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…
Wittmund, M.; Cadet, F.; Davari, M. D.;Learning epistasis and residue coevolution patterns: Current trends and future perspectives for advancing enzyme engineeringACS Catal.1214243-14263(2022)DOI: 10.1021/acscatal.2c01426
Engineering proteins and enzymes with the desired
functionality has broad applications in molecular biology,
biotechnology, biomedical sciences, health, and medicine. The
vastness of protein sequence space and all the possible proteins it
represents can pose a considerable barrier for enzyme engineering
campaigns through directed evolution and rational design. The
nonlinear effects of coevolution between amino acids in protein
sequences complicate this further. Data-driven models increasingly
provide scientists with the computational tools to navigate through
the largely undiscovered forest of protein variants and catch a
glimpse of the rules and effects underlying the topology of sequence
space. In this review, we outline a complete theoretical journey
through the processes of protein engineering methods such as
directed evolution and rational design and reflect on these strategies and data-driven hybrid strategies in the context of sequence
space. We discuss crucial phenomena of residue coevolution, such as epistasis, and review the history of models created over the past
decade, aiming to infer rules of protein evolution from data and use this knowledge to improve the prediction of the structure−
function relationship of proteins. Data-driven models based on deep learning algorithms are among the most promising methods
that can account for the nonlinear phenomena of sequence space to some degree. We also critically discuss the available models to
predict evolutionary coupling and epistatic effects (classical and deep learning) in terms of their capabilities and limitations. Finally,
we present our perspective on possible future directions for developing data-driven approaches and provide key orientation points
and necessities for the future of the fast-evolving field of enzyme engineering.
Publikation
Voiniciuc, C.;Modern mannan: a hemicellulose\'s journeyNew Phytol.2341175-1184(2022)DOI: 10.1111/nph.18091
Hemicellulosic polysaccharides built of b-1,4-linked mannose units have been found throughout the plant kingdom and have numerous industrial applications. Here, I review recent advances in the biosynthesis and modification of plant b-mannans. These matrix polymers can associate with cellulose bundles to impact the mechanical properties of plant fibers or biocomposites. In certain algae, mannan microfibrils even replace cellulose as the dominant structural component of the cell wall. Conversely, patterned galactoglucomannan found in Arabidopsis thaliana seed mucilage significantly modulates cell wall architecture and abiotic stress tolerance despite its relatively low content. I also discuss the subcellular requirements for b-mannan biosynthesis, the increasing number of carbohydrate-active enzymes involved in this process, and the players that continue to be puzzling. I discuss how cellulose synthase-like enzymes elongate (gluco)mannans in orthogonal hosts and highlight the discoveries of plant enzymes that add specific galactosyl or acetyl decorations. Hydrolytic enzymes such as endo-b-1,4-mannanases have recently been involved in a wide range of biological contexts including seed germination, wood formation, heavy metal tolerance, and defense responses. Synthetic biology tools now provide faster tracks to modulate the increasingly-relevant mannan structures for improved plant traits and bioproducts.
Publikation
Balarynová, J.; Klčová, B.; Sekaninová, J.; Kobrlová, L.; Cechová, M. Z.; Krejčí, P.; Leonova, T.; Gorbach, D.; Ihling, C.; Smržová, L.; Trněný, O.; Frolov, A.; Bednář, P.; Smýkal, P.;The loss of polyphenol oxidase function is associated with hilum pigmentation and has been selected during pea domesticationNew Phytol.2351807–1821(2022)DOI: 10.1111/nph.18256
Seed coats serve as protective tissue to the enclosed embryo. As well as mechanical there are also chemical defence functions. During domestication, the property of the seed coat was altered including the removal of the seed dormancy. We used a range of genetic, transcriptomic, proteomic and metabolomic approaches to determine the function of the pea seed polyphenol oxidase (PPO) gene. Sequencing analysis revealed one nucleotide insertion or deletion in the PPO gene, with the functional PPO allele found in all wild pea samples, while most cultivated peas have one of the three nonfunctional ppo alleles. PPO functionality cosegregates with hilum pigmentation. PPO gene and protein expression, as well as enzymatic activity, was downregulated in the seed coats of cultivated peas. The functionality of the PPO gene relates to the oxidation and polymerisation of gallocatechin in the seed coat. Additionally, imaging mass spectrometry supports the hypothesis that hilum pigmentation is conditioned by the presence of both phenolic precursors and sufficient PPO activity. Taken together these results indicate that the nonfunctional polyphenol oxidase gene has been selected during pea domestication, possibly due to better seed palatability or seed coat visual appearance.
Publikation
Rausche, J.; Stenzel, I.; Stauder, R.; Fratini, M.; Trujillo, M.; Heilmann, I.; Rosahl, S.;A phosphoinositide 5-phosphatase from Solanum tuberosum is activated by PAMP-treatment and may antagonize phosphatidylinositol 4,5-bisphosphate at Phytophthora infestans infection sitesNew Phytol.229469-487(2021)DOI: 10.1111/nph.16853
Potato (Solanum tuberosum) plants susceptible to late blight disease caused by the oomycete Phytophthora infestans display enhanced resistance upon infiltration with the pathogen-associated molecular pattern (PAMP), Pep-13. Here, we characterize a potato gene similar to Arabidopsis 5-phosphatases which was identified in transcript arrays performed to identify Pep-13 regulated genes, and termed StIPP.Recombinant StIPP protein specifically dephosphorylated the D5-position of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) in vitro. Other phosphoinositides or soluble inositolpolyphosphates were not converted.When transiently expressed in tobacco (Nicotiana tabacum) pollen tubes, a StIPP-YFP fusion localized to the subapical plasma membrane and antagonized PtdIns(4,5)P2-dependent effects on cell morphology, indicating in vivo functionality. Phytophthora infestans-infection of N. benthamiana leaf epidermis cells resulted in relocalization of StIPP-GFP from the plasma membrane to the extra-haustorial membrane (EHM). Colocalizion with the effector protein RFP-AvrBlb2 at infection sites is consistent with a role of StIPP in the plant–oomycete interaction. Correlation analysis of fluorescence distributions of StIPP-GFP and biosensors for PtdIns(4,5)P2 or phosphatidylinositol 4-phosphate (PtdIns4P) indicate StIPP activity predominantly at the EHM.In Arabidopsis protoplasts, expression of StIPP resulted in the stabilization of the PAMP receptor, FLAGELLIN-SENSITIVE 2, indicating that StIPP may act as a PAMP-induced and localized antagonist of PtdIns(4,5)P2-dependent processes during plant immunity.