Correction to: Communications Biologyhttps://doi.org/10.1038/s42003-022-04141-x, published online 16 November 2022.In the original version of the Article, an incorrect additional description of... Show moreCorrection to: Communications Biologyhttps://doi.org/10.1038/s42003-022-04141-x, published online 16 November 2022.In the original version of the Article, an incorrect additional description of panel b in Figure 1 was included. The following sentence has now been removed:b Lignocellulose is a complex and recalcitrant polymer built up from cellulose, xylan (hemicellulose), and lignin. Its degradation requires the synergistic action of various different enzymes. Show less
Activity-based protein profiling is used to screen lignocellulose-degrading enzymes from the white rot fungus Phanerochaete chrysosporium to identify those specifically active in the presence of... Show moreActivity-based protein profiling is used to screen lignocellulose-degrading enzymes from the white rot fungus Phanerochaete chrysosporium to identify those specifically active in the presence of wood substrate.Activity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts. Show less
Activity-based protein profiling (ABPP) has so far scarcely been applied in Archaea in general and, especially, in extremophilic organisms. We herein isolated a novel Thermococcus strain designated... Show moreActivity-based protein profiling (ABPP) has so far scarcely been applied in Archaea in general and, especially, in extremophilic organisms. We herein isolated a novel Thermococcus strain designated sp. strain 2319x1E derived from the same enrichment culture as the recently reported Thermococcus sp. strain 2319x1. Both strains are able to grow with xylan as the sole carbon and energy source, and for Thermococcus sp. strain 2319x1E (optimal growth at 85°C, pH 6-7), the induction of xylanolytic activity in the presence of xylan was demonstrated. Since the solely sequence-based identification of xylanolytic enzymes is hardly possible, we established a complementary approach by conducting comparative full proteome analysis in combination with ABPP using α- or β-glycosidase selective probes and subsequent mass spectrometry (MS)-based analysis. This complementary proteomics approach in combination with recombinant protein expression and classical enzyme characterization enabled the identification of a novel bifunctional maltose-forming α-amylase and deacetylase (EGDIFPOO_00674) belonging to the GH57 family and a promiscuous β-glycosidase (EGIDFPOO_00532) with β-xylosidase activity. We thereby further substantiated the general applicability of ABPP in archaea and expanded the ABPP repertoire for the identification of glycoside hydrolases in hyperthermophiles. Show less
Woude, L. van der; Piotrowski, M.; Klaasse, G.; Paulus, J.K.; Krahn, D.; Ninck, S.; ... ; Zanten, M. van 2021
This document presents the Bonn PRINTEGER Consensus Statement: Working with Research Integrity-Guidance for research performing organisations. The aim of the statement is to complement existing... Show moreThis document presents the Bonn PRINTEGER Consensus Statement: Working with Research Integrity-Guidance for research performing organisations. The aim of the statement is to complement existing instruments by focusing specifically on institutional responsibilities for strengthening integrity. It takes into account the daily challenges and organisational contexts of most researchers. The statement intends to make research integrity challenges recognisable from the work-floor perspective, providing concrete advice on organisational measures to strengthen integrity. The statement, which was concluded February 7th 2018, provides guidance on the following key issues: § 1. Providing information about research integrity § 2. Providing education, training and mentoring § 3. Strengthening a research integrity culture § 4. Facilitating open dialogue § 5. Wise incentive management § 6. Implementing quality assurance procedures § 7. Improving the work environment and work satisfaction § 8. Increasing transparency of misconduct cases § 9. Opening up research § 10. Implementing safe and effective whistle-blowing channels § 11. Protecting the alleged perpetrators § 12. Establishing a research integrity committee and appointing an ombudsperson § 13. Making explicit the applicable standards for research integrity. Show less
Husaini, A.M.; Morimoto, K.; Chandrasekar, B.; Kelly, S.; Kaschani, F.; Palmero, D.; ... ; Hoorn, R.A.L. van der 2018
The proteasome is a nuclear‐cytoplasmic proteolytic complex involved in nearly all regulatory pathways in plant cells. The three different catalytic activities of the proteasome can have different... Show moreThe proteasome is a nuclear‐cytoplasmic proteolytic complex involved in nearly all regulatory pathways in plant cells. The three different catalytic activities of the proteasome can have different functions, but tools to monitor and control these subunits selectively are not yet available in plant science. Here, we introduce subunit‐selective inhibitors and dual‐color fluorescent activity‐based probes for studying two of the three active catalytic subunits of the plant proteasome. We validate these tools in two model plants and use this to study the proteasome during plant–microbe interactions. Our data reveal that Nicotiana benthamiana incorporates two different paralogs of each catalytic subunit into active proteasomes. Interestingly, both β1 and β5 activities are significantly increased upon infection with pathogenic Pseudomonas syringae pv. tomato DC3000 lacking hopQ1‐1 [PtoDC3000(ΔhQ)] whilst the activity profile of the β1 subunit changes. Infection with wild‐type PtoDC3000 causes proteasome activities that range from strongly induced β1 and β5 activities to strongly suppressed β5 activities, revealing that β1 and β5 activities can be uncoupled during bacterial infection. These selective probes and inhibitors are now available to the plant science community, and can be widely and easily applied to study the activity and role of the different catalytic subunits of the proteasome in different plant species. Show less
Kovacs, J.; Poor, P.; Kaschani, F.; Chandrasekar, B.; Hong, T.N.; Misas-Villamil, J.C.; ... ; Hoorn, R.A.L. van der 2017
