The canonical correlation analysis (CCA) is commonly used to analyze data sets with paired data, e.g. measurements of gene expression and metabolomic intensities of the same experiments. This allows to find interesting relationships between the data sets, e.g. they can be assigned to biological processes. However, it can be difficult to interpret the processes and often the relationships observed are not related to the experimental design but to some unknown parameters.Here we present an extension of the penalized CCA, the supervised penalized approach (spCCA), where the experimental design is used as a third data set and the correlation of the biological data sets with the design data set is maximized to find interpretable and meaningful canonical variables. The spCCA was successfully tested on a data set of Arabidopsis thaliana with gene expression and metabolite intensity measurements and resulted in eight significant canonical variables and their interpretation. We provide an R-package under the GPL license.

Regulation of the expression of nuclear genes encoding chloroplast proteins allows for metabolic adjustment in response to changing environmental conditions. This regulation is linked to retrograde signals that transmit information on the metabolic state of the chloroplast to the nucleus. Transcripts of several APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERF-TFs) were found to respond within 10 min after transfer of low-light-acclimated Arabidopsis thaliana plants to high light. Initiation of this transcriptional response was completed within 1 min after transfer to high light. The fast responses of four AP2/ERF genes, ERF6, RRTF1, ERF104, and ERF105, were entirely deregulated in triose phosphate/phosphate translocator (tpt) mutants. Similarly, activation of MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) was upregulated after 1 min in the wild type but not in the tpt mutant. Based on this, together with altered transcript regulation in mpk6 and erf6 mutants, a retrograde signal transmission model is proposed starting with metabolite export through the triose phosphate/phosphate translocator with subsequent MPK6 activation leading to initiation of AP2/ERF-TF gene expression and other downstream gene targets. The results show that operational retrograde signaling in response to high light involves a metabolite-linked pathway in addition to previously described redox and hormonal pathways.

We sequenced and annotated the complete mitochondrial (mt) genomes of four closely related Rhynchosporium species that diverged ∼14,000–35,000 years ago. During this time frame, three of the mt genomes expanded significantly due to an invasion of introns into three genes (cox1, cox2, and nad5). The enlarged mt genomes contained ∼40% introns compared to 8.1% in uninvaded relatives. Many intron gains were accompanied by co-conversion of flanking exonic regions. The comparative analysis revealed a highly variable set of non-intronic, free-standing ORFs of unknown function (uORFs). This is consistent with a rapidly evolving accessory compartment in the mt genome of these closely related species. Only one free-standing uORF was shared among all mt genomes analyzed. This uORF had a mutation rate similar to the core mt protein-encoding genes, suggesting conservation of function among the species. The nucleotide composition of the core protein-encoding genes significantly differed from those of introns and uORFs. The mt mutation rate was 77 times higher than the nuclear mutation rate, indicating that the phylogeny inferred from mt genes may better resolve the phylogenetic relationships among closely related Rhynchosporium species than phylogenies inferred from nuclear genes.

