Oxidative pathways of deoxyribose and deoxyribonate catabolism

Price, Morgan N.; J, Ray; Iavarone, Anthony T.; Carlson, Hans K.; Ryan, Elizabeth; Malmstrom, Rex R.; Arkin, Adam P.; Deutschbauer, Adam M.

doi:10.1101/205583

Cited by 7 publications

(9 citation statements)

References 44 publications

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“…Overall, the accuracy of iJN1462 is in the range of other high-quality models such as E. coli, 93.4%, (Monk et al, 2017) and Bacillus subtilis, 93.4% (Tanaka et al, 2013). Further model validation was performed using data from BarSeq experiments with P. putida using three different carbon sources: glucose, acetate and p-coumaric acid in minimal media (Rand et al, 2017;Price et al, 2019;Thompson et al, 2019). Sensitivity analysis was performed to identify a proper cut-off of gene fitness that corresponds with gene essentiality in the model (SI 1).…”

Section: Gene Essentiality Data Contextualization Within Ijn1462mentioning

confidence: 99%

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Nogales

Mueller

Guđmundsson

et al. 2019

Environmental Microbiology

149

138

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Genome-scale reconstructions of metabolism are computational species-specific knowledge bases able to compute systemic metabolic properties. We present a comprehensive and validated reconstruction of the biotechnologically relevant bacterium Pseudomonas putida KT2440 that greatly expands computable predictions of its metabolic states. The reconstruction represents a significant reactome expansion over available reconstructed bacterial metabolic networks. Specifically, iJN1462 (i) incorporates several hundred additional genes and associated reactions resulting in new predictive capabilities, including new nutrients supporting growth; (ii) was validated by in vivo growth screens that included previously untested carbon (48) and nitrogen (41) sources; (iii) yielded gene essentiality predictions showing large accuracy when compared with a knockout library and Bar-seq data; and (iv) allowed mapping of its network to 82 P. putida sequenced strains revealing functional core that reflect the large metabolic versatility of this species, including aromatic compounds derived from lignin. Thus, this study provides a thoroughly updated metabolic reconstruction and new computable phenotypes for P. putida, which can be leveraged as a first step toward understanding the pan metabolic capabilities of Pseudomonas.

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Section: Gene Essentiality Data Contextualization Within Ijn1462mentioning

confidence: 99%

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Nogales

Mueller

Guđmundsson

et al. 2019

Environmental Microbiology

149

138

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“…To validate the plate-based assays, we also measured the total concentration of capsaicin in plates with fungal growth via LC-MS. After 10 days of growth, over 99% of the capsaicin had disappeared relative to uninoculated controls ( Figure 6). Previous work has reported potential routes of capsaicin catabolism (Price et al 2019;van den Heuvel et al 2001), but current LC-TOF analysis of spent media could not detect specific masses consistent with predicted degradation products, such as vanillylamine, vanillin, or vanillate ( Supplementary Figure 2A). In Fungal capsaicin plates, a large peak appeared at RT 6.5 that was unique to that condition (Supplementary Figure 2B),…”

Section: Supplementary Figure 1 Zone Of Clearance and Compound Strucmentioning

confidence: 83%

Fungal seed pathogens of wild chili peppers possess multiple mechanisms to tolerate capsaicinoids

Adams

Zimmerman²,

Fenstermacher

et al. 2019

Preprint

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ImportancePlants make chemical compounds to protect themselves. For example, chili peppers produce the spicy compound capsaicin to inhibit animal feeding and pathogen damage. In humans, capsaicin binds to a membrane channel protein, creating the sensation of heat, while in microbes, capsaicin limits energy production by binding respiratory enzymes. However, some data suggest capsaicin also disrupts membranes. Here we studied fungal pathogens (Alternaria, Colletotrichum, Fusarium, and Phomopsis) isolated from a wild chili pepper, Capsicum chacoense. By measuring growth rate in the presence of antibiotics with known respiratory targets, we infer wild plant pathogens may be rich with alternative respiratory enzymes. A zone of clearance around the colonies, as well as LCMS data, further indicate these fungi can break down capsaicin. Lastly, the total inhibitory effect of capsaicin was not fully explained by its effect on respiratory enzymes. Our findings lend credence to studies proposing capsaicin may disrupt cell membranes, with implications for microbiology as well as human health.

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“…Using a barcoded transposon library for parallel fitness assays is an ideal method for the rapid identification of such mutants and is commonly referred to as random barcode transposon sequencing (RB-TnSeq) ( Wetmore et al, 2015 ). This library has been generated for P. putida KT2440 and contains ∼100,000 unique transposon mutants with coverage of most non-essential genes ( Price et al, 2019 ; Thompson et al, 2019 ). By growing these mutants in a pooled format, P. putida mutants that are sensitive to the toxic agents in the supernatant will be outcompeted by more fit strains, and the absolute abundance of each mutant can be determined using Illumina sequencing specific to each barcoded transposon mutant.…”

Section: Resultsmentioning

confidence: 99%

Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria

et al. 2020

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The rhizosphere microbiome (rhizobiome) plays a critical role in plant health and development. However, the processes by which the constituent microbes interact to form and maintain a community are not well understood. To investigate these molecular processes, we examined pairwise interactions between 11 different microbial isolates under select nutrient-rich and nutrient-limited conditions. We observed that when grown with media supplemented with 56 mM glucose, two microbial isolates were able to inhibit the growth of six other microbes. The interaction between microbes persisted even after the antagonistic microbe was removed, upon exposure to spent media. To probe the genetic basis for these antagonistic interactions, we used a barcoded transposon library in a proxy bacterium, Pseudomonas putida, to identify genes which showed enhanced sensitivity to the antagonistic factor(s) secreted by Acinetobacter sp. 02. Iron metabolism-related gene clusters in P. putida were implicated by this systemslevel analysis. The supplementation of iron prevented the antagonistic interaction in the original microbial pair, supporting the hypothesis that iron limitation drives antagonistic microbial interactions between rhizobionts. We conclude that rhizobiome community composition is influenced by competition for limiting nutrients, with implications for growth and development of the plant.

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Oxidative pathways of deoxyribose and deoxyribonate catabolism

Cited by 7 publications

References 44 publications

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Fungal seed pathogens of wild chili peppers possess multiple mechanisms to tolerate capsaicinoids

Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria

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