Clostridium difficile clade 3 (RT023) have a modified cell surface and contain a large transposable island with novel cargo

Shaw, Helen Alexandra; Khodadoost, Ladan; Preston, Mark D.; Corver, Jeroen; Mullany, Peter; Wren, Brendan W.

doi:10.1038/s41598-019-51628-5

Cited by 5 publications

(4 citation statements)

References 41 publications

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“…In Clostridium kluyveri , Seedorf et al identified a siderophore biosynthetic locus and further showed a color change in the Chrome Azurol S (CAS) assay when the strain was grown on iron restricted media (41). The genome of Cd630 does not encode for siderophore biosynthesis genes, but a siderophore locus has been identified in genomes of some C. difficile isolates (11) suggesting that, similar to aerobic bacteria, the majority of anaerobes may use xenosiderophores, while select strains produce their own siderophore(s).…”

Section: Discussionmentioning

confidence: 99%

“…The diversity of siderophores is predicted to be vast (>500 types of siderophores), and siderophores are categorized based on general structure into four groups: hydroxamate, catecholate, phenolate, or mixed (9, 10). While siderophore biosynthesis genes have been identified in some Clade 3 C. difficile genomes, most strains of C. difficile , including the lab strain Cd630, do not encode for siderophore biosynthesis genes (11). The presence of two putative siderophore transporters, in the absence of siderophore biosynthesis genes, suggests most C. difficile strains likely use siderophores produced by other members of the gut microbiota, also known as xenosiderophores.…”

Section: Introductionmentioning

confidence: 99%

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Clostridioides difficileutilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake

Hastie,

Carmichael,

Werner

et al. 2023

Preprint

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Clostridioides difficileremains a public health threat commonly observed following antibiotic use. Due to the importance of iron in many cell processes, most bacteria, includingC. difficile, have multiple mechanisms of acquiring iron. Previous studies have examined ferrous iron uptake inC. difficile, here we focus on the role of siderophores. In a growth assay, we show thatC. difficilecan use a variety of siderophores as the sole iron source. InC. difficile,two ABC transporters induced under low iron conditions are predicted siderophore importers: FhuDBGC and YclNOPQ. We hypothesized that these transporters are responsible for the uptake of the siderophores we tested. To investigate the specificity of these transporters, we purified the substrate binding proteins and examined siderophore binding using thermal shift. We demonstrate increased stability between one siderophore binding protein, FhuD, and the siderophore ferrichrome, suggesting a binding interaction. This specificity correlates with the inability of anΔfhuDBGCmutant to grow efficiently under iron limiting conditions in the presence of ferrichrome. WhileC. difficileused additional siderophores in our growth experiments, we did not observe increased thermal stability between the receptor proteins and any of the other siderophores tested, suggesting these siderophores do not bind these receptors and other siderophore import mechanisms remain to be elucidated. Redundancy in iron acquisition is a microbial survival adaptation to cope with the constant battle for iron within a host. Greater knowledge about howC. difficileacquires iron will provide insight about howC. difficilecolonizes and persists in the colon.IMPORTANCEThis study is the first example ofC. difficilegrowing with siderophores as the sole iron source and describes the characterization of the ferric hydroxamate uptake ABC transporter (FhuDBGC). This transporter shows specificity to the siderophore ferrichrome. While not required for pathogenesis, this transporter highlights the redundancy in iron acquisition mechanisms whichC. difficileuses to compete for iron during an infection.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Clostridioides difficileutilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake

Hastie,

Carmichael,

Werner

et al. 2023

Preprint

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“…91,92 Clostridium difficile has been hypothesized to import siderophores produced by other microorganisms, but not to produce them. However, a recent study conducted by Shaw et al 137 identified a large genetic island from the genome of clade 3-associated strains of C. difficile, which, among other peptides, is predicted to code for the biosynthesis of a Yersiniabactin-like siderophore.…”

