TY  - JOUR
AB  - The importance of RNA-binding proteins (RBPs) for plant responses to environmental stimuli and development is well documented. Insights into the portfolio of RNAs they recognize, however, clearly lack behind the understanding gathered in non-plant model organisms. Here, we characterize binding of the circadian clock-regulated Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 7 (AtGRP7) to its target transcripts. We identified novel RNA targets from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) data using an improved bioinformatics pipeline that will be broadly applicable to plant RBP iCLIP data. 2705 transcripts with binding sites were identified in plants expressing AtGRP7-GFP that were not recovered in plants expressing an RNA-binding dead variant or GFP alone. A conserved RNA motif enriched in uridine residues was identified at the AtGRP7 binding sites. NMR titrations confirmed the preference of AtGRP7 for RNAs with a central U-rich motif. Among the bound RNAs, circadian clock-regulated transcripts were overrepresented. Peak abundance of the LHCB1.1 transcript encoding a chlorophyll-binding protein was reduced in plants overexpressing AtGRP7 whereas it was elevated in atgrp7 mutants, indicating that LHCB1.1 was regulated by AtGRP7 in a dose-dependent manner. In plants overexpressing AtGRP7, the LHCB1.1 half-life was shorter compared to wild-type plants whereas in atgrp7 mutant plants, the half-life was significantly longer. Thus, AtGRP7 modulates circadian oscillations of its in vivo binding target LHCB1.1 by affecting RNA stability.
AU  - Lewinski, M.*
AU  - Steffen, A.*
AU  - Kachariya, N.
AU  - Elgner, M.*
AU  - Schmäl, C.*
AU  - Messini, N.
AU  - Köster, T.*
AU  - Reichel, M.*
AU  - Sattler, M.
AU  - Zarnack, K.*
AU  - Staiger, D.*
C1  - 69053
C2  - 53831
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 203-224
TI  - Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 interaction with its iCLIP target LHCB1.1 correlates with changes in RNA stability and circadian oscillation.
JO  - Plant J.
VL  - 118
IS  - 1
PB  - Wiley
PY  - 2024
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Wind, rain, herbivores, obstacles, neighbouring plants, etc. provide important mechanical cues to steer plant growth and survival. Mechanostimulation to stimulate yield and stress resistance of crops is of significant research interest, yet a molecular understanding of transcriptional responses to touch is largely absent in cereals. To address this, we performed whole-genome transcriptomics following mechanostimulation of wheat, barley, and the recent genome-sequenced oat. The largest transcriptome changes occurred ±25 min after touching, with most of the genes being upregulated. While most genes returned to basal expression level by 1-2 h in oat, many genes retained high expression even 4 h post-treatment in barley and wheat. Functional categories such as transcription factors, kinases, phytohormones, and Ca2+ regulation were affected. In addition, cell wall-related genes involved in (hemi)cellulose, lignin, suberin, and callose biosynthesis were touch-responsive, providing molecular insight into mechanically induced changes in cell wall composition. Furthermore, several cereal-specific transcriptomic footprints were identified that were not observed in Arabidopsis. In oat and barley, we found evidence for systemic spreading of touch-induced signalling. Finally, we provide evidence that both the jasmonic acid-dependent and the jasmonic acid-independent pathways underlie touch-signalling in cereals, providing a detailed framework and marker genes for further study of (a)biotic stress responses in cereals.
AU  - Darwish, E.*
AU  - Ghosh, R.*
AU  - Bentzer, J.*
AU  - Tsardakas Renhuldt, N.*
AU  - Proux-Wera, E.*
AU  - Kamal, N.
AU  - Spannagl, M.
AU  - Hause, B.*
AU  - Sirijovski, N.*
AU  - Van Aken, O.*
C1  - 67816
C2  - 54294
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 282-302
TI  - The dynamics of touch-responsive gene expression in cereals.
JO  - Plant J.
VL  - 116
IS  - 1
PB  - Wiley
PY  - 2023
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.
AU  - Avni, R.*
AU  - Lux, T.
AU  - Minz-Dub, A.*
AU  - Millet, E.*
AU  - Sela, H.*
AU  - Distelfeld, A.*
AU  - Deek, J.*
AU  - Yu, G.*
AU  - Steuernagel, B.*
AU  - Pozniak, C.*
AU  - Ens, J.*
AU  - Gundlach, H.
AU  - Mayer, K.F.X.
AU  - Himmelbach, A.*
AU  - Stein, N.*
AU  - Mascher, M.*
AU  - Spannagl, M.
AU  - Wulff, B.B.H.*
AU  - Sharon, A.*
C1  - 64001
C2  - 52041
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 179-192
TI  - Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement.
JO  - Plant J.
