Joachim Kopka
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View article: Increasing temperatures and CO2 impact on primary and specialized metabolism of Brassica species
Increasing temperatures and CO2 impact on primary and specialized metabolism of Brassica species Open
View article: Positional <scp><sup>13</sup>C</scp> enrichment analysis of aspartate determines <scp>PEPC</scp> activity <i>in vivo</i>
Positional <span><sup>13</sup>C</span> enrichment analysis of aspartate determines <span>PEPC</span> activity <i>in vivo</i> Open
Summary Photoautotrophic organisms fix inorganic carbon (Ci) by RIBULOSE‐1,5‐BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) and PHOSPHOENOLPYRUVATE CARBOXYLASE (PEPC). Monitoring Ci assimilation rates in vivo is a major challenge in analyzin…
View article: Discovery of Species-Specific Peptide Markers for Superseed Authentication Using Targeted LC-MS/MS Proteomics
Discovery of Species-Specific Peptide Markers for Superseed Authentication Using Targeted LC-MS/MS Proteomics Open
The increasing popularity of “superseeds” such as flax, sesame, amaranth and quinoa as functional foods raises the need for robust analytical methods for authentication purposes. In this work, a standardized workflow for the extraction, ch…
View article: Unveiling Potato Cultivars With Microbiome Interactive Traits for Sustainable Agricultural Production
Unveiling Potato Cultivars With Microbiome Interactive Traits for Sustainable Agricultural Production Open
Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive trait (MIT), such…
View article: Sulfate enhances metabolic acclimation under drought stress – a comparative study of grapevine and maize
Sulfate enhances metabolic acclimation under drought stress – a comparative study of grapevine and maize Open
View article: Discovery of Species-Specific Peptide Markers for Superseed Authentication Using Targeted LC-MS/MS Proteomics
Discovery of Species-Specific Peptide Markers for Superseed Authentication Using Targeted LC-MS/MS Proteomics Open
The increasing popularity of “superseeds” such as flax, sesame, amaranth and quinoa as functional foods raises the need of robust analytical methods for authentication purpose. In this work, a standardized workflow for the extraction, char…
View article: Polycomb repressive complex 2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence
Polycomb repressive complex 2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence Open
The seed-to-seedling transition represents a key developmental and metabolic switch in plants. Catabolism of seed storage reserves fuels germination and early seedling emergence until photosynthesis is established. The seed-to-seedling dev…
View article: <i>In vivo</i> RUBISCO activity in <i>Synechocystis</i> is regulated by RuBP availability
<i>In vivo</i> RUBISCO activity in <i>Synechocystis</i> is regulated by RuBP availability Open
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) is the main CO 2 -fixing enzyme on earth and entry point of carbon into the Calvin-Benson-Bassham cycle. Fueled by photosynthesis, C-assimilation by RUBISCO must be tightly controll…
View article: Insights into CPSFL1 Induced Membrane Dynamics: A Multifaceted Regulator Linking Vesicle Formation to Thylakoid Biogenesis
Insights into CPSFL1 Induced Membrane Dynamics: A Multifaceted Regulator Linking Vesicle Formation to Thylakoid Biogenesis Open
Light drives plant life through photosynthesis, a process that takes place in the thylakoid membrane of the chloroplast, an organelle of cyanobacterial origin. The formation of thylakoid membranes within the chloroplast involves the eukary…
View article: Remodelled ribosomal populations synthesize a specific proteome in proliferating plant tissue during cold
Remodelled ribosomal populations synthesize a specific proteome in proliferating plant tissue during cold Open
Plant acclimation occurs through system-wide mechanisms that include proteome shifts, some of which occur at the level of protein synthesis. All proteins are synthesized by ribosomes. Rather than being monolithic, transcript-to-protein tra…
View article: Guard Cell‐Specific Metabolic Responses to Drought Stress in Maize
Guard Cell‐Specific Metabolic Responses to Drought Stress in Maize Open
Understanding crop responses to drought stress is crucial for securing future agricultural productivity. Guard cells regulate transpiration and thus the yield burden under drought conditions. Therefore, the influence of repeated drought st…
View article: Dynamic photosynthetic labeling and carbon-positional mass spectrometry monitor in vivo RUBISCO carbon assimilation rates
Dynamic photosynthetic labeling and carbon-positional mass spectrometry monitor in vivo RUBISCO carbon assimilation rates Open
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) is the most abundant enzyme and CO2 bio-sequestration system on Earth. Its in vivo activity is usually determined by 14CO2 incorporation into 3-phosphoglycerate (3PGA). However, the…
View article: Increasing Temperatures and Co2 Impact on Primary and Specialized Metabolism of Brassica Species
Increasing Temperatures and Co2 Impact on Primary and Specialized Metabolism of Brassica Species Open
View article: Grapevine and maize: Two guard cell shaped strategies to cope with repeated drought stress
Grapevine and maize: Two guard cell shaped strategies to cope with repeated drought stress Open
Adaptation of crops to recurrent drought stress is crucial for maintaining agricultural productivity and achieving food security under changing climate. Guard cells, pivotal regulators of plant water usage and assimilation, are central to …
View article: Detailed Profiling of 17-Hydroxygeranyllinalool Diterpene Glycosides from Nicotiana Species Reveals Complex Reaction Networks of Conjugation Isomers
Detailed Profiling of 17-Hydroxygeranyllinalool Diterpene Glycosides from Nicotiana Species Reveals Complex Reaction Networks of Conjugation Isomers Open