Hypericum riparium A. Chev. is a Cameroonian medicinal plant belonging to the family Guttiferae. Chemical investigation of the methanol extract of the stem bark of H. riparium led to the isolation of four natural products, 7,7′-dihydroxy-6,6′-biscoumarin (1), 7,7′-dihydroxy-8,8′-biscoumarin (2), 7-methoxy-6,7′-dicoumarinyl ether (3), 2′-hydroxy-5′-(7″-methoxycoumarin-6″-yl)-4′-methoxyphenylpropanoic acid (4), together with one known 7,7′-dimethoxy-6,6′-biscoumarin (5), two flavones, 2′-methoxyflavone (6) and 3′-methoxy flavone (7), and two steroids, stigmast-4-en-3-one (8) and ergosta-4,6,8,22-tetraen-3-one (9). In addition, tetradecanoic acid (10), n-pentadecanoic acid (11), hexadecanoic acid (12), cis-10-heptadecenoic acid (13), octadecanoic acid (14) campesterol (15), stigmasterol (16), β-sitosterol (17), stigmastanol (18), β-eudesmol (19), 1-hexadecanol (20), and 1-octadecanol (21) were identified by GC–MS analysis. Compound 4 consists of a phenylpropanoic acid derivative fused with a coumarin unit, while compounds 2 and 3 are rare members of C8–C8′ and C7–O–C6 linked biscoumarins. Their structures were elucidated by UV, IR, extensive 1D- and 2D-NMR experiments and electrospray (ESI) high resolution mass spectrometry (MS) including detailed MS/MS studies. This is the first report on the isolation of biscoumarins from the genus Hypericum, although simple coumarin derivatives have been reported from this genus in the literature. The cytotoxic activities of compounds 2–5 were evaluated against the human prostate cancer cell line PC-3 and the colon cancer cell line HT-29. They do not exhibit any significant cytotoxic activity.

To explore the chemical composition of root exudates of the model plant Arabidopsis thaliana a workflow for nontargeted metabolite profiling of the semipolar fraction of root exudates was developed. It comprises hydroponic plant cultivation and sampling of root exudates under sterile conditions, sample preparation by solid-phase extraction and analysis by reversed-phase UPLC/ESI-QTOFMS. Following the established workflow, root exudates of six-week-old plants were profiled and a set of reproducibly occurring molecular features was compiled. To structurally elucidate the corresponding metabolites, accurate mass tandem mass spectrometry and on-line hydrogen/deuterium exchange were applied. Currently, a total of 103 compounds were detected and annotated by elemental composition of which more than 90 were structurally characterized or classified. Among them, 42 compounds were rigorously identified using an authenticated standard. The compounds identified so far include nucleosides, deoxynucleosides, aromatic amino acids, anabolites and catabolites of glucosinolates, dipeptides, indolics, salicylic and jasmonic acid catabolites, coumarins, mono-, di- and trilignols, hydroxycinnamic acid derivatives and oxylipins and exemplify the high chemical diversity of plant root exudates.

GC/EI-MS-based metabolite profiling of derivatized polar fractions of crude plant extracts typically reveals several hundred components. Thereof, only up to one half can be identified using mass spectral and retention index libraries, the rest remains unknown. In the present work, the utility of GC/APCI(+)-QTOFMS for the annotation of unknown components was explored. Hence, EI and APCI(+) mass spectra of ~100 known components were extracted from GC/EI-QMS and GC/APCI(+)-QTOFMS profiles obtained from a methoximated and trimethylsilylated root extract of Arabidopsis thaliana. Based on this reference set, adduct and fragment ion formation under APCI(+) conditions was examined and the calculation of elemental compositions evaluated. During these studies, most of the components formed dominating protonated molecular ions. Despite the high mass accuracy (|Δm| ≤ 3 mDa) and isotopic pattern accuracy (mSigma ≤ 30) the determination of a component’s unique native elemental composition requires additional information, namely the number of trimethylsilyl and methoxime moieties as well as the analysis of corresponding collision-induced dissociation (CID) mass spectra. After all, the reference set was used to develop a strategy for the pairwise assignment of EI and APCI(+) mass spectra. Proceeding from these findings, the annotation of unidentified components detected by GC/EI-QMS using GC/APCI(+)-QTOFMS and corresponding deuterated derivatization reagents was attempted. For a total of 25 unknown components, pairs of EI and APCI(+) mass spectra were compiled and elemental compositions determined. Integrative interpretation of EI and CID mass spectra resulted in 14 structural hypotheses, of which seven were confirmed using authenticated standards.