VL  - 110
IS  - 1
PB  - Wiley
PY  - 2022
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - The green alga Chlamydomonas reinhardtii is one of the most studied microorganisms in photosynthesis research and for biofuel production. A detailed understanding of the dynamic regulation of its carbon metabolism is therefore crucial for metabolic engineering. Post-translational modifications can act as molecular switches for the control of protein function. Acetylation of the ɛ-amino group of lysine residues is a dynamic modification on proteins across organisms from all kingdoms. Here, we performed a mass spectrometry-based profiling of proteome and lysine acetylome dynamics in Chlamydomonas under varying growth conditions. Chlamydomonas liquid cultures were transferred from mixotrophic (light and acetate as carbon source) to heterotrophic (dark and acetate), or photoautotrophic (light only) growth conditions for 30 h before harvest. In total, 5863 protein groups and 1376 lysine acetylation sites were identified with a FDR < 1 %. As a major result of this study, our data shows that dynamic changes in abundance of lysine acetylation on various enzymes involved in photosynthesis, fatty acid metabolism, and the glyoxylate cycle are depending on acetate and light. Exemplary determination of acetylation site stoichiometries revealed particularly high occupancy levels on K175 of the large subunit of RuBisCO and K99 and K340 of peroxisomal citrate synthase, respectively, under heterotrophic conditions. The lysine acetylation stoichiometries correlated with increased activities of cellular citrate synthase, and the known inactivation of the Calvin-Benson cycle under heterotrophic conditions. In conclusion, the newly identified dynamic lysine acetylation sites may have a great potential for genetic engineering of metabolic pathways in Chlamydomonas.
AU  - Füßl, M.*
AU  - König, A.-C.
AU  - Eirich, J.*
AU  - Hartl, M.*
AU  - Kleinknecht, L.*
AU  - Bohne, A.V.*
AU  - Harzen, A.*
AU  - Kramer, K.*
AU  - Leister, D.*
AU  - Nickelsen, J.*
AU  - Finkemeier, I.*
C1  - 63438
C2  - 51534
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 261-277
TI  - Dynamic light- and acetate-dependent regulation of the proteome and lysine acetylome of Chlamydomonas.
JO  - Plant J.
VL  - 109
IS  - 1
PB  - Wiley
PY  - 2022
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic diversity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic diversity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic diversity available in PGRs and to transfer it into elite breeding pools. Here, a diverse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced-representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic diversity, sources of new allelic diversity and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research, and promote breeding in the future by allowing for the targeted introduction of novel allelic diversity into elite wheat breeding pools.
AU  - Lehnert, H.*
AU  - Berner, T.*
AU  - Lang, D.
AU  - Beier, S.*
AU  - Stein, N.*
AU  - Himmelbach, A.*
AU  - Kilian, B.*
AU  - Keilwagen, J.*
C1  - 66164
C2  - 53102
SP  - 897-918
TI  - Insights into breeding history, hotspot regions of selection and untapped allelic diversity for bread wheat breeding.
JO  - Plant J.
VL  - 112
IS  - 4
PY  - 2022
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Plants interact with other organisms employing volatile organic compounds (VOCs). The largest group of plant-released VOCs are terpenes, comprised of isoprene, monoterpenes and sesquiterpenes. Mono- and sesquiterpenes are well known communication compounds in plant-insect interactions whereas the smallest, most commonly emitted terpene, isoprene, is rather assigned a function in combating abiotic stresses. Recently, it has become evident that different volatile terpenes also act as plant-to-plant signaling cues. Upon being perceived, specific volatile terpenes can sensitize distinct signaling pathways in receiver plant cells, which in turn trigger plant innate immune responses. This vastly extends the range of action of volatile terpenes that not only protect plants from various biotic and abiotic stresses, but also convey information about environmental constraints within and between plants. As a result, plant-insect and plant-pathogen interactions, which are believed to influence each other through phytohormone cross talk, are likely equally sensitive to reciprocal regulation via volatile terpene cues. Here, we review the current knowledge of terpenes as volatile semiochemicals and discuss why and how volatile terpenes make good signaling cues. We discuss how volatile terpenes may be perceived by plants, what are possible downstream signaling events in receiver plants, and how responses to different terpene cues might interact to orchestrate the net plant response to multiple stresses. Finally, we discuss how the signal can be further transmitted to the community level leading to a mutually beneficial community scale response or distinct signaling with near kin.
AU  - Rosenkranz, M.
AU  - Chen, Y.
AU  - Zhu, P.
AU  - Vlot, A.C.
C1  - 62744
C2  - 51040
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  -  617-631
TI  - Volatile terpenes - mediators of plant-to-plant communication.
JO  - Plant J.
VL  - 108
IS  - 3
PB  - Wiley
PY  - 2021
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Transport Protein Particle II (TRAPPII) is essential for exocytosis, endocytosis, protein sorting and cytokinesis. In spite of a considerable understanding of its biological role, little information is known about Arabidopsis TRAPPII complex topology and molecular function. In this study, independent proteomic approaches initiated with TRAPP components or Rab-A GTPase variants converge on the TRAPPII complex. We show that the Arabidopsis genome encodes the full complement of 13 TRAPPC subunits, including four previously unidentified components. A dimerization model is proposed to account for binary interactions between TRAPPII subunits. Preferential binding to dominant negative (GDP-bound) versus wild-type or constitutively active (GTP-bound) RAB-A2a variants discriminates between TRAPPII and TRAPPIII subunits and shows that Arabidopsis complexes differ from yeast but resemble metazoan TRAPP complexes. Analyzes of Rab-A mutant variants in trappii backgrounds provide genetic evidence that TRAPPII functions upstream of RAB-A2a, allowing us to propose that TRAPPII is likely to behave as a guanine nucleotide exchange factor (GEF) for the RAB-A2a GTPase. GEFs catalyze exchange of GDP for GTP; the GTP-bound, activated, Rab then recruits a diverse local network of Rab effectors to specify membrane identity in subsequent vesicle fusion events. Understanding GEF-Rab interactions will be crucial to unravel the co-ordination of plant membrane traffic.
AU  - Kalde, M.*
AU  - Elliott, L.*
AU  - Ravikumar, R.*
AU  - Rybak, K.*
AU  - Altmann, M.
