Elisabeth C Lowe

Newcastle University | NCL

Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified an uncharacterised transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full...

Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified a novel transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive...

Mycobacterial glycolipids are important cell envelope structures that drive host-pathogen interactions. Arguably, the most important amongst these are lipoarabinomannan (LAM) and its precursor, lipomannan (LM); both are trafficked out of the bacterium to the host via completely unknown mechanisms. An important class of exported LM/LAM is the capsul...

Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the d-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arab...

Division and degradation of bacterial cell walls requires coordinated action from a myriad of enzymes. This particularly applies to the elaborate cell walls of acid-fast organisms such as Mycobacterium tuberculosis, which consist of a multi-layered cell wall that contains an unusual glycan called arabinogalactan. Enzymes that cleave the D-arabinan...

Degradation of complex carbohydrates in the gut is a key trait of Bacteroides species. Some glycans are metabolised selfishly releasing few or no oligosaccharide breakdown products from complex polysaccharides, whereas others release oligosaccharides and cross feed other microbes. The outer cell wall of many fungi commonly found in the gut consists...

Microbiomes and their enzymes process many of the nutrients accessible in the gastrointestinal tract of bilaterians and play an essential role in host health and nutrition. In this review, we describe recent insights into nutrient processing in microbiomes across three exemplary yet contrasting gastrointestinal ecosystems (humans, ruminants and ins...

Marine bacteria that produce an enormous panoply of glycan-degrading enzymes are identified as having a role in releasing fixed carbon present in glycan-rich cell walls of brown algae.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Glycans are the major carbon sources available to the human colonic microbiota. Numerous N-glycosylated proteins are found in the human gut, from both dietary and host sources, including immunoglobulins such as IgA that are secreted into the intestine at high levels. Here, we show that many mutualistic gut Bacteroides spp. have the capacity to util...

Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a β1,3-galactan backbone and β1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mechanisms by which nutritionally re...

The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaom...

The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaom...

Interactions between the host and its microbiota are of mutual benefit and promote health. Complex molecular pathways underlie this dialog, but the identity of microbe-derived molecules that mediate the mutualistic state remains elusive. Helicobacter hepaticus is a member of the mouse intestinal microbiota that is tolerated by the host. In the abse...

Significance The major nutrients available to the human microbiota are complex carbohydrates. Host glycans are important to this microbial community, particularly when dietary carbohydrates are scarce. The host glycans heparin and heparan sulfate are high-priority carbohydrates for Bacteroides thetaiotaomicron , a member of the human microbiota. Th...

Glycans are major nutrients available to the human gut microbiota (HGM). The Bacteroides are generalist glycan degraders and this function is mediated largely by polysaccharide utilization loci (PULs). The genomes of several Bacteroides species contain a PUL, PUL1,6-beta;-glucan, that was predicted to target mixed linked plant 1,3;1,4-beta-glucans....

Nature Communications 6 Article number: 748110.1038/ncomms8481 (2015); Published June262015; Updated February052016 The financial support for the work described in this Article was not fully acknowledged. The Acknowledgements should have included the following:This work was supported in part by a grant to H.J.G., B.H. and N.T. (European Union's Se...

The complex carbohydrates accessible to the distal gut microbiota (DGM) are key drivers in determining the structure of this ecosystem. Typically, plant cell wall polysaccharides and recalcitrant starch (i.e. dietary fibre), in addition to host glycans are considered the primary nutrients for the DGM; however, we recently demonstrated that α-mannan...

The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. beta-mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by glycoside hydrolases, although a family of glycoside phosphorylase...

The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members...

Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the micr...

Cells respond to nutrient availability by expressing nutrient catabolic genes. We report that the regulator controlling utilization of chondroitin sulfate (CS) in the mammalian gut symbiont Bacteroides thetaiotaomicron is activated by an intermediate in CS breakdown rather than CS itself. We determine that the rate-determining enzyme in CS breakdow...

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallog...

Signaling across the membrane in response to extracellular stimuli is essential for survival of all cells. In bacteria, responses to environmental changes are predominantly mediated by two-component systems, which are typically composed of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. In the human gut symbiont Ba...

Additional Results and Discussion of the B. thetaiotaomicron and B. ovatus plant cell wall degrading mechanisms. (DOC)

Schematic of B. thetaiotaomicron PULs involved in plant glycan metabolism. (A) Eight HTCS-associated B. thetaiotaomicron PULs involved in plant pectin degradation. The HTCS genes (pink boxes) that were disrupted by plasmid insertions are labeled with an “Ω” symbol; black symbols indicate no phenotype was observed; red symbols indicate HTCS mutants...