Background: Specialised anti-herbivory metabolites are abundant in the solanaceous genus Nicotiana. These metabolites include the large family of 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs). Many HGL-DTGs occur exclusively wi…
View article: PRC2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence
PRC2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence Open
Seed-to-seedling transition represents a key developmental and metabolic switch in plants. Catabolism of seed storage reserves fuels germination and early seedling emergence until photosynthesis is established. The developmental transition…
View article: Membrane protein provision controls prothylakoid biogenesis in tobacco etioplasts
Membrane protein provision controls prothylakoid biogenesis in tobacco etioplasts Open
The cytochrome b559 heterodimer is a conserved component of photosystem II whose physiological role in photosynthetic electron transfer is enigmatic. A particularly puzzling aspect of cytochrome b559 has been its presence in etiolated seed…
View article: Unveiling potato cultivars with microbiome interactive traits for sustainable agricultural production
Unveiling potato cultivars with microbiome interactive traits for sustainable agricultural production Open
Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive traits (MITs), su…
View article: Metabolomic analysis of grapes and leaves from symptomatic and asymptomatic Vitis vinifera grapevines with Esca disease
Metabolomic analysis of grapes and leaves from symptomatic and asymptomatic Vitis vinifera grapevines with Esca disease Open
Esca is a grapevine trunk disease spreading in vineyards worldwide, and of rising concern since no efficient treatment is available to mitigate its impact. Trunks, grapes and leaves from symptomatic and asymptomatic Aragonês vines were col…
View article: Convergence and molecular evolution of floral fragrance after independent transitions to self-fertilization
Convergence and molecular evolution of floral fragrance after independent transitions to self-fertilization Open
Studying the independent evolution of similar traits provides valuable insights into the ecological and genetic factors driving phenotypic evolution.1 The transition from outcrossing to self-fertilization is common in plant evol…
View article: Positional<sup>13</sup>C Enrichment Analysis of Aspartate by GC-MS to Determine PEPC Activity<i>In Vivo</i>
Positional<sup>13</sup>C Enrichment Analysis of Aspartate by GC-MS to Determine PEPC Activity<i>In Vivo</i> Open
Photoautotrophic organisms fix inorganic carbon (Ci) by two enzymes, ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) and phosphoenolpyruvate carboxylase (PEPC). RUBISCO assimilates Ci (CO2) into the 1-C position of 3-phosphoglyce…
View article: Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance
Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance Open
View article: PEPc-mediated CO2 assimilation provides carbons to gluconeogenesis and the TCA cycle in both dark-exposed and illuminated guard cells
PEPc-mediated CO2 assimilation provides carbons to gluconeogenesis and the TCA cycle in both dark-exposed and illuminated guard cells Open
Evidence suggests that guard cells have higher rate of phosphoenolpyruvate carboxylase (PEPc)-mediated dark CO2 assimilation than mesophyll cells. However, it is unknown which metabolic pathways are activated following dark CO2 assimilatio…
View article: Metabolomic Analysis of Grapes and Leaves from Symptomatic and Asymptomatic Vitis Vinifera Grapevines with Esca Disease
Metabolomic Analysis of Grapes and Leaves from Symptomatic and Asymptomatic Vitis Vinifera Grapevines with Esca Disease Open
View article: Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome
Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome Open
Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. M…
View article: Different metabolic adaptation strategies after overwintering in<i>Eutrema</i>sp. and<i>Arabidopsis</i>accessions under field conditions in Germany
Different metabolic adaptation strategies after overwintering in<i>Eutrema</i>sp. and<i>Arabidopsis</i>accessions under field conditions in Germany Open
Successful overwintering is a prerequisite for high fitness in temperate perennials and winter annuals and is highly dependent on increased freezing tolerance and timely balancing of deacclimation with growth resumption in spring. To asses…
View article: Dynamics of ribosome composition and ribosomal protein phosphorylation in immune signaling in <i>Arabidopsis thaliana</i>
Dynamics of ribosome composition and ribosomal protein phosphorylation in immune signaling in <i>Arabidopsis thaliana</i> Open
In plants, the detection of microbe-associated molecular patterns (MAMPs) induces primary innate immunity by the activation of mitogen-activated protein kinases (MAPKs). We show here that the MAMP-activated MAPK MPK6 not only modulates def…
View article: The serine–glycine–one-carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development
The serine–glycine–one-carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development Open
L-serine (Ser) and L-glycine (Gly) are critically important for the overall functioning of primary metabolism. We investigated the interaction of the phosphorylated pathway of Ser biosynthesis (PPSB) with the photorespiration-associated gl…
View article: Supplemental data for: Chapter 6: Effect of PLC-overexpression on the metabolome of Arabidopsis roots and shoots in response to mild drought stress
Supplemental data for: Chapter 6: Effect of PLC-overexpression on the metabolome of Arabidopsis roots and shoots in response to mild drought stress Open
Supplemental tables for metabolomic data of PLC-OEs exposed to drought stress
View article: Remodelled Ribosomes Synthesise a Specific Proteome in Proliferating Plant Tissue during Cold
Remodelled Ribosomes Synthesise a Specific Proteome in Proliferating Plant Tissue during Cold Open
Plant acclimation to low temperatures occurs through system-wide mechanisms that include proteome shifts, some of which occur at the level of protein synthesis. All proteins are synthesised by ribosomes. Rather than being monolithic, trans…