AU  - Klaeger, S.*
AU  - Wiese, C.*
AU  - Abele, M.*
AU  - Al, B.*
AU  - Kalbfuß, N.*
AU  - Qi, X.*
AU  - Steiner, A.*
AU  - Meng, C.*
AU  - Zheng, H.*
AU  - Kuster, B.*
AU  - Falter-Braun, P.
AU  - Ludwig, C.*
AU  - Moore, I.*
AU  - Assaad, F.F.*
C1  - 56560
C2  - 47137
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 279-297
TI  - Interactions between Transport Protein Particle (TRAPP) complexes and Rab GTPases in Arabidopsis.
JO  - Plant J.
VL  - 100
IS  - 2
PB  - Wiley
PY  - 2019
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.
AU  - Bolger, A.M.*
AU  - Poorter, H.*
AU  - Dumschott, K.*
AU  - Bolger, M.E.*
AU  - Arend, D.*
AU  - Osorio, S.*
AU  - Gundlach, H.
AU  - Mayer, K.F.X.
AU  - Lange, M.*
AU  - Scholz, U.*
AU  - Usadel, B.*
C1  - 54892
C2  - 45933
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 182-198
TI  - Computational aspects underlying genome to phenome analysis in plants.
JO  - Plant J.
VL  - 97
IS  - 1
PB  - Wiley
PY  - 2018
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Human adenovirus (HAdV) E1B-55K is a multifunctional regulator of productive viral replication and oncogenic transformation in nonpermissive mammalian cells. These functions depend on E1B-55K's posttranslational modification with the SUMO protein and its binding to HAdV E4orf6. Both early viral proteins recruit specific host factors to form an E3 ubiquitin ligase complex that targets antiviral host substrates for proteasomal degradation. Recently, we reported that the PML-NB associated factor Daxx represses efficient HAdV productive infection and is proteasomally degraded via a SUMO-E1B-55K-dependent, E4orf6-independent pathway, the details of which remained to be established. RNF4, a cellular SUMO-targeted ubiquitin ligase (STUbL), induces ubiquitinylation of specific SUMOy lated proteins and plays an essential role during DNA repair. Here, we show that E1B-55K recruits RNF4 to the insoluble nuclear matrix fraction of the infected cell to support RNF4/Daxx association, promoting Daxx PTM and thus inhibiting this antiviral factor. Removing RNF4 from infected cells using RNA interference resulted in blocking the proper establishment of viral replication centers and significantly diminished viral gene expression. These results provide a model for how HAdV antagonize the antiviral host responses by exploiting the functional capacity of cellular STUbLs. Thus, RNF4 and its STUbL function represent a positive factor during lytic infection and a novel candidate for future therapeutic antiviral intervention strategies.IMPORTANCE Daxx is a PML-NB-associated transcription factor that was recently shown to repress efficient HAdV productive infection. To counteract this antiviral measurement during infection, Daxx is degraded via a novel pathway including viral E1B-55K and host proteasomes. This virus-mediated degradation is independent of the classical HAdV E3 ubiquitin ligase complex, which is essential during viral infection to target other host antiviral substrates. To maintain a productive viral life cycle, HAdV E1B-55K early viral protein inhibits the chromatin-remodeling factor Daxx in a SUMO-dependent manner. In addition, viral E1B-55K protein recruits the STUbL RNF4 and sequesters it into the insoluble fraction of the infected cell. E1B-55K promotes complex formation between RNF4-and E1B-55K-targeted Daxx protein, supporting Daxx posttranslational modification prior to functional inhibition. Hence, RNF4 represents a novel host factor that is beneficial for HAdV gene expression by supporting Daxx counteraction. In this regard, RNF4 and other STUbL proteins might represent novel targets for therapeutic intervention.
AU  - Perroud, P.F.*
AU  - Haas, F.B.*
AU  - Hiss, M.*
AU  - Ullrich, K.K.*
AU  - Alboresi, A.*
AU  - Amirebrahimi, M.*
AU  - Barry, K.*
AU  - Bassi, R.*
AU  - Bonhomme, S.*
AU  - Chen, H.*
AU  - Coates, J.*
AU  - Fujita, T.*
AU  - Guyon-Debast, A.*
AU  - Lang, D.
AU  - Lin, J.*
AU  - Lipzen, A.*
AU  - Nogué, F.*
AU  - Oliver, M.J.*
AU  - Ponce de León, I.*
AU  - Quatrano, R.S.*
AU  - Rameau, C.*
AU  - Reiss, B.*
AU  - Reski, R.*
AU  - Ricca, M.*
AU  - Saidi, Y.*
AU  - Sun, N.*
AU  - Szövényi, P.*
AU  - Sreedasyam, A.*
AU  - Grimwood, J.*
AU  - Stacey, G.*
AU  - Schmutz, J.*
AU  - Rensing, S.A.*
C1  - 53442
C2  - 44869
CY  - 1752 N St Nw, Washington, Dc 20036-2904 Usa
SP  - 168-182
TI  - The Physcomitrella patens gene atlas project: Large-scale RNA-seq based expression data.
JO  - Plant J.
VL  - 95
IS  - 1
PB  - Amer Soc Microbiology
PY  - 2018
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene-and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
AU  - Lang, D.
AU  - Ullrich, K.K.*
AU  - Murat, F.*
AU  - Fuchs, J.*
AU  - Jenkins, J.*
AU  - Haas, F.B.*
AU  - Piednoël, M.*
AU  - Gundlach, H.
