Structure and assembly of the S-layer determine virulence in C. difficile

Many bacteria and archaea possess a cell surface layer – S-layer – made of a 2D protein array that covers the entire cell. As the outermost component of the cell envelope, S-layers play crucial roles in many aspects of cell physiology. Importantly, many clinically relevant bacterial pathogens possess a distinct S-layer that forms an initial interface with the host, making it a potential target for development of species-specific antimicrobials. Targeted therapeutics are particularly important for antibiotic resistant pathogens such as Clostridioides difficile, the most frequent cause of hospital acquired diarrhea, which relies on disruption of normal microbiota through antibiotic usage. Despite the ubiquity of S-layers, only partial structural information from a very limited number of species is available and their function and organization remains poorly understood. Here we report the first complete atomic level structure and in situ assembly model of an S-layer from a bacterial pathogen and reveal its role in disease severity. SlpA, the main C. difficile S-layer protein, assembles through tiling of triangular prisms abutting the cell wall, interlocked by distinct ridges facing the environment. This forms a tightly packed array, unlike the more porous S-layer models previously described. We report that removing one of the SlpA ridge features dramatically reduces disease severity, despite being dispensable for overall SlpA structure and S-layer assembly. Remarkably, the effect on disease severity is independent of toxin production and bacterial colonization within the mouse model of disease. Our work combines X-ray and electron crystallography to reveal a novel S-layer organization in atomic detail, highlighting the need for multiple technical approaches to obtain structural information on these paracrystalline arrays. These data also establish a direct link between specific structural elements of S-layer and virulence for the first time, in a crucial paradigm shift in our understanding of C. difficile disease, currently largely attributed to the action of potent toxins. This work highlights the crucial role of S-layers in pathogenicity and the importance of detailed structural information for providing new therapeutic avenues, targeting the S-layer. Understanding the interplay between S-layer and other virulence factors will further enhance our ability to tackle pathogens carrying an S-layer. We anticipate that this work provides a solid basis for development of new, C. difficile-specific therapeutics, targeting SlpA structure and S-layer assembly to reduce the healthcare burden of these infections.

Prediction of photoperiodic regulators from quantitative gene circuit models

Photoperiod sensors allow physiological adaptation to the changing seasons. The external coincidence hypothesis postulates that a light-responsive regulator is modulated by a circadian rhythm. Sufficient data are available to test this quantitatively in plants, though not yet in animals. In Arabidopsis, the clock-regulated genes CONSTANS (CO) and FLAVIN, KELCH, F-BOX (FKF1) and their lightsensitive proteins are thought to form an external coincidence sensor. We use 40 timeseries of molecular data to model the integration of light and timing information by CO, its target gene FLOWERING LOCUS T (FT), and the circadian clock. Among other predictions, the models show that FKF1 activates FT. We demonstrate experimentally that this effect is independent of the known activation of CO by FKF1, thus we locate a major, novel controller of photoperiodism. External coincidence is part of a complex photoperiod sensor: modelling makes this complexity explicit and may thus contribute to crop improvement

CCP4 Cloud for structure determination and project management in macromolecular crystallography

Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.The following funding is acknowledged: Biotechnology and Biological Sciences Research Council (grant No. BB/L007037/1; grant No. BB/S007040/1; grant No. BB/S007083/1; grant No. BB/S005099/1; grant No. BB/S007105/1; award No. BBF020384/1); Medical Research Council (grant No.MC_UP_A025_1012; grant No. MC_U105184325); Ro¨ntgenA˚ ngstro¨m Cluster (grant No. 349-2013-597); Nederlandse Wetenschappelijke Organisatie (grant No. TKI 16219)

Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota

International audienceSulfated glycans are ubiquitous nutrient sources for microbial communities that have co-evolved with eukaryotic hosts. Bacteria metabolise sulfated glycans by deploying carbohydrate sulfatases that remove sulfate esters. Despite the biological importance of sulfatases, the mechanisms underlying their ability to recognise their glycan substrate remain poorly understood. Here, we utilise structural biology to determine how sulfatases from the human gut microbiota recognise sulfated glycans. We reveal 7 new carbohydrate sulfatase structures span four S1 sulfatase subfamilies. Structures of S1_16 and S1_46 represent the first structures of these subfamilies. Structures of S1_11 and S1_15 demonstrate how non-conserved regions of the protein drive specificity towards related but distinct glycan targets. Collectively, these data reveal that Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: https://www.springernature.com/gp/open-research/policies/accepted-manuscript-term

E. coli metabolic protein aldehydealcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed

It is becoming increasingly evident that a high degree of regulation is involved in the protein synthesis machinery entailing more interacting regulatory factors. A multitude of proteins have been identified recently which show regulatory function upon binding to the ribosome. Here, we identify tight association of a metabolic protein aldehyde-alcohol dehydrogenase E (AdhE) with the E. coli 70S ribosome isolated from cell extract under low salt wash conditions. Cryo-EM reconstruction of the ribosome sample allows us to localize its position on the head of the small subunit, near the mRNA entrance. Our study demonstrates substantial RNA unwinding activity of AdhE which can account for the ability of ribosome to translate through downstream of at least certain mRNA helices. Thus far, in E. coli, no ribosome-associated factor has been identified that shows downstream mRNA helicase activity. Additionally, the cryo-EM map reveals interaction of another extracellular protein, outer membrane protein C (OmpC), with the ribosome at the peripheral solvent side of the 50S subunit. Our result also provides important insight into plausible functional role of OmpC upon ribosome binding. Visualization of the ribosome purified directly from the cell lysate unveils for the first time interactions of additional regulatory proteins with the ribosom

Moclobemide excretion in human breast milk

1 Six lactating white women, aged 24-36 years, received a single oral dose of 300 mg moclobemide, between 09.00 h and 11.00 h, 3 to 5 days after the delivery of a full term neonate. 2 Complete milk collections were obtained before, 3, 6, 9, 12 and 24 h after drug administration by means of a breast pump. Venous blood samples were drawn before, and 0.5, 1, 3, 4.5, 6, 9, 12, 24 h post-dosing. 3 Moclobemide, and its major metabolite (Ro 12-8095) were measured in milk and plasma samples using h.p.l.c. The active metabolite (Ro 12-5637) could only be detected in plasma. 4 Moclobemide and its metabolites were not detectable in 24 h plasma samples. Cmax, tmax and t½h for moclobemide were (mean ± s.d.) 2.70 ± 1.24 mg l-1, 2.03 ± 1.19 h and 2.26 ± 0.26 h, respectively. 5 The concentrations of moclobemide and Ro 12-8095 in milk were highest at 3 h after drug administration and the drug and metabolite were not detectable after 12 h. Ro 12-5637 was not detected in any milk sample. The percentages of the dose excreted as moclobemide and Ro 12-8095 were (mean ± s.d.) 0.057 ± 0.020% and 0.031 ± 0.011%, respectively. An average 3.5 kg breast-fed neonate would therefore be exposed to only a 0.05 mg kgmoclobemide dose (approximately 1% of the maternal dose on the mg kg-' basis)

Trends of the Major Porin Gene (ompF) Evolution: Insight from the Genus Yersinia

OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species