Plant natural products (PNPs) are unique in that they represent a vast array of different structural features, ranging from relatively simple molecules to very complex ones. Given the fact that many plant secondary metabolites exhibit profound biological activity, they are frequently used as fragrances and flavors, medicines, as well as industrial chemicals. As the intricate structures of PNPs often cannot be mimicked by chemical synthesis, the original plant providers constitute the sole source for their industrial, large‐scale production. However, sufficient supply is not guaranteed for all molecules of interest, making the development of alternative production systems a priority. Modern techniques, such as genome mining and thorough biochemical analysis, have helped us gain preliminary understanding of the enzymatic formation of the valuable ingredients in planta. Herein, we review recent advances in the application of biocatalytical processes, facilitating generation of complex PNPs through utilization of plant‐derived specific enzymes and combinatorial biochemistry. We further evaluate the options of employing heterologous organisms harboring PNP biosynthetic pathways for the production of secondary metabolites of interest.

The phytohormone jasmonate (JA) plays essential roles in plant growth, development and defense. In response to the JA signal, the CORONATINE INSENSITIVE 1 (COI1)-based SCF complexes recruit JASMONATE ZIM-domain (JAZ) repressors for ubiquitination and degradation, and subsequently regulate their downstream signaling components essential for various JA responses. Tremendous progress has been made in understanding the JA signaling pathway and its crosstalk with other phytohormone pathways during the past two decades. Recent studies have revealed that a variety of positive and negative regulators act as targets of JAZs to control distinctive JA responses, and that JAZs and these regulators function as crucial interfaces to mediate synergy and antagonism between JA and other phytohormones. Owing to different regulatory players in JA perception and JA signaling, a fine-tuning of JA-dependent processes in plant growth, development and defense is achieved. In this review, we will summarize the latest progresses in JA signaling and its crosstalk with gibberellin and ethylene.

Scald caused by Rhynchosporium commune is an important foliar disease of barley. Insertion mutagenesis of R. commune generated a nonpathogenic fungal mutant which carries the inserted plasmid in the upstream region of a gene named PFP1. The characteristic feature of the gene product is an Epc-N domain. This motif is also found in homologous proteins shown to be components of histone acetyltransferase (HAT) complexes of fungi and animals. Therefore, PFP1 is suggested to be the subunit of a HAT complex in R. commune with an essential role in the epigenetic control of fungal pathogenicity. Targeted PFP1 disruption also yielded nonpathogenic mutants which showed wild-type-like growth ex planta, except for the occurrence of hyphal swellings. Complementation of the deletion mutants with the wild-type gene reestablished pathogenicity and suppressed the hyphal swellings. However, despite wild-type-level PFP1 expression, the complementation mutants did not reach wild-type-level virulence. This indicates that the function of the protein complex and, thus, fungal virulence are influenced by a position-affected long-range control of PFP1 expression.

Transient infiltrations in tobacco are commonly used in plant studies, but the host response to different disarmed Agrobacterium strains is not fully understood. The present study shows that pretreatment with disarmed Agrobacterium tumefaciens GV3101 primes the defense response to subsequent infection by Pseudomonas syringae in Nicotiana tabacum. The presence of a trans-zeatin synthase (tzs) gene in strain GV3101 may be partly responsible for the priming response, as the tzs-deficient Agrobacterium sp. strain LBA4404 only weakly imparts such responses. Besides inducing the expression of defense-related genes like PR-1 and NHL10, GV3101 pretreatment increased the expression of tobacco mitogen-activated protein kinase (MAPK) pathway genes like MEK2, WIPK (wound-induced protein kinase), and SIPK (salicylic acid-induced protein kinase). Furthermore, the GV3101 strain showed a stronger effect than the LBA4404 strain in activating phosphorylation of the tobacco MAPK, WIPK and SIPK, which presumably prime the plant immune machinery. Lower doses of exogenously applied cytokinins increased the activation of MAPK, while higher doses decreased the activation, suggesting a balanced level of cytokinins is required to generate defense response in planta. The current study serves as a cautionary warning for plant researchers over the choice of Agrobacterium strains and their possible consequences on subsequent pathogen-related studies.