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A prototypic ARC that implements all specification standards accordingly

Cofunctioning of bacterial exometabolites drives root microbiota establishment

Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare.

Genome sequencing of blackcurrant (Ribes nigrum)

Algae cultures were grown mixotrophically (TAP). After 24h of 35°C/40°C the cells were shifted back to room temperature for 48h. 'omics samples were taken.

early maturity 7 controls photoperiodic flowering in barley by modifying the diurnal expression pattern of the major photoperiod response gene Ppd-H1.

Pangenome of Camellia sinensis

early maturity 7 controls photoperiodic flowering in barley by modifying the diurnal expression pattern of the major photoperiod response gene Ppd-H1.

This is the ARC resulting from the Start Here guide in the DataPLANT Knowledge Base.

This ARC presents diverse data from MibiNet members to illustrate the application of MibiNet-specific SWATE templates and showcase examples of metadata annotation.

The iron-containing porphyrin heme is of high interest for the food industry for the production of artificial meat as well as for medical applications, e.g. for anemia treatment. Recently, the biotechnological platform strain Corynebacterium glutamicum has emerged as a promising host for animal-free heme production. Beyond engineering of complex heme biosynthetic pathways, improving heme export offers significant yet untapped potential for enhancing production strains. In this study, a growth-coupled biosensor was designed to impose a selection pressure on the increased expression of the hrtBA operon encoding an ABC-type heme exporter in C. glutamicum. For this purpose, the promoter region PhrtB was replaced with that of the growth-regulating genes pfkA (phosphofructokinase) and aceE (pyruvate dehydrogenase), creating biosensor strains with a selection pressure for hrtBA activation. Resulting sensor strains were used for plate-based selections and for a repetitive batch f(luorescent)ALE using a robotics platform. Genome sequencing of isolated clones featuring increased hrtBA expression revealed three distinct mutational hotspots: (i) chrS, (ii) chrA, and (iii) cydD. Mutations in the genes of the ChrSA two-component system, which regulates hrtBA in response to heme levels, were identified as a promising target to enhance export activity. Furthermore, causal mutations within cydD, encoding an ABC-transporter essential for cytochrome bd oxidase assembly, were confirmed by the construction of a deletion mutant, which showed strongly increased hrtBA expression as well as increased cellular heme levels. These results further support the proposed role of CydDC as a heme transporter. Mutations identified in this study therefore underline the potential of biosensor-based growth coupling and provide promising engineering targets to improve microbial heme production.

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota

A systematic overexpression approach reveals native targets to increase squalene production in Synechocystis sp. PCC 6803

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis

This ARC is based on the research of Mönchgesang et al. 2016, who performed a metabolite profiling of 19 Arabidopsis thaliana accessions. The natural variability of root metabolic patterns was analyzed between different accessions, with the result that plant-to-plant variability is greater than natural variation between accessions and non-biological variation between experimental batches.

A prototypic ARC that implements all specification standards accordingly

Crassulacean acid metabolism (CAM) has evolved as a water-saving strategy, and its engineering into crops offers an opportunity to improve their water use efficiency. This requires a comprehensive understanding of the regulation of the CAM pathway. Here, we use the facultative CAM species Talinum triangulare as a model in which CAM can be induced rapidly by exogenous abscisic acid. RNA sequencing and metabolite measurements were employed to analyse the changes underlying CAM induction and identify potential CAM regulators. Non-negative matrix factorization followed by k-means clustering identified an early CAM-specific cluster and a late one, which was specific for the early light phase. Enrichment analysis revealed abscisic acid metabolism, WRKY-regulated transcription, sugar and nutrient transport, and protein degradation in these clusters. Activation of the CAM pathway was supported by up-regulation of phosphoenolpyruvate carboxylase, cytosolic and chloroplastic malic enzymes, and several transport proteins, as well as by increased end-of-night titratable acidity and malate accumulation. The transcription factors HSFA2, NF-YA9, and JMJ27 were identified as candidate regulators of CAM induction. With this study we promote the model species T. triangulare, in which CAM can be induced in a controlled way, enabling further deciphering of CAM regulation.

Cofunctioning of bacterial exometabolites drives root microbiota establishment