Biology subjects

Shaw, S.

Publications and source records attributed to Shaw, S..

25 records · Page 2Linked to original sources

bioRxiv2023

Structure of the Commander endosomal trafficking complex linked to X-linked intellectual disability/Ritscher-Schinzel syndrome

The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two subassemblies; Retriever composed of VPS35L, VPS26C and VPS29, and the CCC complex which contains ten subunits COMMD1-COMMD10 and two coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy and in silico predictions we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilised by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a sixteenth subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.

biochemistry↗

bioRxiv2021

Distribution, organization and expression of genes concerned with anaerobic lactate-utilization in human intestinal bacteria

Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analysis was performed for two prominent lactate-utilizing species from the human gut, Anaerobutyricum soehngenii and Coprococcus catus, during growth on lactate, hexose sugar, or hexose plus lactate. In A. soehngenii L2-7, six genes of the lct cluster including NAD-independent D-lactate dehydrogenase (i-LDH) were co-ordinately upregulated during growth on equimolar D and L-lactate (DL-lactate). Upregulated genes included an acyl-CoA dehydrogenase related to butyryl-CoA dehydrogenase, which may play a role in transferring reducing equivalents between reduction of crotonyl-CoA and oxidation of lactate. Genes upregulated in C. catus GD/7 included a six-gene cluster (lap) encoding propionyl CoA-transferase, a putative lactoyl-CoA epimerase, lactoyl-CoA dehydratase and lactate permease, and two unlinked acyl-CoA dehydrogenase genes that are candidates for acryloyl-CoA reductase. An i-LDH homolog in C. catus is encoded by a separate, partial lct, gene cluster, but not upregulated on lactate. While C. catus converts three mols of DL-lactate via the acrylate pathway to two mols propionate and one mol acetate, some of the acetate can be re-used with additional lactate to produce butyrate. A key regulatory difference is that while glucose partially repressed lct cluster expression in A. soehngenii, there was no repression of lactate utilization genes by fructose in the non-glucose utilizer C. catus. This implies that bacteria such as C. catus might be more important in curtailing lactate accumulation in the gut. Impact statementLactate can be produced as a fermentation by-product by many gut bacteria but has the potential to perturb intestinal microbial communities by lowering luminal pH, and its accumulation has been linked to a range of deleterious health outcomes. Fortunately, in healthy individuals, lactate tends not to accumulate as it is consumed by cross-feeding lactate-utilizing bacteria, which can convert it into the beneficial short chain fatty acids butyrate and propionate. Lactate-utilizing gut bacteria are therefore promising candidates for potential development as novel probiotics. However, lactate-utilizers are taxonomically diverse, and the genes that underpin utilization of lactate by these specialized gut bacteria are not fully understood. In this study we used transcriptomics to compare gene expression profiles of Anaerobutyricum soehngenii and Coprococcus catus, two prominent lactate-utilizing species in the human gut, during growth on lactate alone, sugar alone, or sugar plus lactate. The results revealed strong upregulation of key, but distinct, gene clusters that appear to be responsible for lactate utilization by these, and other, gut bacterial species. Our results therefore increase mechanistic understanding of different lactate utilization pathways used by gut bacteria, which may help to inform selection of optimal lactate-utilizing species for development as novel therapeutics against colonic microbiota perturbations. Data summaryNovel draft genomes generated for this study have been made available from GenBank (https://www.ncbi.nlm.nih.gov/bioproject/) under BioProject number PRJNA701799. RNA-seq data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-10136. Further details of additional existing genomic data that were analyzed in this project are given in Table 1 and Table S2. O_TBL View this table: org.highwire.dtl.DTLVardef@13fd07borg.highwire.dtl.DTLVardef@90796dorg.highwire.dtl.DTLVardef@1140a60org.highwire.dtl.DTLVardef@b53597org.highwire.dtl.DTLVardef@d16268_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONNew and existing strains used for in vitro cultivation studies in this work, and their corresponding genomes. "N/A" indicates no genome available for this strain, which was used for in vitro work only. The full list of strains used for genomic-based analyses is shown in Table S2. C_TABLECAPTION C_TBL

microbiology↗

bioRxiv2021

Crosstalk between enterocytes and innate lymphoid cells drives early IFN-g-mediated control of Cryptosporidium

The intestinal parasite, Cryptosporidium, is a major contributor to global child mortality and causes opportunistic infection in immune deficient individuals. Innate resistance to Cryptosporidium, which specifically invades enterocytes, is dependent on the production of IFN-{gamma}, yet whether enterocytes contribute to parasite control is poorly understood. In this study, utilizing the natural mouse pathogen, Cryptosporidium tyzzeri, we show that epithelial-derived IL-18 synergized with IL-12 to stimulate innate lymphoid cell (ILC) production of IFN-{gamma}. This innate IFN-{gamma} was required for early parasite control. Loss of STAT1 in enterocytes, but not dendritic cells or macrophages, antagonized early parasite control. Transcriptional profiling of enterocytes from infected mice identified an IFN-{gamma} signature and enrichment of anti-microbial effectors like IDO, GBP and IRG. Deletion experiments identified a role for Irgm1/m3 in parasite control. Thus, enterocytes promote ILC production of IFN-{gamma} that acts on enterocytes to restrict the growth of C. tyzzeri.

