Search bioRxiv⌕ Search

Biology subjects

Rohr, A. K.

Publications and source records attributed to Rohr, A. K..

5 recordsLinked to original sources

Conserved copper(I)-binding auxiliary domains link virulence-associated LPMOs to copper homeostasis in the intestinal environment

Multidomain lytic polysaccharide monooxygenases (LPMOs) are widely distributed in human pathogenic bacteria and increasingly recognized for promoting host interactions and virulence. Recent work has shown that immunizing mice with CbpD, a trimodular LPMO from Pseudomonas aeruginosa, provides protection against lethal P. aeruginosa infection. In several human intestinal pathogenic bacteria, LPMOs occur as tetra- and pentamodular proteins and their ability to interact with the host and facilitate virulence has primarily been ascribed to their ability to bind to N-acetylglucosamine containing glycans. Recently, AlphaFold predictions and substrate-binding studies of the Vibrio cholerae colonization factor GbpA suggested the presence of a copper-binding site in its non-catalytic third domain. In light of the recent demonstration that MUC2, the primary intestinal mucin, harbors two conserved and distinct copper binding sites for Cu(II) and Cu(I), we hypothesized that the auxiliary non-catalytic copper-binding domains of intestinal LPMOs evolved as a response to the intestinal environment. Here, we examine GbpA and homologous multidomain LPMOs from food-borne intestinal disease-causing Gram-positive bacteria from the genera Bacillus and Listeria. By combining mutagenesis with biochemical, spectroscopic, and computational approaches, we demonstrate that these multidomain LPMOs contain conserved, yet structurally distinct copper(I)-binding motifs on their non-catalytic third domain. A comprehensive review and reassessment of the literature spanning the past two decades reveals consistent links between the copper-binding ability of these LPMOs and host-pathogen interactions. Thus, our findings link these LPMOs to copper management in the intestine, offering an explanation for why their unique architecture is preserved across different bacterial lineages causing intestinal disease.

biochemistry↗

Redox robustness drives LPMO evolution

Enzymes known as lytic polysaccharide monooxygenases (LPMOs) are exceptionally powerful small redox enzymes that master the controlled generation and productive use of potentially damaging hydroxyl radicals in what is essentially a H2O2-driven peroxygenase reaction. We have used ancestral sequence reconstruction and enzyme resurrection to unravel evolutionary steps leading to this unprecedented catalytic power. Real-time monitoring of copper re-oxidation and amino acid radical formation showed evolutionary improvement of both the capacity to avoid futile turnover of H2O2 and the ability to scavenge damaging radicals resulting from such turnover through a hole hopping pathway. These results show how selective pressure imposed by the need for generating a highly oxidizing intermediate shapes metalloenzymes, involving large parts of the enzyme, well beyond the catalytic center.

evolutionary biology↗

Human gut Faecalibacterium prausnitzii deploy a highly efficient conserved system to cross-feed on β-mannan-derived oligosaccharides

