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…
Zheng, K.; Lyu, J. C.; Thomas, E. L.; Schuster, M.; Sanguankiattichai, N.; Ninck, S.; Kaschani, F.; Kaiser, M.; Hoorn, R. A.;The proteome of agroinfiltrated Nicotiana benthamiana is shaped by extensive protein processingbioRxiv(2024)DOI: 10.1101/2023.11.02.565301
Processing by proteases irreversibly regulates the fate of plant proteins and hampers the production of recombinant protein in plants, yet only few processing events have been described in agroinfiltrated Nicotiana benthamiana, which has emerged as a favorite transient protein expression platform in plant science and molecular pharming. Here, we used in-gel digests and mass spectrometry to monitor the migration and topography of 5,040 plant proteins of agroinfiltrated N. benthamiana within a protein gel. By plotting the peptides over the gel slices, we generated peptographs that reveal where which part of each protein was detected within the protein gel. These data uncovered that 60% of the detected proteins have proteoforms that migrate at lower than predicted molecular weights, implicating extensive proteolytic processing. For instance, this analysis confirms the proteolytic removal and degradation of autoinhibitory prodomains of most but not all proteases, and revealed differential processing within pectinemethylesterase and lipase families. This analysis also uncovered intricate processing of glycosidases and uncovered that ectodomain shedding might be common for a diverse range of receptor-like kinases. Transient expression of double-tagged candidate proteins confirmed various processing events in vivo. This extensive proteomic dataset can be investigated further and demonstrates that most plant proteins are proteolytically processed and implicates an extensive proteolytic machinery shaping the proteome of agroinfiltrated N. benthamiana.
Preprints
Mekkaoui, K.; Baral, R.; Smith, F.; Klein, M.; Feussner, I.; Hause, B.;Unraveling the role of 12-cis-oxo-phytodienoic acid in the wound response of Arabidopsis thaliana: Insights from transcriptomic and complementation studiesbioRxiv(2024)DOI: 10.1101/2024.03.22.586262
In addition to jasmonoyl-isoleucine (JA-Ile), a well-established signaling molecule for plant growth and defense, its precursor, cis-12-oxo-phytodienoic acid (OPDA), is thought to possess independent signaling functions. Its perception in vascular plants is still uncharacterized. Several OPDA functions in Arabidopsis were inferred from a mutant that is affected in the function of the OPDA REDUCTASE3 (OPR3), catalyzing the conversion of OPDA within peroxisomes. Recently, opr3 plants were found to accumulate JA-Ile via a cytosolic OPR2-mediated bypass. Given the uncoupling of OPDA and JA biosynthesis in the JA-deficient mutant opr2opr3, potential OPDA signaling was investigated by a transcriptome approach comparing wild type, opr2opr3 and the JA- and OPDA-deficient mutantallene oxide synthase. Dissecting the wound response of seedlings revealed that OPDA lacked a transcriptional signature, and that previously characterized OPDA-response genes were wound-induced independently of OPDA. Exogenous application of OPDA to opr2opr3 seedlings led to JA-Ile formation and signaling even in absence of OPR2 and OPR3 and resulted in activation of sulfur assimilation. These divergent responses to endogenously synthesized and applied OPDA suggest a compartmentalization of endogenous OPDA which was investigated by a trans-organellar complementation approach. OPR3 complemented the opr2opr3 mutant in terms of fertility and wound-induced JA-Ile production irrespective of its subcellular localization. In vitro enzymatic activity of OPR3, however, showed conversion of OPDA and 4,5-didehydro-JA (4,5-ddh-JA), therefore not allowing to conclude which compound is translocated. Dissecting the conversion of either OPDA or 4,5-ddh-JA by OPR2 and OPR1 organelle variants pointed to a strong OPDA compartmentalization supporting its lacking signaling capacity.
Preprints
Medina-Ortiz, D.; Khalifeh, A.; Anvari-Kazemabad, H.; Davari, M. D.;Interpretable and explainable predictive machine learning models for data-driven protein engineeringbioRxiv(2024)DOI: 10.1101/2024.02.18.580860
Protein engineering using directed evolution and (semi)rational design has emerged as a powerful strategy for optimizing and enhancing enzymes or proteins with desired properties. Integrating artificial intelligence methods has further enhanced and accelerated protein engineering through predictive models developed in data-driven strategies. However, the lack of explainability and interpretability in these models poses challenges. Explainable Artificial Intelligence addresses the interpretability and explainability of machine learning models, providing transparency and insights into predictive processes. Nonetheless, there is a growing need to incorporate explainable techniques in predicting protein properties in machine learning-assisted protein engineering. This work explores incorporating explainable artificial intelligence in predicting protein properties, emphasizing its role in trustworthiness and interpretability. It assesses different machine learning approaches, introduces diverse explainable methodologies, and proposes strategies for seamless integration, improving trust-worthiness. Practical cases demonstrate the explainable model’s effectiveness in identifying DNA binding proteins and optimizing Green Fluorescent Protein brightness. The study highlights the utility of explainable artificial intelligence in advancing computationally assisted protein design, fostering confidence in model reliability.
Preprints
Liu, Q.; Neefjes, A. C. M.; Kobylinska, R.; Mugford, S. T.; Marzo, M.; Canham, J.; Schuster, M.; Hoorn, R. A.; Chen, Y.; Hogenhout, S. A.;Aphid effectors suppress plant immunity via recruiting defence proteins to processing bodiesbioRxiv(2024)DOI: 10.1101/2024.11.20.624400
Aphids are small insects that have developed specialized mouthparts and effector proteins to establish long-term relationships with plants. The peach-potato aphid, Myzus persicae, is a generalist, feeding on many plant species and capable of transmitting numerous pathogens. This study reveals how host-responsive cathepsins B (CathB) in the oral secretions of M. persicae facilitate aphid survival by modulating plant immune responses. Aphid CathB localize to processing bodies (p-bodies) and recruit key immune regulators EDS1, PAD4, and ADR1 to these bodies, suppressing plant defenses. A plant protein, Acd28.9 (Hsp20 family), counteracts this CathB activity and contributes to plant resistance to aphids. These findings highlight a novel role for p-bodies in plant immunity and uncover a plant resistance mechanism to aphid infestation.