immunology↗

bioRxiv2021

Cyclic AMP signalling and glucose metabolism mediate pH taxis by African trypanosomes

The collective movement of African trypanosomes on semi-solid surfaces, known as social motility, is presumed to be due to migration factors and repellents released by the parasites. Here we show that procyclic (insect midgut) forms acidify their environment as a consequence of glucose metabolism, generating pH gradients by diffusion. Early and late procyclic forms exhibit self-organising properties on agarose plates. While early procyclic forms are repelled by acid and migrate outwards, late procyclic forms remain at the inoculation site. Furthermore, trypanosomes respond to exogenously formed pH gradients, with both early and late procyclic forms being attracted to alkali. pH taxis is mediated by multiple cyclic AMP effectors: deletion of one copy of adenylate cyclase ACP5, or both copies of the cyclic AMP response protein CARP3, abrogates the response to acid, while deletion of phosphodiesterase PDEB1 completely abolishes pH taxis. The ability to sense pH is biologically relevant as trypanosomes experience large changes as they migrate through their tsetse host. Supporting this, a CARP3 null mutant is severely compromised in its ability to establish infections in flies. Based on these findings, we propose that the expanded family of adenylate cyclases in trypanosomes might govern other chemotactic responses in their two hosts.

microbiology↗

bioRxiv2020

Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease

The myxozoan parasite, Tetracapsuloides bryosalmonae has a two-host life cycle alternating between freshwater bryozoans and salmonid fish. Infected fish can develop Proliferative Kidney Disease (PKD), characterised by a gross lymphoid-driven kidney pathology in wild and farmed salmonids. To facilitate an in-depth understanding of T. bryosalmonae-host interactions, we have adopted a two-host parasite transcriptome sequencing approach to minimize host contamination in the absence of a complete T. bryosalmonae genome. Parasite contigs common to both infected hosts (the intersect transcriptome; 7,362 contigs) were typically AT-rich (60-75% AT). 5,432 contigs within the intersect were annotated with 1,930 unannotatde contigs encoding for unknown transcripts. We have focused on transcripts encoding proteins involved in; nutrient acquisition, host-parasite interactions, development, and cell-to-cell communication or proteins of unknown function, establishing their potential importance in each host by RT-qPCR. Host-specific expression profiles were evident, particularly in transcripts encoding proteases and proteins involved in lipid metabolism, cell adhesion, and development. We confirm for the first time the presence of homeobox proteins and a frizzled homologue in myxozoan parasites. The novel insights into myxozoan biology that this study reveals will help to focus research in developing future disease control strategies.

genomics↗

bioRxiv2019

Domestication of Campylobacter jejuni NCTC 11168

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37{degrees}C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains.\n\nImpact statementIn this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 reference Campylobacter genomes and compare them with observable differences in common laboratory phenotypes.\n\nData summaryShort read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467).\n\nAll assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact: https://microreact.org/project/NCTC11168.\n\nRepositoriesShort read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467; Table S1).\n\nThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2018

High throughput screen identifies IFN-γ-dependent inhibitors of Toxoplasma gondii growth

Toxoplasma gondii is an obligate intracellular parasite capable of causing severe disease due to congenital infection and in patients with compromised immune systems. Control of infection is dependent on a robust Th1 type immune response including production of interferon gamma (IFN-{gamma}), which is essential for control. IFN-{gamma} activates a variety of anti-microbial mechanisms in host cells, which are then able to control intracellular parasites such as T. gondii. Despite the effectiveness of these pathways in controlling acute infection, the immune system is unable to eradicate chronic infections that can persist for life. Similarly, while antibiotic treatment can control acute infection, it is unable to eliminate chronic infection. To identify compounds that would act synergistically with IFN-{gamma}, we performed a high-throughput screen of diverse small molecule libraries to identify inhibitors of T. gondii. We identified a number of compounds that inhibited parasite growth in vitro at low M concentrations and that demonstrated enhanced potency in the presence of low level of IFN-{gamma}. A subset of these compounds act by enhancing the recruitment of LC3 to the parasite-containing vacuole, suggesting they work by an autophagy-related process, while others were independent of this pathway. The pattern of IFN-{gamma}-dependence was shared among the majority of analogs from 6 priority scaffolds and analysis of structure activity relationships for one such class revealed specific stereochemistry associated with this feature. Identification of these IFN-{gamma}-dependent leads may lead to development of improved therapeutics due to their synergistic interactions with immune responses.

microbiology↗