AU  - Van Bel, M.*
AU  - Meyberg, R.*
AU  - Vives, C.*
AU  - Morata, J.*
AU  - Symeonidi, A.*
AU  - Hiss, M.*
AU  - Muchero, W.*
AU  - Kamisugi, Y.*
AU  - Saleh, O.*
AU  - Blanc, G.*
AU  - Decker, E.L.*
AU  - van Gessel, N.*
AU  - Grimwood, J.*
AU  - Hayes, R.D.*
AU  - Graham, S.W.*
AU  - Gunter, L.E.*
AU  - McDaniel, S.*
AU  - Hoernstein, S.N.W.*
AU  - Larsson, A.*
AU  - Li, F.W.*
AU  - Perroud, P.F.*
AU  - Phillips, J.A.*
AU  - Ranjan, P.*
AU  - Rokshar, D.S.*
AU  - Rothfels, C.J.*
AU  - Schneider, L.*
AU  - Shu, S.Q.*
AU  - Stevenson, D.W.*
AU  - Thümmler, F.*
AU  - Tillich, M.*
AU  - Villarreal A, J.C.*
AU  - Widiez, T.*
AU  - Wong, G.K.*
AU  - Wymore, A.*
AU  - Zhang, Y.*
AU  - Zimmer, A.D.*
AU  - Quatrano, R.S.*
AU  - Mayer, K.F.X.
AU  - Goodstein, D.*
AU  - Casacuberta, J.M.*
AU  - Vandepoele, K.*
AU  - Reski, R.*
AU  - Cuming, A.C.*
AU  - Tuskan, J.*
AU  - Maumus, F.*
AU  - Salse, J.*
AU  - Schmutz, J.*
AU  - Rensing, S.A.*
C1  - 52547
C2  - 44060
CY  - Hoboken
SP  - 515-533
TI  - The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
JO  - Plant J.
VL  - 93
IS  - 3
PB  - Wiley
PY  - 2017
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole-genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full-length pseudogenes (11 015) have preferentially retained their exon-intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense-response were found to be under-represented in cultivated barley, we detected several defense-related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles. The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non-random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations.
AU  - Prade, V.M.
AU  - Gundlach, H.
AU  - Twardziok, S.O.
AU  - Chapman, B.*
AU  - Tan, C.S.*
AU  - Langridge, P.*
AU  - Schulman, A.H.*
AU  - Stein, N.*
AU  - Waugh, R.*
AU  - Zhang, G.*
AU  - Platzer, M.*
AU  - Li, C.*
AU  - Spannagl, M.
AU  - Mayer, K.F.X.
C1  - 52479
C2  - 44003
CY  - Hoboken
SP  - 502-514
TI  - The pseudogenes of barley.
JO  - Plant J.
VL  - 93
IS  - 3
PB  - Wiley
PY  - 2017
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun (WGS) sequencing of the 7.9 Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27,784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants (SNVs) and short insertions/deletions (indels) in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600,843 markers which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
AU  - Bauer, E.*
AU  - Schmutzer, T.*
AU  - Barilar, I.*
AU  - Mascher, M.*
AU  - Gundlach, H.
AU  - Martis, M.M.
AU  - Twardziok, S.O.
AU  - Hackauf, B.*
AU  - Gordillo, A.*
AU  - Wilde, P.*
AU  - Schmidt, M.*
AU  - Korzun, V.*
AU  - Mayer, K.F.X.
AU  - Schmid, K.*
AU  - Schön, C.C.*
AU  - Scholz, U.*
C1  - 50309
C2  - 42086
SP  - 853-869
TI  - Towards a whole-genome sequence for rye (Secale cereale L.).
JO  - Plant J.
VL  - 89
PY  - 2016
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Here we report the draft genome sequence of perennial ryegrass (Lolium perenne), an economically important forage and turf grass species widely cultivated in temperate regions worldwide. It is classified along with wheat, barley, oats and Brachypodium distachyon in the Pooideae sub-family of the grass family (Poaceae). Transcriptome data was used to identify 28,455 gene models, and we utilize macro-co-linearity between perennial ryegrass and barley, and synteny within the grass family to establish a synteny-based linear gene order. The gametophytic self-incompatibility (SI) mechanism enables the pistil of a plant to reject self-pollen and therefore promote outcrossing. We have used the sequence assembly to characterise transcriptional changes in the stigma during pollination with both compatible and incompatible pollen. Characterisation of the pollen transcriptome identified homologs to pollen allergens from a range of species, many of which were expressed to very high levels in mature pollen grains, and potentially involved in the SI mechanism. The genome sequence provides a valuable resource for future breeding efforts based on genomic prediction, and will accelerate the development of varieties for more productive grasslands.
AU  - Byrne, S.L.*
AU  - Pfeifer, M.*
AU  - Nagy, I.*
AU  - Armstead, I.*
AU  - Swain, S.*
AU  - Studer, B.*
AU  - Mayer, K.F.X.
AU  - Campbell, J.D.*
AU  - Czaban, A.*
AU  - Hentrup, S.*
AU  - Panitz, F.*
AU  - Bendixen, C.*
AU  - Hedegaard, J.*
AU  - Caccamo, M.*
AU  - Asp, T.*
C1  - 46927
C2  - 39040
SP  - 816-826
TI  - A synteny-based draft genome sequence of the forage grass Lolium perenne.
