Mimicking the human environment in mice reveals that inhibiting biotin biosynthesis is effective against antibiotic-resistant pathogens

Carfrae, Lindsey A; MacNair, Craig R.; Brown, Christopher M.; Tsai, Caressa N.; Weber, Brent S.; Zlitni, Soumaya; Rao, Vishwas N; Chun, Joshua; Junop, M.S.; Coombes, Brian K.; Brown, Eric D.

doi:10.1038/s41564-019-0595-2

Cited by 33 publications

(61 citation statements)

References 48 publications

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“…These nine mutants all corresponded to genes involved in vitamin biosynthesis. Vitamin requirements for E. coli growth can be extremely low; for example, an E. coli ΔbioA mutant requires only 0.2 to 0.4 ng/ml to restore growth ( 58 ). Because trace amounts of vitamins can supplement the growth of these auxotrophs, we suggest that it can lead to variable growth findings.…”

Section: Discussionmentioning

confidence: 99%

“…In our study, we identified 342 genes that were conditionally essential dependent on the carbon source available and 74 genes that were essential in MOPS minimal media regardless of carbon source. Although knowledge of the nutrient composition available to pathogens at various sites of infection is an emerging field of study ( 6 , 58 , 70 , 71 ), the data generated here may have value to help us understand the set of unique targets that are practicable in the context of antibacterial drug discovery. This information could generate new hypotheses for drug target validation studies and could catalyze the creation of unique screening platforms for identifying compounds that are uniquely antibacterial at specific sites of infections ( 72 – 74 ).…”

Section: Discussionmentioning

confidence: 99%

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Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments

Tong

French

Zahed

et al. 2020

mBio

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Central metabolism is a topic that has been studied for decades, and yet, this process is still not fully understood in Escherichia coli, perhaps the most amenable and well-studied model organism in biology. To further our understanding, we used a high-throughput method to measure the growth kinetics of each of 3,796 E. coli single-gene deletion mutants in 30 different carbon sources. In total, there were 342 genes (9.01%) encompassing a breadth of biological functions that showed a growth phenotype on at least 1 carbon source, demonstrating that carbon metabolism is closely linked to a large number of processes in the cell. We identified 74 genes that showed low growth in 90% of conditions, defining a set of genes which are essential in nutrient-limited media, regardless of the carbon source. The data are compiled into a Web application, Carbon Phenotype Explorer (CarPE), to facilitate easy visualization of growth curves for each mutant strain in each carbon source. Our experimental data matched closely with the predictions from the EcoCyc metabolic model which uses flux balance analysis to predict growth phenotypes. From our comparisons to the model, we found that, unexpectedly, phosphoenolpyruvate carboxylase (ppc) was required for robust growth in most carbon sources other than most trichloroacetic acid (TCA) cycle intermediates. We also identified 51 poorly annotated genes that showed a low growth phenotype in at least 1 carbon source, which allowed us to form hypotheses about the functions of these genes. From this list, we further characterized the ydhC gene and demonstrated its role in adenosine efflux. IMPORTANCE While there has been much study of bacterial gene dispensability, there is a lack of comprehensive genome-scale examinations of the impact of gene deletion on growth in different carbon sources. In this context, a lot can be learned from such experiments in the model microbe Escherichia coli where much is already understood and there are existing tools for the investigation of carbon metabolism and physiology (1). Gene deletion studies have practical potential in the field of antibiotic drug discovery where there is emerging interest in bacterial central metabolism as a target for new antibiotics (2). Furthermore, some carbon utilization pathways have been shown to be critical for initiating and maintaining infection for certain pathogens and sites of infection (3–5). Here, with the use of high-throughput solid medium phenotyping methods, we have generated kinetic growth measurements for 3,796 genes under 30 different carbon source conditions. This data set provides a foundation for research that will improve our understanding of genes with unknown function, aid in predicting potential antibiotic targets, validate and advance metabolic models, and help to develop our understanding of E. coli metabolism.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments

Tong

French

Zahed

et al. 2020

mBio

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“…Of note, biotin levels available in humans may be substantially lower than in mice, as a recent study showed a 40‐fold higher biotin concentration in mouse plasma compared to human plasma (Carfrae et al, ). In line with this, the same study showed that growth of bacterial pathogens, which lack biotin transporters and are deficient in biotin biosynthesis, is diminished in human plasma, but not mouse (Carfrae et al, ).…”

Section: Discussionmentioning

confidence: 99%

Fungal biotin homeostasis is essential for immune evasion after macrophage phagocytosis and virulence

Sprenger

Hartung

Allert

et al. 2020

Cellular Microbiology

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Biotin is an important cofactor for multiple enzymes in central metabolic processes.While many bacteria and most fungi are able to synthesise biotin de novo, Candida spp. are auxotrophic for this vitamin and thus require efficient uptake systems to facilitate biotin acquisition during infection. Here we show that Candida glabrata and Candida albicans use a largely conserved system for biotin uptake and regulation, consisting of the high-affinity biotin transporter Vht1 and the transcription factor Vhr1. Both species induce expression of biotin-metabolic genes upon in vitro biotin depletion and following phagocytosis by macrophages, indicating low biotin levels in the Candida-containing phagosome. In line with this, we observed reduced intracellular proliferation of both Candida cells pre-starved of biotin and deletion mutants lacking VHR1 or VHT1 genes. VHT1 was essential for the full virulence of C. albicans during systemic mouse infections, and the lack of VHT1 led to reduced fungal burden in C. glabrata-infected brains and C. albicans-infected brains and kidneys. Together, our data suggest a critical role of Vht1-mediated biotin acquisition for C. glabrata and C. albicans during intracellular growth in macrophages and systemic infections. K E Y W O R D S biotin, Candida albicans, Candida glabrata, macrophage, metabolism, virulence

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“…105 This is consistent with other research that shows biotin biosynthesis is essential under host-relevant conditions. 106 Since biotin levels are 40-fold higher in mouse plasma than in human plasma, biotin biosynthesis has been overlooked as a potential drug target in P. aeruginosa and other species due to the use of mouse models for preclinical studies. 106 Injection of streptavidin temporarily lowers mouse plasma biotin levels to a range within that of human levels, allowing for the development of a physiologically relevant model to test the antipseudomonal activity of biotin inhibitors.…”

Section: Using Conditionally Essential Genes To Find New Targetsmentioning

confidence: 99%

How to kill Pseudomonas—emerging therapies for a challenging pathogen

Yaeger

Coles

Chan

et al. 2021

Annals of the New York Academy of Sciences

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As the number of effective antibiotics dwindled, antibiotic resistance (AR) became a pressing concern. Some Pseudomonas aeruginosa isolates are resistant to all available antibiotics. In this review, we identify the mechanisms that P. aeruginosa uses to evade antibiotics, including intrinsic, acquired, and adaptive resistance. Our review summarizes many different approaches to overcome resistance. Antimicrobial peptides have potential as therapeutics with low levels of resistance evolution. Rationally designed bacteriophage therapy can circumvent and direct evolution of AR and virulence. Vaccines and monoclonal antibodies are highlighted as immune-based treatments targeting specific P. aeruginosa antigens. This review also identifies promising drug combinations, antivirulence therapies, and considerations for new antipseudomonal discovery. Finally, we provide an update on the clinical pipeline for antipseudomonal therapies and recommend future avenues for research.

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Mimicking the human environment in mice reveals that inhibiting biotin biosynthesis is effective against antibiotic-resistant pathogens

Cited by 33 publications

References 48 publications

Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments

Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments

Fungal biotin homeostasis is essential for immune evasion after macrophage phagocytosis and virulence

How to kill Pseudomonas—emerging therapies for a challenging pathogen

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