Section: Uptake Of Free Inorganic Ironmentioning

confidence: 99%

The battle for iron in enteric infections

et al. 2020

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Iron is an essential element for almost all living organisms, but can be extremely toxic in high concentrations. All organisms must therefore employ homeostatic mechanisms to finely regulate iron uptake, usage and storage in the face of dynamic environmental conditions. The critical step in mammalian systemic iron homeostasis is the fine regulation of dietary iron absorption. However, as the gastrointestinal system is also home to >10 14 bacteria, all of which engage in their own programmes of iron homeostasis, the gut represents an anatomical location where the interkingdom fight for iron is never-ending. Here, we explore the molecular mechanisms of, and interactions between, host and bacterial iron homeostasis in the gastrointestinal tract. We first detail how mammalian systemic and cellular iron homeostasis influences gastrointestinal iron availability. We then focus on two important human pathogens, Salmonella and Clostridia; despite their differences, they exemplify how a bacterial pathogen must navigate and exploit this web of iron homeostasis interactions to avoid host nutritional immunity and replicate successfully. We then reciprocally explore how iron availability interacts with the gastrointestinal microbiota, and the consequences of this on mammalian physiology and pathogen iron acquisition. Finally, we address how understanding the battle for iron in the gastrointestinal tract might inform clinical practice and inspire new treatments for important diseases.

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“…For example, ICE often encode resistance to antibiotics; e.g., Tn916, and Tn5397 (tetracycline resistance). A large ICE, 023_CTnT found in C. difficile clade 3 strains contains genes encoding a sortase, putative sortase substrates, lantibiotic ABC transporters and a putative siderophore biosynthetic cluster (Shaw et al, 2019). Similar genes are found throughout the gut microbiome indicating that ICE have a role in allowing organisms to adapt to their local environment and can transfer through the gut microbiome.…”

Section: Introductionmentioning

confidence: 99%

Removal of mobile genetic elements from the genome of Clostridioides difficile and the implications for the organism’s biology

Hussain,

Nubgan,

Rodríguez

et al. 2024

Front. Microbiol.

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Clostridioides difficile is an emerging pathogen of One Health significance. Its highly variable genome contains mobile genetic elements (MGEs) such as transposons and prophages that influence its biology. Systematic deletion of each genetic element is required to determine their precise role in C. difficile biology and contribution to the wider mobilome. Here, Tn5397 (21 kb) and ϕ027 (56 kb) were deleted from C. difficile 630 and R20291, respectively, using allele replacement facilitated by CRISPR-Cas9. The 630 Tn5397 deletant transferred PaLoc at the same frequency (1 × 10−7) as 630 harboring Tn5397, indicating that Tn5397 alone did not mediate conjugative transfer of PaLoc. The R20291 ϕ027 deletant was sensitive to ϕ027 infection, and contained two unexpected features, a 2.7 kb remnant of the mutagenesis plasmid, and a putative catalase gene adjacent to the deleted prophage was also deleted. Growth kinetics of R20291 ϕ027 deletant was similar to wild type (WT) in rich medium but marginally reduced compared with WT in minimal medium. This work indicates the commonly used pMTL8000 plasmid series works well for CRISPR-Cas9-mediated gene deletion, resulting in the largest deleted locus (56.8 kb) described in C. difficile. Removal of MGEs was achieved by targeting conjugative/integrative regions to promote excision and permanent loss. The deletants created will be useful strains for investigating Tn5397 or ϕ027 prophage contribution to host virulence, fitness, and physiology, and a platform for other mutagenesis studies aimed at functional gene analysis without native transposon or phage interference in C. difficile 630 and R20291.

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Clostridium difficile clade 3 (RT023) have a modified cell surface and contain a large transposable island with novel cargo

Cited by 5 publications

References 41 publications

Clostridioides difficileutilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake

Clostridioides difficileutilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake

The battle for iron in enteric infections

Removal of mobile genetic elements from the genome of Clostridioides difficile and the implications for the organism’s biology

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