JO  - Plant J.
VL  - 84
IS  - 4
PY  - 2015
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Given the potential health benefits of polyphenolic compounds in the diet, there is a growing interest in the generation of food crops enriched with health-protective flavonoids. We undertook a series of metabolite analyses of tomatoes ectopically expressing the Delila and Rosea1 transcription factor genes from snapdragon, paying particular attention to changes in phenylpropanoids compared to controls. These analyses revealed multiple changes including depletion of rutin and naringenin-chalcone, enhanced levels of anthocyanins and phenylacylated flavonol derivatives. We isolated and characterised the chemical structures of the two most abundant anthocyanins which were shown by nuclear magnetic resonance spectroscopy to be delphinidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside and petunidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside. By performing RNA sequencing on both the purple fruit and wild type fruit we collected important information concerning the relative expression of both structural and transcription factor genes. Integrative analysis of the transcript and metabolite datasets provided compelling evidence of the nature of all genes involved in anthocyanin biosynthesis including those encoding species-specific anthocyanin decoration enzymes. One gene, SlFdAT1 (Solyc12g088170), predicted to encode a flavonoid-3-O-rutinoside-4'''-phenylacyltransferase was characterized by assays of recombinant protein and overexpression assays in tobacco. The combined data are discussed in the context of both our current understanding of phenylpropanoid metabolism in Solanaceous species, and evolution of flavonoid decorating enzymes and their transcriptional networks in different plant species.
AU  - Tohge, T.*
AU  - Zhang, Y.*
AU  - Peterek, S.*
AU  - Matros, A.*
AU  - Rallapalli, G.*
AU  - Tandrón, Y.A.*
AU  - Butelli, E.*
AU  - Kallam, K.*
AU  - Hertkorn, N.
AU  - Mock, H.P.*
AU  - Martin, C.*
AU  - Fernie, A.R.*
C1  - 45475
C2  - 37353
CY  - Hoboken
SP  - 686-704
TI  - Ectopic expression of snapdragon transcription factors facilitates the identification of genes encoding enzymes of anthocyanin decoration in tomato.
JO  - Plant J.
VL  - 83
IS  - 4
PB  - Wiley-blackwell
PY  - 2015
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Sulfur plays a crucial role in protein structure and function, redox status and plant biotic stress responses. However, our understanding of sulfur metabolism is limited to identified pathways. In this study, we used a high-resolution Fourier transform mass spectrometric approach in combination with stable isotope labeling to describe the sulfur metabolome of Arabidopsis thaliana. Databases contain roughly 300 sulfur compounds assigned to Arabidopsis. In comparative analyses, we showed that the overlap of the expected sulfur metabolome and the mass spectrometric data was surprisingly low, and we were able to assign only 37 of the 300 predicted compounds. By contrast, we identified approximately 140 sulfur metabolites that have not been assigned to the databases to date. We used our method to characterize the γ-glutamyl transferase mutant ggt4-1, which is involved in the vacuolar breakdown of glutathione conjugates in detoxification reactions. Although xenobiotic substrates are well known, only a few endogenous substrates have been described. Among the specifically altered sulfur-containing masses in the ggt4-1 mutant, we characterized one endogenous glutathione conjugate and a number of further candidates for endogenous substrates. The small percentage of predicted compounds and the high proportion of unassigned sulfur compounds identified in this study emphasize the need to re-evaluate our understanding of the sulfur metabolome.
AU  - Gläser, K.*
AU  - Kanawati, B.
AU  - Kubo, T.*
AU  - Schmitt-Kopplin, P.
AU  - Grill, E.*
C1  - 28611
C2  - 33483
SP  - 31-45
TI  - Exploring the Arabidopsis sulfur metabolome.
JO  - Plant J.
VL  - 77
IS  - 1
PB  - Wiley-Blackwell
PY  - 2014
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A utilizing Whole Genome Profiling (WGP(™) ). The Bacterial Artificial Chromosome (BAC) contig assembly tools FingerPrinted Contig (FPC) and Linear Topological Contig (LTC) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that LTC created a highly robust assembly compared to those formed by FPC. The LTC assemblies contained 1217 contigs for the short and 1113 contigs for long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to "decoration" of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for sequencing of wheat chromosome 6A and is of immediate use for map-based isolation of agronomically important genes/Quantitative Trait Loci located on this chromosome.
AU  - Poursarebani, N.*
AU  - Nussbaumer, T.
AU  - Šimková, H.*
AU  - Safar, J.*
AU  - Witsenboer, H.*
AU  - van Oeveren, J.*
AU  - International Wheat Genome Sequencing Consortium (Schnurbusch, T.)
AU  - Dolezel, J.*
AU  - Mayer, K.F.X.
AU  - Stein, N.*
C1  - 31541
C2  - 34540
CY  - Hoboken
SP  - 334-347
TI  - Whole Genome Profiling (WGP™) and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.
JO  - Plant J.
VL  - 79
IS  - 2
PB  - Wiley-Blackwell
PY  - 2014
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Owing to duplication events in its progenitor, more than 90% of the genes in the Arabidopsis thaliana genome are members of multigene families. A set of 2108 gene families, each consisting of precisely two unlinked paralogous genes, was identified in the nuclear genome of A.thaliana on the basis of sequence similarity. A systematic method for the creation of double knock-out lines for such gene pairs, designated as DUPLO lines, was established and 200 lines are now publicly available. Their initial phenotypic characterisation led to the identification of seven lines with defects that emerge only in the adult stage. A further six lines display seedling lethality and 23 lines were lethal before germination. Another 14 lines are known to show phenotypes under non-standard conditions or at the molecular level. Knock-out of gene pairs with very similar coding sequences or expression profiles is more likely to produce a mutant phenotype than inactivation of gene pairs with dissimilar profiles or sequences. High coding sequence similarity and highly similar expression profiles are only weakly correlated, implying that promoter and coding regions of these gene pairs display different degrees of diversification.
