Rhys Grinter

Rhys Grinter
Monash University (Australia) · Department of Microbiology

BSc PhD

About

113
Publications
15,991
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1,525
Citations
Additional affiliations
October 2010 - January 2015
University of Glasgow
Position
  • PhD Student

Publications

Publications (113)
Article
Full-text available
Iron is a limiting nutrient in bacterial infection putting it at the centre of an evolutionary arms race between host and pathogen. Gram-negative bacteria utilize TonB-dependent outer membrane receptors to obtain iron during infection. These receptors acquire iron either in concert with soluble iron-scavenging siderophores or through direct interac...
Article
Full-text available
Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the environment is often mediated by TonB-dependent transporters (TBDTs), which are β-barrel proteins that form sophisticated channels in the outer membrane. Repo...
Article
Full-text available
Bacteria have evolved sophisticated uptake machineries in order to obtain the nutrients required for growth. Gram-negative plant pathogens of the genus Pectobacterium obtain iron from the protein ferredoxin, which is produced by their plant hosts. This iron-piracy is mediated by the ferredoxin uptake system (Fus), a gene cluster encoding proteins t...
Preprint
Full-text available
F420 is a low-potential redox cofactor used by diverse bacteria and archaea. In mycobacteria, this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and activation of the clinical antitubercular prodrugs pretomanid and delamanid. A recent biochemical study proposed a revised biosynthesis pathway for F420 in...
Article
Full-text available
In order to survive in mixed microbial communities, some species of fungi secrete coprogens, siderophores that facilitate capture of the scarce nutrient iron. The TonB-dependent transporter FhuE is integrated in the outer membrane of Gram-negative bacteria and has been reported to scavenge these fungally produced coprogens. In this work, an Escheri...
Preprint
Full-text available
CRISPR-Cas systems are transformative tools for gene editing which can be tuned or controlled by anti-CRISPRs (Acrs) - phage derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that are capable of inhibiting biotechnologically relevant CRISPR systems are relatively rare and challenging to discover. To overcome this limitation, we de...
Preprint
Full-text available
Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode transporters capable of extracting the iron-containing cofactor heme directly from host proteins. Pathoge...
Preprint
Full-text available
Rumen microbiota enable ruminants to grow on fibrous plant materials but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species...
Article
Full-text available
Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeF...
Article
Full-text available
Haemoglobin (Hb) is a vital oxygen carrier in vertebrates. Low blood Hb levels may indicate anaemia or genetic disorders, while its presence in the lower digestive system suggests colon cancer. Detecting and quantifying human Hb is essential for medical diagnostics. A nanobody‐based sandwich‐ELISA test was recently developed utilising llama‐derived...
Preprint
Full-text available
PQQ is a soluble redox cofactor used by diverse bacteria to oxidise fuel compounds as a source of electrons for the respiratory chain. Many Gram-negative bacteria that encode PQQ- dependent enzymes do not possess the biosynthetic machinery for its production and instead obtain it from the environment. To achieve this the bacterium Escherichia coli...
Preprint
Full-text available
Cryo-electron microscopy (Cryo-EM) single particle analysis (SPA) has become a major structural biology technique in recent years. High-resolution cryo-EM typically requires higher voltage cryo-TEMs with coherent FEG sources, stable columns, autoloader systems and direct electron detectors. These setups are specialised for Cryo-EM work and are expe...
Article
Full-text available
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...
Article
Full-text available
Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear...
Chapter
MoCu]‐dependent carbon monoxide dehydrogenases (Mo‐CODH) catalyze the hydroxylation of CO, which produces CO 2 and consumes H 2 O in the process. Aerobic carbon monoxide oxidizing bacteria and archaea use Mo‐CODH to generate energy by providing the respiratory chain with CO‐derived electrons, and aerobic CO‐oxidizers that possess the genes for CO 2...