Dissecting the in vivo expression of EC 3.2.1.8 (endo-1,4-β-xylanase). (A) Gene expression in E2 fecal samples was evaluated by microbial RNA-Seq. After data from all 12 species in the model human gut microbiome were binned by EC number annotation and normalized (i.e., data were “community-normalized” at the level of ECs), a significant decrease in...

Comparison of homologous PULs between B. thetaiotaomicron and B. ovatus. Dark green lines delineate “homologous PULs.” Light green lines delineate “probably homologous PULs.” Yellow lines delineate genes immediately adjacent to PULs that are syntenic best Blast hits. Gray lines delineate genes within homologous PULs that are not best Blast hits. (P...

Microarray datasets used in this study. All GeneChip data used in this study are available from the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/projects/geo/) under the indicated accession number. (PDF)

Primers used in this study. Sequences recognized by restriction enzymes used for molecular cloning are underlined. (PDF)

Activity and specificity of the family 1 polysaccharide lyase BT4116. Homogalacturonan (HG; non-methyl esterified) and rhamnogalacturonan I (RG) at 5 mg ml−1 were digested with 1 µM BT4116 in 20 mM Tris pH 8.0, 1 mM CaCl2 for 1 h at 37°C. TLC plates were analyzed in a solvent system of ethyl acetate, acetic acid, formic acid, and water (9∶3∶1∶4) an...

Glycan degrading enzymes encoded in B. thetaiotaomicron and B. ovatus PULs. Glycan degrading enzymes are listed as annotated in the CAZy database [14]. Predicted target linkages are based on the known activities within each CAZy family and the linkages known to be present in the substrate presented for growth. (PDF)

Supplier information for carbohydrate growth array. (PDF)

A Venn diagram of B. thetaiotaomicron genes that respond to plant and host glycans in vitro and in vivo. Comparison of genes from three different classes of growth conditions: in vitro growth on purified plant glycans; in vitro growth on purified host glycans; and in vivo growth in the ceca of mono-associated gnotobiotic mice consuming a diet rich...

Growth curves of B. thetaiotaomicron HTCS mutants on various pectins. In each panel, the growth profile of one or more HTCS mutants is compared directly to wild-type B. thetaiotaomicron. Six individual replicate cultures (200 µl each, in the same 96-well plate) were averaged to generate each curve. Error bars represent the standard deviation of eac...

Schematic of B. ovatus PULs involved in plant glycan metabolism. Seven B. ovatus PULs involved in hemicellulose or homogalacturonan degradation. Each gene is drawn to scale as a rectangle with its orientation indicated by the closed triangle. Dashed lines are used to connect linear segments and do not represent actual genomic distance. Genes that w...

ITC data showing binding of the periplasmic domains of plant glycan PUL associated HTCS to their activating oligosaccharide signals. The upper parts of each panel show the raw binding heats and the lower parts the integrated heats fit to a single site (BACOVA_04394 and BACOVA_02740) or two-site (BT0366 and BACOVA_02097) binding model. (EPS)

B. thetaiotaomicron genes with altered expression in vitro during growth on plant and host glycans or in vivo in mono-associated gnotobiotic mice fed a plant glycan rich diet. Genes are separated according to the Venn diagram sectors delineated in Figure S4. Values shown are the mean fold differences compared to expression during growth in MM-G; on...

Hybrid two-component system mutants analyzed in this study. (PDF)

B. ovatus genes with altered expression in vitro during growth on plant glycans or in mice fed a plant glycan rich diet. Mean fold differences in expression compared to growth on minimal medium plus glucose are noted. “Sector” designations for each sub-list refer to the Venn diagram in Figure S6. (PDF)

Putative PULs identified in the B. ovatus ATCC8384 genome. B. ovatus PULs that contain genes expressed in vivo in the ceca of mice fed a plant rich diet are indicated in the final column. Abbreviations and notes: extracytoplasmic function sigma factor, ECF; hybrid two-component system, HTCS; regulators with homology to other families of PUL-associa...

A Venn diagram of B. ovatus genes that respond to plant glycans in vitro and in vivo. Comparison of genes from two different classes of growth conditions: in vitro growth on purified plant glycans; in vivo growth in the ceca of mice consuming a plant-rich diet. All genes summarized exhibited ≥10-fold increased (“up”) or decreased (“down”) expressio...

Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in...

Selenate reductase (SER) from Thauera selenatis is a periplasmic enzyme that has been classified as a type II molybdoenzyme. The enzyme comprises three subunits SerABC, where SerC is an unusual b-heme cytochrome. In the present work the spectropotentiometric characterization of the SerC component and the identification of redox partners to SER are...

Cytochrome c', a c-type cytochrome with unique spectroscopic and magnetic properties, has been characterized in a variety of denitrifying and photosynthetic bacteria. Cytochrome c' has a role in defence and/or removal of NO but the mechanism of action is not clear. To examine the function of cytochrome c' from Neisseria meningitidis, the protein wa...