AU  - Bolle, C.*
AU  - Huep, G.*
AU  - Kleinbolting, N.*
AU  - Haberer, G.
AU  - Mayer, K.F.X.
AU  - Leister, D.*
AU  - Weisshaar, B.*
C1  - 25972
C2  - 32037
SP  - 157-171
TI  - GABI-DUPLO: A collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana.
JO  - Plant J.
VL  - 75
IS  - 1
PB  - Wiley-Blackwell
PY  - 2013
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.
AU  - Mascher, M.*
AU  - Richmond, T.A.*
AU  - Gerhardt, D.J.*
AU  - Himmelbach, A.*
AU  - Clissold, L.*
AU  - Sampath, D.*
AU  - Ayling, S.*
AU  - Steuernagel, B.*
AU  - Pfeifer, M.
AU  - D'Ascenzo, M.*
AU  - Akhunov, E.D.*
AU  - Hedley, P.E.*
AU  - Gonzales, A.M.*
AU  - Morrell, P.L.*
AU  - Kilian, B.*
AU  - Blattner, F.R.*
AU  - Scholz, U.*
AU  - Mayer, K.F.X.
AU  - Flavell, A.J.*
AU  - Muehlbauer, G.J.*
AU  - Waugh, R.*
AU  - Jeddeloh, J.A.*
AU  - Stein, N.*
C1  - 27210
C2  - 32564
SP  - 494-505
TI  - Barley whole exome capture: A tool for genomic research in the genus Hordeum and beyond.
JO  - Plant J.
VL  - 76
IS  - 3
PB  - Wiley-Blackwell
PY  - 2013
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.
AU  - Mascher, M.*
AU  - Muehlbauer, G.J.*
AU  - Rokhsar, D.S.*
AU  - Chapman, J.*
AU  - Schmutz, J.*
AU  - Barry, K.*
AU  - Muñoz-Amatriaín, M.*
AU  - Close, T.J.*
AU  - Wise, R.P.*
AU  - Schulman, A.H.*
AU  - Himmelbach, A.*
AU  - Mayer, K.F.X.
AU  - Scholz, U.*
AU  - Poland, J.A.*
AU  - Stein, N.*
AU  - Waugh, R.*
C1  - 27949
C2  - 32873
SP  - 718-727
TI  - Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
JO  - Plant J.
VL  - 76
IS  - 4
PB  - Wiley-Blackwell
PY  - 2013
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Wheat is the third most important crop for human nutrition in the world. The availability of high resolution genetic and physical maps and ultimately a complete genome sequence holds great promises for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat genome (∼17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status together impede the genome sequencing of this important crop species. Here we describe the application of mitotic chromosome flow sorting to separately purify and then shotgun sequence a pair of telocentric chromosomes which together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated the construction of an ordered gene map of chromosome 4A, embracing ≥85% of its total gene content. It has also allowed for the precise localization of the various translocation and inversion breakpoints on chromosome 4A which differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of 4A along with the emerging sequences of homoeologous wheat chromosome groups 4, 5, and 7 represent unique resources that will, among other, allow to generate new insights into evolutionary dynamics between the homoeologous chromosomes and syntenic chromosomal regions.
AU  - Hernandez, P.*
AU  - Martis, M.M.
AU  - Dorado, G.*
AU  - Pfeifer, M.
AU  - Gálvez, S.*
AU  - Schaaf, S.
AU  - Jouve, N.*
AU  - Šimková, H.*
AU  - Valárik, M.*
AU  - Dolezel, J.*
AU  - Mayer, K.F.X.
C1  - 6669
C2  - 29086
SP  - 377-386
TI  - Next generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content.
JO  - Plant J.
VL  - 69
IS  - 3
PB  - Wiley-Blackwell
PY  - 2012
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Plants perceive UV-B radiation as an informational signal by a pathway involving UVR8 as UV-B photoreceptor, activating photomorphogenic and acclimation responses. In contrast, the response to UV-B as an environmental stress involves mitogen-activated protein kinase (MAPK) signalling cascades. Whereas the perception pathway is plant specific, the UV-B stress pathway is more broadly conserved. Knowledge of the UV-B stress-activated MAPK signalling pathway in plants is limited, and its potential interplay with the UVR8-mediated pathway has not been defined. Here, we show that loss of MAP kinase phosphatase 1 in the mutant mkp1 results in hypersensitivity to acute UV-B stress, but without impairing UV-B acclimation. The MKP1-interacting proteins MPK3 and MPK6 are activated by UV-B stress and are hyperactivated in mkp1. Moreover, mutants mpk3 and mpk6 exhibit elevated UV-B tolerance and partially suppress the UV-B hypersensitivity of mkp1. We show further that the MKP1-regulated stress-response MAPK pathway is independent of the UVR8 photoreceptor, but that MKP1 also contributes to survival under simulated sunlight. We conclude that, whereas UVR8-mediated acclimation in plants promotes UV-B-induced defence measures, MKP1-regulated stress signalling results when UV-B protection and repair are insufficient and damage occurs. The combined activity of these two mechanisms is crucial to UV-B tolerance in plants.