Preprint
Diverse bacteria and archaea use atmospheric carbon monoxide (CO) as an energy source during long-term survival. This process enhances the biodiversity of soil and marine ecosystems globally and removes 250 million tonnes of a toxic, climate-relevant pollutant from the atmosphere each year. Bacteria use [MoCu]-carbon monoxide dehydrogenases (Mo-COD...
Article
Full-text available
The splitting of hydrogen (H 2) is an energy-yielding process, which is important for both biological systems and as a means of providing green energy. In biology, this reaction is mediated by enzymes called hydrogenases, which utilise complex nickel and iron cofactors to split H 2 and transfer the resulting electrons to an electron-acceptor. These...
Preprint
Full-text available
In soil ecosystems, obligately aerobic bacteria survive oxygen deprivation (hypoxia) by entering non-replicative persistent states. Little is known about how these bacteria rewire their metabolism to stay viable in these states. The model obligate aerobe Mycobacterium smegmatis maintains redox homeostasis during hypoxia by mediating fermentative hy...
Preprint
Full-text available
Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe]-hydrogenases were thought to be restricted to anaerobic bacteria and eukaryotes. Here we show that archaea encode diverse, active, and ancient lineages of [FeFe...
Article
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures...
Article
Full-text available
Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments. Atmospheric H2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfam...
Preprint
Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Though recently discovered, trace gas oxidation is now recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosyste...
Preprint
Diverse aerobic bacteria use atmospheric H 2 as an energy source for growth and survival. This recently discovered yet globally significant process regulates the composition of the atmosphere, enhances soil biodiversity, and drives primary production in certain extreme environments. Atmospheric H 2 oxidation has been attributed to still uncharacter...
Preprint
Helicobacter pylori infection is the main cause of gastric cancer. Vacuolating cytotoxin A (VacA) is a H. pylori pore-forming toxin and a key determinant of gastric cancer risk. VacA is secreted as an 88-kDa polypeptide (p88) that upon interaction with host cells induces cytotoxic effects, including cell vacuolation and mitochondrial dysfunction. T...
Article
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial...
Article
Full-text available
Significance Diverse microbial life has been detected in the cold desert soils of Antarctica once thought to be barren. Here, we provide metagenomic, biogeochemical, and culture-based evidence that Antarctic soil microorganisms are phylogenetically and functionally distinct from those in other soils and adopt various metabolic and ecological strate...
Article
Full-text available
The biological and functional significance of selected CASP14 targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of prot...
Article
Full-text available
Acinetobacter baumannii is a high-risk pathogen due to the rapid global spread of multidrug-resistant lineages. Its phylogenetic divergence from other ESKAPE pathogens means that determinants of its antimicrobial resistance can be difficult to extrapolate from other widely studied bacteria. A recent study showed that A. baumannii upregulates produc...
Article
Full-text available
Carbon monoxide (CO) gas is infamous for its acute toxicity. This toxicity predominantly stems from its tendency to form carbonyl complexes with transition metals, thus inhibiting the heme-prosthetic groups of proteins, including respiratory terminal oxidases. While CO has been proposed as an antibacterial agent, the evidence supporting its toxicit...
Article
Full-text available
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis, and xenobiotic biodegradation. In the last five y...
Article
Full-text available
Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how so...
Preprint
Full-text available
Acinetobacter baumannii is a high-risk pathogen due to the rapid global spread of multi-drug resistant lineages. Its phylogenetic divergence from other ESKAPE pathogens means that determinants of its antimicrobial resistance can be difficult to extrapolate from other widely studied bacteria. A recent study showed that A. baumannii upregulates produ...
Preprint
Full-text available
1 A surprising diversity and abundance of microorganisms resides in the cold desert 2 soils of Antarctica. The metabolic processes that sustain them, however, are poorly 3 understood. In this study, we used metagenomic and biogeochemical approaches to 4 study the microbial communities in 16 physicochemically diverse mountainous and 5 glacial soils...