{beta}-Mannans are hemicelluloses that are abundant in modern diets as components in seed endosperms and common additives in processed food. Currently, the collective understanding of {beta}-mannan saccharification in the human colon is limited to a few keystone species, which presumably liberate low-molecular-weight mannooligosaccharide fragments that become directly available to the surrounding microbial community. Here we show that a dominant butyrate-producer in the human gut, Faecalibacterium prausnitzii, is able to acquire and degrade various {beta}-mannooligosaccharides ({beta}-MOS), which are derived by the primary mannanolytic activity of neighboring gut microbiota. Detailed biochemical analyses of selected protein components from their two {beta}-mannooligosaccharides ({beta}-MOS) utilization loci (FpMULs) supported a concerted model whereby the imported {beta}-MOS are stepwise disassembled intracellularly by highly adapted enzymes. Coculturing experiments of F. prausnitzii with the primary degrader Bacteroides ovatus on polymeric {beta}-mannan resulted in syntrophic growth and production of butyrate, thus confirming the high efficiency of the FpMULs uptake system. Genomic comparison with human F. prausnitzii strains and analyses of 2441 public human metagenomes revealed that FpMULs are highly conserved and distributed worldwide. Together, our results provide a significant advance in the knowledge of {beta}-mannans metabolism and the degree to which its degradation is mediated by cross-feeding interactions between prominent beneficial microbes in the human gut. ImportanceCommensal butyrate-producing bacteria belonging to the Firmicutes phylum are abundant in the human gut and are crucial for maintaining health. Currently, insight is lacking into how they target otherwise indigestible dietary fibers and into the trophic interactions they establish with other glycan degraders in the competitive gut environment. By combining cultivation, genomic and detailed biochemical analyses this work reveals the mechanism enabling F. prausnitzii, as a model clostridial cluster IV Firmicute, to cross-feed and access {beta}-mannan-derived oligosaccharides released in the gut ecosystem by the action of primary degraders. A comprehensive survey of human gut metagenomes shows that FpMULs are ubiquitous in human populations globally, highlighting the importance of microbial metabolism of {beta}-mannans/{beta}-MOS as a common dietary component. Our findings provide a mechanistic understanding of the {beta}-MOS utilization capability by F. prausnitzii that may be exploited to select dietary formulations specifically boosting this beneficial symbiont, thus butyrate production, in the gut.

microbiology↗

Molecular mechanism of the chitinolytic monocopper peroxygenase reaction

Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of monocopper enzymes, broadly distributed across the Tree of Life. We recently reported that LPMOs can use H2O2 as an oxidant, revealing a novel reaction pathway. Here, we aimed to elucidate the H2O2-mediated reaction mechanism with experimental and computational approaches. In silico studies suggest that a network of hydrogen bonds, involving both the enzyme and the substrate, brings H2O2 into a strained reactive conformation, and guides the derived hydroxyl radical towards formation of a copper-oxyl intermediate. The initial H2O2 homolytic cleavage and subsequent hydrogen atom abstraction from chitin by the copper-oxyl intermediate are suggested to be the main energy barriers. Under single turnover conditions, stopped-flow fluorimetry demonstrates that LPMO-Cu(II) reduction to Cu(I) is a fast process compared to the re-oxidation reactions. We found that re-oxidation of LPMO-Cu(I) is 2000-fold faster with H2O2 than with O2, the latter being several orders of magnitude slower than rates reported for other monooxygenases. In agreement with the notion of ternary complex formation, when chitin is added, re-oxidation by H2O2 is accelerated whereas that by O2 slows. Simulations indicated that Glu60, a highly-conserved residue, gates the access to the confined active site and constrains H2O2 during catalysis, and Glu60 mutations significantly decreased the enzyme performance. By providing molecular and kinetic insights into the peroxygenase activity of chitinolytic LPMOs, this study will aid the development of applications of enzymatic and synthetic copper catalysis and contribute to understanding pathogenesis, notably chitinolytic plant defenses against fungi and insects. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/541292v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@92826org.highwire.dtl.DTLVardef@12b0a19org.highwire.dtl.DTLVardef@a3fa2aorg.highwire.dtl.DTLVardef@17cfa80_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Fenton-type chemistry by a copper enzyme: molecular mechanism of polysaccharide oxidative cleavage

The discovery of Lytic Polysaccharide Monooxygenases (LPMOs) has been instrumental for the development of economically sustainable lignocellulose biorefineries. Despite the obvious importance of these exceptionally powerful redox enzymes, their mode of action remains enigmatic and their activity and stability under process conditions are hard to control. By using enzyme assays, mass spectrometry and experiments with labeled oxygen atoms, we show that H2O2, and not O2 as previously thought, is the co-substrate of LPMOs. By controlling H2O2 supply, stable reaction kinetics and high enzymatic rates are achieved, the LPMOs work under anaerobic conditions, and the need for adding stoichiometric amounts of reductants is alleviated. These results offer completely new perspectives regarding the mode of action of these unique mono-copper enzymes, the enzymatic conversion of biomass in Nature, and industrial biorefining.

biochemistry↗