AU  - González Besteiro, M.A.*
AU  - Bartel, S.*
AU  - Albert, A.
AU  - Ulm, R.*
C1  - 5626
C2  - 29160
SP  - 727-737
TI  - Arabidopsis MAP kinase phosphatase 1 and its target MAP kinases 3 and 6 antagonistically determine UV-B stress tolerance, independent of the UVR8 photoreceptor pathway.
JO  - Plant J.
VL  - 68
IS  - 4
PB  - Blackwell Publishing
PY  - 2011
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - The introduction of apomixis - seed formation without fertilization - into crop plants is a long-held goal of breeding research, since it would allow for the ready fixation of heterozygosity. The genetic basis of apomixis, whether of the aposporous or the diplosporous type, is still only poorly understood. Hypericum perforatum (St John's wort), a plant with a small genome and a short generation time, can be aposporous and/or parthenogenetic, and so represents an interesting model dicot for apomixis research. Here we describe a genetic analysis which first defined and then isolated a locus (designated HAPPY for Hypericum APOSPORY) associated with apospory. Amplified fragment length polymorphism (AFLP) profiling was used to generate a cleaved amplified polymorphic sequence (CAPS) marker for HAPPY which co-segregated with apospory but not with parthenogenesis, showing that these two components of apomixis are independently controlled. Apospory was inherited as a dominant simplex gene at the tetraploid level. Part of the HAPPY sequence is homologous to the Arabidopsis thaliana gene ARI7 encoding the ring finger protein ARIADNE7. This protein is predicted to be involved in various regulatory processes, including ubiquitin-mediated protein degradation. While the aposporous and sexual alleles of the HAPPY component HpARI were co-expressed in many parts of the plant, the gene product of the apomict's allele is truncated. Cloning HpARI represents the first step towards the full characterization of HAPPY and the elucidation of the molecular mechanisms underlying apomixis in H. perforatum.
AU  - Schallau, A.*
AU  - Arzenton, F.*
AU  - Johnston, A.J.*
AU  - Hähnel, U.*
AU  - Koszegi, D.*
AU  - Blattner, F.R.*
AU  - Altschmied, L.*
AU  - Haberer, G.
AU  - Barcaccia, G.*
AU  - Bäumlein, H.*
C1  - 4730
C2  - 28214
CY  - USA
SP  - 773-784
TI  - Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L.
JO  - Plant J.
VL  - 62
IS  - 5
PB  - Wiley-Blackwell Publishing
PY  - 2010
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - ABI1, a protein phosphatase 2C, is a key component of ABA signal transduction in Arabidopsis that regulates numerous ABA responses, such as stomatal closure, seed germination and inhibition of vegetative growth. The abi1-1 mutation, so far the only characterized dominant allele for ABI1, impairs ABA responsitivity in both seeds and vegetative tissues. The site of action of ABI1 is unknown. We show that there is an essential requirement for nuclear localization of abi1 to confer insensitivity towards ABA responses. Transient analyses in protoplasts revealed a strict dependence of wild-type ABI1 and mutant abi1 on a functional nuclear localization sequence (NLS) for regulating ABA-dependent gene expression. Arabidopsis lines with ectopic expression of various abi1 forms corroborated the necessity of a functional NLS to control ABA sensitivity. Disruption of the NLS function in abi1 rescued ABA-controlled gene transcription to wild-type levels, but also attenuated abi1-conferred insensitivity towards ABA during seed germination, root growth and stomatal movement. The mutation in the PP2C resulted in a preferential accumulation of the protein in the nucleus. Application of a proteosomal inhibitor led to both a preferential nuclear accumulation of ABI1 and an enhancement of PP2C-dependent inhibitory action on the ABA response. Thus, abi1-1 acts as a hypermorphic allele, and ABI1 reprograms sensitivity towards ABA in the nucleus.
AU  - Moes, D.*
AU  - Himmelbach, A.*
AU  - Korte, A.*
AU  - Haberer, G.
AU  - Grill, E.*
C1  - 4528
C2  - 25509
SP  - 806-819
TI  - Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis.
JO  - Plant J.
VL  - 54
IS  - 5
PB  - Blackwell
PY  - 2008
SN  - 0960-7412
ER  - 

TY  - JOUR
AU  - Vandenabeele, S.*
AU  - Vanderauwera, S.*
AU  - Vuylsteke, M.*
AU  - Rombauts, S.*
AU  - Langebartels, C.
AU  - Seidlitz, H.K.
AU  - Zabeau, M.*
AU  - van Montagu, M.*
AU  - Inzé, D.*
AU  - van Breusegem, F.*
C1  - 2977
C2  - 22148
SP  - 45-58
TI  - Catalase deficiency drastically affects gene expression induced by high light in Arabidopsis thaliana.
JO  - Plant J.
VL  - 39
PY  - 2004
SN  - 0960-7412
ER  - 

TY  - JOUR
AU  - Zhang, H.*
AU  - Screenivasulu, N.*
AU  - Weschke, W.*
AU  - Stein, N.*
AU  - Rudd, S.
AU  - Radchuk, V.*
AU  - Potokina, E.*
AU  - Scholz, U.*
AU  - Schweizer, P.*
AU  - Zierold, U.*
AU  - Langridge, P.*
C1  - 1509
C2  - 22223
SP  - 276-290
TI  - Large-scale analysis of the barley transcriptome based on expressed sequence tags.