Article
Full-text available
Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great interest given the substantial drag forces and torques they face when moving down the spinning flagellum. We show that the main capsid and auxiliary protein...
Article
Full-text available
Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 prod...
Article
Full-text available
Mycobacteria are major environmental microorganisms and cause many significant diseases, including tuberculosis. Mycobacteria make an unusual vitamin-like compound, F 420 , and use it to both persist during stress and resist antibiotic treatment. Understanding how mycobacteria make F 420 is important, as this process can be targeted to create new d...
Article
Full-text available
The outer membrane of Gram-negative bacteria is highly impermeable to hydrophilic molecules of larger than 600 Da, protecting these bacteria from toxins present in the environment. In order to transport nutrients across this impermeable membrane, Gram-negative bacteria utilize a diverse family of outer-membrane proteins called TonB-dependent transp...
Preprint
Full-text available
Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 prod...
Preprint
Full-text available
Carbon monoxide (CO) is a gas infamous for its acute toxicity. The toxicity of CO predominantly stems from its tendency to form carbonyl complexes with transition metals, thus inhibiting the heme-prosthetic groups of proteins, including the terminal oxidases of the respiratory chain. While CO has been proposed as an antibacterial agent, the evidenc...
Article
Full-text available
Fucosylation of the inner-most N-acetylglucosamine (GlcNAc) of N-glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N-glycans. This simple modification can dramatically affect the activities and half-lives of glycoproteins, effects that are relevant to understanding the invasiveness of some cancers,...
Preprint
Fucosylation of the inner-most N-acetyl-glucosamine (GlcNAc) of N-glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N-glycans. This simple modification can have a dramatic impact on the activity and half-life of glycoproteins. These effects are relevant to understanding the invasiveness of some canc...
Preprint
The outer membrane of Gram-negative bacteria is highly impermeable to hydrophilic molecules larger than 600 Da, protecting these bacteria from toxins present in the environment. In order to transport nutrients across this impermeable membrane, Gram-negative bacteria utilise a diverse family of outer-membrane proteins called TonB-dependent transport...
Article
Full-text available
The plant pathogen, Pseudomonas syringae (Ps), together with related Ps species, infect and attack a wide range of agronomically important crops, including tomato, kiwifruit, pepper, olive and soybean, causing economic losses. Currently, chemicals and introduced resistance genes are used to protect plants against these pathogens but have limited su...
Article
Full-text available
The ferric iron uptake (Fiu) transporter from Escherichia coli functions in the transport of iron-catecholate complexes across the bacterial outer membrane, providing the bacterium with iron, which is essential for growth. Recently, it has become clear that Fiu also represents a liability for E. coli because its activity allows the import of antimi...
Article
Full-text available
To persist when nutrient sources are limited, aerobic soil bacteria metabolize atmospheric hydrogen (H2). This process is the primary sink in the global H2 cycle and supports the productivity of microbes in oligotrophic environments. H2-metabolizing bacteria possess [NiFe]-hydrogenases that oxidize H2 to subatmospheric concentrations. The soil sapr...
Article
Full-text available
The discovery of a Salmonella‐targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi‐like bacteriophage (phage) engage with bacterial flagellae. The long tail fibre seen on Chi‐like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the ident...
Article
Full-text available
Carotenoid coloration is widely recognized as a signal of individual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the put...
Preprint
Full-text available
Aerobic soil bacteria metabolize atmospheric hydrogen (H2) to persist when nutrient sources are limited. This process is the primary sink in the global H2 cycle and supports the productivity of microbes in oligotrophic environments. To mediate this function, bacteria possess [NiFe]-hydrogenases capable of oxidising H2 to subatmospheric concentratio...
Preprint
Full-text available
The Ferric Iron Uptake (Fiu) transporter from Escherichia coli functions in the transport of iron-catecholate complexes across the bacterial outer membrane, providing the bacterium with iron which is an essential element for growth. Recently, it became clear that Fiu also represents a liability: its activity allows the import of antimicrobial compo...
