Geschmack ist vorhersagbar: Mit FlavorMiner. FlavorMiner heißt das Tool, das IPB-Chemiker und Partner aus Kolumbien jüngst entwickelt haben. Das Programm kann, basierend auf maschinellem Lernen (KI), anhand der…
Seit Februar 2021 bietet Wolfgang Brandt, ehemaliger Leiter der Arbeitsgruppe Computerchemie am IPB, sein Citizen Science-Projekt zur Pilzbestimmung an. Dafür hat er in regelmäßigen Abständen öffentliche Vorträge zur Vielfalt…
The HD-ZIP class I transcription factor, HvHOX1 (Homeobox 1) or VRS1 (Vulgare Row-type Spike 1 or Six-rowed Spike 1), regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic function of HvHOX1 and HvHOX2 during spikelet development is still fragmentary. Here, we show that compared to HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of these genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
Publikation
Ninck, S.; Halder, V.; Krahn, J. H.; Beisser, D.; Resch, S.; Dodds, I.; Scholtysik, R.; Bormann, J.; Sewald, L.; Gupta, M. D.; Heilmann, G.; Bhandari, D. D.; Morimoto, K.; Buscaill, P.; Hause, B.; van der Hoorn, R. A. L.; Kaschani, F.; Kaiser, M.;Chemoproteomics Reveals the Pan-HER Kinase Inhibitor Neratinib To Target an Arabidopsis Epoxide Hydrolase Related to Phytohormone SignalingACS Chem. Biol.181076-1088(2023)DOI: 10.1021/acschembio.2c00322
Plant phytohormone pathways are regulated by an intricate network of signaling components and modulators, many of which still remain unknown. Here, we report a forward chemical genetics approach for the identification of functional SA agonists in Arabidopsis thaliana that revealed Neratinib (Ner), a covalent pan-HER kinase inhibitor drug in humans, as a modulator of SA signaling. Instead of a protein kinase, chemoproteomics unveiled that Ner covalently modifies a surface-exposed cysteine residue of Arabidopsis epoxide hydrolase isoform 7 (AtEH7), thereby triggering its allosteric inhibition. Physiologically, the Ner application induces jasmonate metabolism in an AtEH7-dependent manner as an early response. In addition, it modulates PATHOGENESIS RELATED 1 (PR1) expression as a hallmark of SA signaling activation as a later effect. AtEH7, however, is not the exclusive target for this physiological readout induced by Ner. Although the underlying molecular mechanisms of AtEH7-dependent modulation of jasmonate signaling and Ner-induced PR1-dependent activation of SA signaling and thus defense response regulation remain unknown, our present work illustrates the powerful combination of forward chemical genetics and chemical proteomics for identifying novel phytohormone signaling modulatory factors. It also suggests that marginally explored metabolic enzymes such as epoxide hydrolases may have further physiological roles in modulating signaling.
Publikation
Rajakumara, E.; Abhishek, S.; Nitin, K.; Saniya, D.; Bajaj, P.; Schwaneberg, U.; Davari, M. D.;Structure and cooperativity in substrate–enzyme interactions: Perspectives on enzyme engineering and inhibitor designACS Chem. Biol.17266-280(2022)DOI: 10.1021/acschembio.1c00500
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure–function relationship, cooperativity in binding of substrates, and dynamics of substrate–enzyme–cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure–activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes’ structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
Publikation
Bittner, A.; Hause, B.; Baier, M.;Cold-priming causes oxylipin dampening during the early cold and light response of Arabidopsis thalianaJ. Exp. Bot.727163-7179(2021)DOI: 10.1093/jxb/erab314
Abstract
The comparison of transcriptome time-courses of the first 2 h of the cold or highlight response of 24 h cold primed and naive Arabidopsis thaliana showed that priming quickly modifies gene expression in a trigger-specific manner. It dampened up- as well as down-regulation of genes in the cold and in the light. 1/3 of the priming-regulated genes were jasmonate sensitive, including the full set of genes required for oxylipin biosynthesis. qPCR-based analysis in wildtype plants and mutants demonstrated that OPDA (12-oxo phytenoic acid) biosynthesis relative to the jasmonic acid (JA) availability controls dampening of the genes for oxylipin biosynthetic enzymes: Gene regulation in oxylipin biosynthesis mutants more strongly depended on the biosynthesis of the JA precursor OPDA than on its conversion to JA. Additionally, priming-dependent dampening during triggering was more linked to OPDA than to JA level regulation and spray application of OPDA prior to triggering counteracted gene dampening. In contrast to cold-priming induced dampening of ZAT10, priming regulation of the oxylipin hub was insensitive to priming-induced accumulation of thylakoid ascorbate peroxidase and mediated by modulation of the oxylipin sensitivity of genes for OPDA biosynthesis.