JO  - Plant J.
VL  - 40
PY  - 2004
SN  - 0960-7412
ER  - 

TY  - JOUR
AU  - Dat, J.F.*
AU  - Pellinen, R.*
AU  - Beeckman, T.*
AU  - van de Cotte, B.*
AU  - Langebartels, C.
AU  - Kangasjärvi, J.*
AU  - Inzé, D.*
AU  - van Breusegem, F.*
C1  - 2003
C2  - 21820
SP  - 621-632
TI  - Changes in hydrogen peroxide homeostasis trigger an active cell death process in tobacco.
JO  - Plant J.
VL  - 33
PY  - 2003
SN  - 0960-7412
ER  - 

TY  - JOUR
AU  - Foissner, I.*
AU  - Wendehenne, D.*
AU  - Langebartels, C.
AU  - Durner, J.
C1  - 21837
C2  - 20056
SP  - 817-824
TI  - In vivo imaging of an elicitor-induced nitric oxide burst in tobacco.
JO  - Plant J.
VL  - 23
PY  - 2000
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Stress ethylene emission is positively correlated with ozone sensitivity in various plant species, indicating that ethylene may be involved in the control of ozone damage. This study shows that ozone exposure of tomato plants for 5 h at 85 nl l−1 and above leads to leaf injury within 24 h. 1-aminocyclopropane-1-carboxylic acid (ACC) content and ACC synthase activity were accordingly elevated within 1–2 h. Pre-treatment of leaves with inhibitors of ACC synthase and ACC oxidase significantly inhibited the evolution of ethylene and reduced ozone-induced visible damage. Transcript levels for only one out of three S-adenosyl-l-methionine (SAM) synthetase genes (SAM3), and one out of four ACC synthase genes (LE-ACS2) were induced by ozone (maximum at 2 h). Treatment with protein kinase (K-252a) and phosphatase inhibitors (calyculin A) revealed that ACC synthase activity was additionally regulated by protein phosphorylation/dephosphorylation. Transcripts of ACC oxidase (pTOM13 cDNA probe) displayed the fastest response of the parameters tested (maximum at 30 min), suggesting a regulatory role for ACC oxidase in ethylene formation of ozone-exposed plants. The results demonstrate a highly selective ozone response by ethylene biosynthetic genes which resembles that of plant—pathogen interactions.
AU  - Tuomainen J.*
AU  - Betz, C.*
AU  - Kangasjärvi, J.*
AU  - Ernst, D.
AU  - Langebartels, C.
AU  - Sandermann, H.
C1  - 46466
C2  - 0
SP  - 1151-1162
TI  - Ozone induction of ethylene emission in tomato plants: Regulation by differential accumulation of transcripts for the biosynthetic enzymes.
JO  - Plant J.
VL  - 12
IS  - 5
PY  - 1997
SN  - 0960-7412
ER  - 

TY  - JOUR
AB  - Nitrite reductase is an enzyme in the nitrate assimilatory pathway whose expression is induced upon the addition of nitrate. Furthermore, it is known to be located in chloroplasts in leaves and plastids in roots. A 3.1 kb 5′ upstream region of the spinach nitrite reductase (NiR) gene promoter was shown previously to confer nitrate inducibility on the β-glucuronidase (GUS) reporter gene expression in both the leaves and the roots of transgenic tobacco plants. In the present study, this 3.1 kb promoter fragment as well as a series of promoter deletion constructs, fused to a GUS gene, were utilized to delineate the region of NiR promoter involved in nitrate regulation of NiR expression by studying the cellular localization of NiR-GUS expression as well as its regulation by nitrate. In plants carrying the longest promoter fragment (-3100 from the transcription start site) and promoter sequences progressively deleted to -330 bp, the expression of GUS was markedly increased in the presence of nitrate, and this expression was found to occur in mesophyll cells in leaves and in the vascular tissues of stem and roots. When nitrate was added to NiR-GUS plants grown in the absence of nitrate, significant levels of GUS activity could be seen in the roots after 2 h and in the leaves after 6 h. Furthers 5′ deletion of the promoter to -200 bp abolished the nitrate induction of GUS expression, indicating that the 130 bp region of the nitrite reductase promoter located between -330 and -200 is required for full nitrate-inducible tissue-specific expression.
AU  - Rastogi, R.*
AU  - Back, E.
AU  - Schneiderbauer, A.
AU  - Bowsher, C.G.*
AU  - Moffatt, B.A.*
AU  - Rothstein, S.J.*
C1  - 34152
C2  - 38976
SP  - 317-326
TI  - A 330 bp region of the spinach nitrite reductase gene promoter directs nitrate-inducible tissue-specific expression in transgenic tobacco.
JO  - Plant J.
VL  - 4
IS  - 2
PY  - 1993
SN  - 0960-7412
ER  - 

TY  - JOUR
AU  - Siefert, F.
AU  - Langebartels, C.
AU  - Boller, T.
AU  - Grossmann, K.
C1  - 20587
C2  - 13797
SP  - 431-440
TI  - Are Ethylene and 1-Aminocyclopropane-1-Carboxylic Acid Involved in the Induction of Chitinase  and ß-1,3-Glucanase Activity in Sunflower Cell Suspension Cultures?.
JO  - Plant J.
VL  - 192
PY  - 1993
SN  - 0960-7412
ER  -