Preprint
Full-text available
Carotenoid coloration is widely recognized as a signal of individual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the put...
Preprint
Full-text available
Pseudomonas syringae ( Ps ) and related plant pathogenic bacteria are responsible for losses in diverse crops such as tomato, kiwifruit, pepper, olive and soybean. Current solutions, involving the use of chemicals and the introduction of resistance genes, have enjoyed only limited success and may have adverse environmental impacts. Consequently, th...
Article
Full-text available
A grand challenge in microbiology is to understand how the dormant majority lives. In natural environments, most microorganisms are not growing and instead exist in a spectrum of dormant states. Despite this, most research on microbial metabolism continues to be growth-centric, and many overlook the fact that dormant cells require energy for mainte...
Presentation
Full-text available
The translocation and assembly module (TAM) plays a role in the transport and insertion of proteins into the bacterial outer membrane. TamB, a component of this system spans the periplasmic space to engage with its partner protein TamA. Finally we present the crystal structure of TamB amino acids 963–1,138. This region represents half of the conser...
Data
Structural comparisons of the catalytic lobes of MPP and FusC. The β-subunit of MPP houses the active site and is represented here in silver coloring. The side-chains of catalytically important residues are shown as sticks, with the metal (Zn2+) cofactor designated as a gray sphere. The equivalent domain of FusC is represented in yellow, and its st...
Data
FusC:ferredoxin interface statistics. (PDF)
Data
Disparate acquisition of fusC genes in Klebsiella spp. Klebsiella genome sequences were visualized using Figtree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/). Each terminal node, representing a genome, was colored according to the geographical location for the isolate, based on metadata obtained from the NCBI Pathogen Detection project datab...
Data
Biophysical characterization of purified FusC. Analytical-SEC (upper panel) and analytical ultracentrifugation (lower panel) showing that purified FusC is a monomer of approximately 104 kDa. SEC, size-exclusion chromatography. (PDF)
Data
Data underlying this paper. (XLSX)
Data
Sequence accession data for plants M16 sequences used in the CLANS analysis. CLANS, cluster analysis of sequences. (PDF)
Data
Data underlying this paper. (XLSX)
Data
The FusC:ferredoxin crystal structure electron density. Stereo electron density and model of the refined FusC:ferredoxin crystal structures. Density was prepared through generation of a composite omit map and is contoured to 1.0 σ. (PDF)
Data
Cocrystallization and structural modeling are consistent in suggesting a partial unfolding of ferredoxin in the FusC:ferredoxin complex. (A) The crystal structure of full-length Arabidopsis ferredoxin (4ZHO), docked into the FusC cavity by superimposition with the ferredoxin fragment located at binding site F2. This docking results in a large numbe...
Data
FusC:ferredoxin crystallographic data collection and refinement statistics. (PDF)
Article
Full-text available
The translocation and assembly module (TAM) plays a role in the transport and insertion of proteins into the bacterial outer membrane. TamB, a component of this system spans the periplasmic space to engage with its partner protein TamA. Despite efforts to characterize the TAM, the structure and mechanism of action of TamB remained enigmatic. Here w...
Article
Full-text available
Helicobacter pylori is a gram-negative bacterial pathogen that chronically inhabits the human stomach. To survive and maintain advantage, it has evolved unique host–pathogen interactions mediated by Helicobacter-specific proteins in the bacterial outer membrane. These outer membrane proteins (OMPs) are anchored to the cell surface via a C-terminal...
Data
Animation of FusA and NMA analysis of the FusA-PM1fer ferredoxin complex. FusA is initially shown as a Jones's rainbow cartoon representation, then for the NMA simulations of the docking derived FusA-PM1fer complex: FusA is represented in a surface representation, coloured white, while the PM1fer is shown in a cartoon representation coloured red. T...
Data
Structural coordinates representing the HADDOCK generated docking solutions between FusA and Arabidopsis Ferredoxin docking, cluster 1.