New tricks for the glycyl radical enzyme family

Backman, Lindsey R. F.; Funk, Michael A.; Dawson, Christopher D.; Drennan, Catherine L.

doi:10.1080/10409238.2017.1373741

Cited by 77 publications

(137 citation statements)

References 126 publications

(230 reference statements)

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“…In terms of gene network interactions and function of the rumen microbiome, we found that Glycyl Radical and Peptidase function, were positively correlated to each other. The Ruminococcaceae family undergo changes with the inclusion of NA and had a positivel correlation with the abundance of protein Glycyl Radical genes, which are found to contribute to environmental resilience, and are also potentially related with VFA production [42]. The abundance of Prevotellaceae was negatively correlated with Ruminococcaceae; the two major bacterial families found in our study.…”

Section: Discussionsupporting

confidence: 46%

Natural Plant-Based Additives Can Improve Ruminant Performance by Influencing the Rumen Microbiome

Ornaghi¹,

Prado²,

Ramos³

et al. 2020

Preprint

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Background The use of synthetic compounds as growth promoters in animal production, is now limited or even banned by health agencies globally due to human safety concerns. In feedlot cattle, when using high grain diets, it is necessary to supplement the diet with compounds capable of modulating the rumen in order to reduce the incidence of acidosis and improve growth. In this context, natural substances have become promising substitutes. The objective of this study was to evaluate the effects of a natural additive blend (NA) on animal performance, the rumen microbiome and ingestive behavior in 40 young bulls.Results The initial and final average body weight was similar (P > 0.05) for all diets, although average daily gain increased linearly (P < 0.01) when NA was fed. However, feed efficiency improved linearly (P < 0.05) by including NA in the diet. Principal volatile fatty acid: acetic, butyric, isovaleric and valeric decreased linearly (P < 0.02) following NA addition. Similarly, NA addition linearly decreased (P < 0.02) the acetate/propionate ratio. The propionate and isobutyric acid concentrations showed a positive quadratic effect (P < 0.05). Furthermore, NA addition reduced ammonia concentrations (P < 0.001) and ruminal pH was not affected (P > 0.05) by the diets. The rumen microbiome was significantly different between beef cattle fed the different treatments (P < 0.05), with a reduction in the archaea, and within the Clostridium, Robinsoniella, Acidaminococcus, Acetitomaculum, Succinimonas and Weissella (P < 0.05) seen when NA was fed. The functional capacity of the rumen microbiome was affected following NA supplementation. Overall, we observed Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding; RecG, N-terminal antiparallel four helix bundle; Transposase, ISC1217; Restriction endonuclease, type II, XamI; Acyl-protein synthetase, LuxE; ABC-2 transporter; which could be related to the natural additives mechanism of action.Conclusions Animal performance was improved in a dose-dependent manner by natural additive addition to the diet of bulls. These beneficial effects are correlated to changes in the rumen microbiome. Our findings suggest that the natural additive blend used in this study could be used as an alternative natural substitute to synthetic antibiotics for animal production.

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Section: Discussionsupporting

confidence: 46%

Natural Plant-Based Additives Can Improve Ruminant Performance by Influencing the Rumen Microbiome

Ornaghi¹,

Prado²,

Ramos³

et al. 2020

Preprint

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“…is an abundant glycyl radical enzyme (GRE) 139,140 that catalyzes degradation of choline to trimethylamine (TMA) and acetaldehyde in the human gut microbiome (Scheme 2). After formation of a stable α-carbon glycyl radical at G821 by an activating enzyme, CutD, 74 the formation of a short-lived and reactive cysteine radical, C489, has been proposed 73,74 that can then initiate choline decomposition via C-H abstraction.…”

Section: Cutc (Ref 138)mentioning

confidence: 99%

Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation

et al. 2019

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“…CutC (ref. 138) is an abundant glycyl radical enzyme (GRE) 139,140 that catalyzes degradation of choline to trimethylamine (TMA) and acetaldehyde in the human gut microbiome (Scheme 2). After formation of a stable α-carbon glycyl radical at G821 by an activating enzyme, CutD, 74 the formation of a short-lived and reactive cysteine radical, C489, has been proposed 73,74 that can then initiate choline decomposition via C-H abstraction.…”

Section: View Article Onlinementioning

confidence: 99%

Revealing Quantum Mechanical Effects in Enzyme Catalysis with Large-Scale Electronic Structure Simulation

Yang¹,

Mehmood²,

Wang³

et al. 2018

Preprint

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<div><div><div><p>Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.</p></div></div></div>

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New tricks for the glycyl radical enzyme family

Cited by 77 publications

References 126 publications

Natural Plant-Based Additives Can Improve Ruminant Performance by Influencing the Rumen Microbiome

Natural Plant-Based Additives Can Improve Ruminant Performance by Influencing the Rumen Microbiome

Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation

Revealing Quantum Mechanical Effects in Enzyme Catalysis with Large-Scale Electronic Structure Simulation

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