Biology subjects

van den Berg, B.

Publications and source records attributed to van den Berg, B..

24 records · Page 2Linked to original sources

bioRxiv2020

Insights into glycan import by a prominent gut symbiont

In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the {beta}2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to [~]2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.

microbiology↗

bioRxiv2020

Acquisition of ionic copper by a bacterial outer membrane protein

Copper, while toxic in excess, is an essential micronutrient in all kingdoms of life due to its essential role in the structure and function of many proteins. Proteins mediating ionic copper import have been characterised in detail for eukaryotes, but much less so for prokaryotes. In particular, it is still unclear whether and how Gram-negative bacteria acquire ionic copper. Here we show that Pseudomonas aeruginosa OprC is an outer membrane, TonB-dependent transporter that is conserved in many Proteobacteria and which mediates acquisition of both reduced and oxidised ionic copper via an unprecedented CxxxM-HxM metal binding site. Crystal structures of wild type and mutant OprC variants with silver and copper suggest that acquisition of Cu(I) occurs via a surface-exposed "methionine track" leading towards the principal metal binding site. Together with whole-cell copper quantitation and quantitative proteomics in a murine lung infection model, our data identify OprC as an abundant component of bacterial copper biology that may enable copper acquisition under a wide range of conditions. SignificanceCopper is an essential metal in biology due to its role in the structure and function of many proteins. Despite this, it is not very clear how bacteria acquire copper, especially for Gram-negative organisms. In this study we show that the outer membrane protein OprC has an unusual metal binding site that allows OprC to bind both reduced and oxidised ionic copper near-irreversibly. Given the versatility of OprC, its presence in many Proteobacteria and its abundance during lung infection in mice, our study shows that OprC is an important component of prokaryote copper biology that warrants further study to uncover its regulation and to assess its role in bacterial virulence.

microbiology↗

bioRxiv2020

Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion

In modern societies, biodegradation of hydrophobic pollutants generated by industry is important for environmental and human health. In Gram-negative bacteria, biodegradation depends on facilitated diffusion of the pollutant substrates into the cell, mediated by specialised outer membrane (OM) channels. Here we show, via a combined experimental and computational approach, that the uptake of monoaromatic hydrocarbons such as toluene in Pseudomonas putida F1 (PpF1) occurs via lateral diffusion through FadL channels. Contrary to classical diffusion channels via which polar substrates move directly into the periplasmic space, PpF1 TodX and CymD direct their hydrophobic substrates into the OM via a lateral opening in the channel wall, bypassing the polar barrier formed by the lipopolysaccharide leaflet on the cell surface. Our study suggests that lateral diffusion of hydrophobic molecules is the modus operandi of all FadL channels, with potential implications for diverse areas such as biodegradation, quorum sensing and gut biology.

microbiology↗

bioRxiv2019

Dynamic oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis

Porphyromonas gingivalis, an asaccharolytic Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases, such as rheumatoid arthritis, cardiovascular disease and Alzheimers disease. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how those peptides enter the cell is not clear. Here we identify RagAB as the outer membrane importer for peptides. X-ray crystal structures show that the transporter forms a dimeric RagA2B2 complex with the RagB substrate binding surface-anchored lipoprotein forming a closed lid on the TonB-dependent transporter RagA. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a \"pedal bin\" nutrient uptake mechanism. Together with mutagenesis, peptide binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic OM oligopeptide acquisition machine with considerable substrate selectivity that is essential for the efficient utilisation of proteinaceous nutrients by P. gingivalis.

microbiology↗

bioRxiv2019

Caffeine boosts preparatory attention for reward-related stimulus information

Both the intake of caffeine-containing substances and the prospect of reward for performing a cognitive task have been associated with improved behavioral performance. To investigate the possible common and interactive influences of caffeine and reward-prospect on preparatory attention, we tested 24 participants during a 2-session experiment in which they performed a cued-reward color-word Stroop task. On each trial, participants were presented with a cue to inform them whether they had to prepare for presentation of a Stroop stimulus and whether they could receive a reward if they performed well on that trial. Prior to each session, participants received either coffee with caffeine (3 mg/kg bodyweight) or with placebo (3 mg/kg bodyweight lactose). In addition to behavioral measures, electroencephalography (EEG) measures of electrical brain activity were recorded. Results showed that both the intake of caffeine and the prospect of reward improved speed and accuracy, with the effects of caffeine and reward-prospect being additive on performance. Neurally, reward-prospect resulted in an enlarged contingent negative variation (CNV) and reduced posterior alpha power (indicating increased cortical activity), both hallmark neural markers for preparatory attention. Moreover, the CNV enhancement for reward-prospect trials was considerably more pronounced in the caffeine condition as compared to the placebo condition. These results thus suggest that caffeine intake boosts preparatory attention for task-relevant information, especially when performance on that task can lead to reward.

neuroscience↗

bioRxiv2018

A multidisciplinary approach towards identification of novel antibiotic scaffolds for Acinetobacter baumannii

Research efforts to discover potential new antibiotics for Gram-negative bacteria suffer from high attrition rates due to the synergistic action of efflux systems and the limited permeability of the outer membrane (OM). One potential strategy to overcome the OM permeability barrier is to identify small molecules that are natural substrates for abundant OM channels, and to use such compounds as scaffolds for the design of efficiently-permeating antibacterials. Here we present a multidisciplinary approach to identify such potential small-molecule scaffolds. Focusing on the pathogenic bacterium Acinetobacter baumannii, we use OM proteomics to identify DcaP as the most abundant channel under various conditions that are relevant for infection. High-resolution X-ray structure determination of DcaP surprisingly reveals a trimeric, porin-like structure and suggests that dicarboxylic acids are potential transport substrates. Electrophysiological experiments and allatom molecular dynamics simulations confirm this notion and provide atomistic information on likely permeation pathways and energy barriers for several small molecules, including a clinically-relevant {beta}-lactamase inhibitor. Our study provides a general blueprint for the identification of molecular scaffolds that will inform the rational design of future antibacterials.

microbiology↗