitt-Kopplin, P.
AU  - Schäffner, A.
C1  - 6852
C2  - 29355
SP  - 4124-4145
TI  - The Arabidopsis glucosyltransferase UGT76B1 conjugates isoleucic acid and modulates plant defense and senescence.
JO  - Plant Cell
VL  - 23
IS  - 11
PB  - American Society of Plant Biologists
PY  - 2011
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were sampled per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely diverse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.
AU  - Wicker, T.*
AU  - Mayer, K.F.X.
AU  - Gundlach, H.
AU  - Martis, M.M.
AU  - Steuernagel, B.*
AU  - Scholz, U.*
AU  - Šimková, H.*
AU  - Kubaláková, M.*
AU  - Choulet, F.*
AU  - Taudien, S.*
AU  - Platzer, M.*
AU  - Feuillet, C.*
AU  - Fahima, T.*
AU  - Budak, H.*
AU  - Dolezel, J.*
AU  - Keller, B.*
AU  - Stein, N.*
C1  - 6260
C2  - 29083
SP  - 1706-1718
TI  - Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives.
JO  - Plant Cell
VL  - 23
IS  - 5
PB  - Amer Soc Plant Biologists
PY  - 2011
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - The role of reactive oxygen and nitrogen species in local and systemic defense reactions is well documented. NPR1 and TGA1 are key redox-controlled regulators of systemic acquired resistance in plants. NPR1 monomers interact with the reduced form of TGA1, which targets the activation sequence-1 (as-1) element of the promoter region of defense proteins. Here, we report the effect of the physiological nitric oxide donor S-nitrosoglutathione on the NPR1/TGA1 regulation system in Arabidopsis thaliana. Using the biotin switch method, we demonstrate that both NPR1 and TGA1 are S-nitrosylated after treatment with S-nitrosoglutathione. Mass spectrometry analyses revealed that the Cys residues 260 and 266 of TGA1 are S-nitrosylated and S-glutathionylated even at GSNO concentrations in the low micromolar range. Furthermore, we showed that S-nitrosoglutathione protects TGA1 from oxygen-mediated modifications and enhances the DNA binding activity of TGA1 to the as-1 element in the presence of NPR1. In addition, we observed that the translocation of NPR1 into the nucleus is promoted by nitric oxide. Taken together, our results suggest that nitric oxide is a redox regulator of the NPR1/TGA1 system and that they underline the importance of nitric oxide in the plant defense response.
AU  - Lindermayr, C.
AU  - Sell, S.
AU  - Müller, B.*
AU  - Leister, D.*
AU  - Durner, J.
C1  - 5548
C2  - 27604
SP  - 2894-2907
TI  - Redox regulation of the NPR1-TGA1 system of Arabidopsis thaliana by nitric oxide.
JO  - Plant Cell
VL  - 22
IS  - 8
PB  - American Society of Plant Biologists
PY  - 2010
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Several factors regulate plant organ growth polarity. tortifolia2 (tor2), a right-handed helical growth mutant, has a conservative replacement of Arg-2 with Lys in the alpha-tubulin 4 protein. Based on a published high-resolution (2.89 angstrom) tubulin structure, we predict that Arg-2 of alpha-tubulin forms hydrogen bonds with the GTPase domain of beta-tubulin, and structural modeling suggests that these contacts are interrupted in tor2. Consistent with this, we found that microtubule dynamicity is reduced in the tor2 background. We investigated the developmental origin of the helical growth phenotype using tor2. One hypothesis predicts that cell division patterns cause helical organ growth in Arabidopsis thaliana mutants. However, cell division patterns of tor2 root tips appear normal. Experimental uncoupling of cell division and expansion suggests that helical organ growth is based on cell elongation defects only. Another hypothesis is that twisting is due to inequalities in expansion of epidermal and cortical tissues. However, freely growing leaf trichomes of tor2 mutants show right-handed twisting and cortical microtubules form left-handed helices as early as the unbranched stage of trichome development. Trichome twisting is inverted in double mutants with tor3, a left-handed mutant. Single tor2 suspension cells also exhibit handed twisting. Thus, twisting of tor2 mutant organs appears to be a higher-order expression of the helical expansion of individual cells.
AU  - Buschmann, H.
AU  - Hauptmann, M.
AU  - Niessing, D.
AU  - Lloyd, C.W.*
AU  - Schäffner, A.
C1  - 597
C2  - 26700
SP  - 2090-2106
TI  - Helical growth of the Arabidopsis mutant tortifolia2 does not depend on cell division patterns but involves handed twisting of isolated cells.
JO  - Plant Cell
VL  - 21
IS  - 7
PB  - American Society of Plant Biologists
PY  - 2009
SN  - 1040-4651
ER  - 

TY  - JOUR
AB  - Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. Surprisingly, we found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. From the inferred phylogeny of all Arabidopsis and rice RLK/Pelle members, we estimated that the common ancestor of Arabidopsis and rice had >440 RLK/Pelles and that largescale expansions of certain RLK/Pelle members and fusions of novel domains have occurred in both the Arabidopsis and rice lineages since their divergence. In addition, the extracellular domains have higher nonsynonymous substitution rates than the intracellular domains, consistent with the role of extracellular domains in sensing diverse signals. The lineage-specific expansions in Arabidopsis can be attributed to both tandem and large-scale duplications, whereas tandem duplication seems to be the major mechanism for recent expansions in rice. Interestingly, although the RLKs that are involved in development seem to have rarely been duplicated after the Arabidopsis-rice split, those that are involved in defense/disease resistance apparently have undergone many duplication events. These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes.
AU  - Shiu, S.-H.*
AU  - Karlsowski, W.M.
AU  - Pan, R.*
AU  - Tzeng, Y.-H.*
AU  - Mayer, K.F.X.
AU  - Li, W.-H.*
C1  - 2738
C2  - 22217
SP  - 1220-1234
TI  - Comparative analysis of the receptor-like kinase family in Arabidopsis and rice.
JO  - Plant Cell
VL  - 16
IS  - 5
PB  - Amer. Soc. Plant Biologists
PY  - 2004
SN  - 1040-4651
ER  - 

TY  - JOUR
AU  - Javot, H.*
AU  - Lauvergeat, V.*
AU  - Santoni, V.*
AU  - Martin-Laurent, F.*
AU  - Güclü, J.*
AU  - Vinh, J.*
AU  - Heyes, J.*
AU  - Franck, K.I.
AU  - Schäffner, A.
AU  - Bouchez, D.*
AU  - Maurel, C.*
C1  - 22160
C2  - 20856
SP  - 509-522
TI  - Role of a Single Aquaporin Isoform in Root Water Uptake.
JO  - Plant Cell
VL  - 15
PY  - 2003
SN  - 1040-4651
ER  - 

TY  - JOUR
AU  - Overmyer, K.*
AU  - Tuominen, H.*
AU  - Kettunen, R.*
AU  - Betz, C.
AU  - Langebartels, C.
AU  - Sandermann, H.
AU  - Kangasjärvi, J.*
C1  - 21846
C2  - 20047
SP  - 1849-1862
TI  - Ozone-Sensitive Arabidopsis rcd1 Mutant Reveals Opposite Roles for Ethylene and Jasmonate Signaling Pathways in Regulating Superoxide-Dependent Cell Death.
JO  - Plant Cell
VL  - 12
PY  - 2000
SN  - 1040-4651
ER  -