Biosynthesis and bioengineering of antibiotics in Burkholderia species

The emergence of antibiotic resistance combined with the decline in the discovery of novel antibiotic scaffolds has led to an urgent need for the development of effective antimicrobial treatments. Recently a Gram-negative genus of bacteria, Burkholderia, has been shown to be an untapped source of antimicrobial compounds. Two such compounds produced by Burkholderia are gladiolin and enacyloxin IIa (figure 1), which are active against the multidrug resistant pathogens Mycobacterium tuberculosis and Acinetobacter baumannii respectively. Both compounds are assembled by polyketide synthases, but there are parts of the biosynthesis of both natural products that are not well understood. Figure 1 The structures of gladiolin and enacyloxin IIa. The installation of the E,Z-diene motif in gladiolin (red, figure 1) was investigated using an intact protein MS-based assay with chemically synthesized polyketide intermediate mimics. The diene was shown to be installed by an unprecedented double dehydration, which appears to be conserved for the installation of dienes in some other polyketide natural products based on bioinformatics analyses. The biosynthesis of the dihydroxycyclohexanecarboxylic acid (DHCCA) unit of enacyloxin IIa (blue, figure 1) was also investigated using in vitro biochemical assays. The initial hypothesis for the pathway was shown to be incorrect, and the elucidation of the correct pathway also led to the discovery of a new potential biocatalyst. Using multiple biosynthetic engineering strategies that rely upon a thorough understanding of enacyloxin IIa biosynthesis, a library of enacyloxin IIa analogues was generated. This provided useful structure-activity relationship (SAR) data with regards to the binding of enacyloxin IIa to its target, EF-Tu. Five enacyloxin IIa analogues were also generated which had improved biological activity. These analogues may provide a platform for the rational engineering of improved enacyloxin IIa analogues harboring more complex structural changes

NMR-based assignment of isoleucine vs allo-isoleucine stereochemistry

A simple 1H and 13C NMR spectrometric analysis is demonstrated that permits differentiation of isoleucine and allo-isoleucine residues by inspection of the chemical shift and coupling constants of the signals associated with the proton and carbon at the α-stereocentre. This is applied to the estimation of epimerisation during metal-free N-arylation and peptide coupling reactions

Inflammation and premature ageing in chronic kidney disease

Persistent low-grade inflammation and premature ageing are hallmarks of the uremic phenotype and contribute to impaired health status, reduced quality of life, and premature mortality in chronic kidney disease (CKD). Because there is a huge global burden of disease due to CKD, treatment strategies targeting inflammation and premature ageing in CKD are of particular interest. Several distinct features of the uremic phenotype may represent potential treatment options to attenuate the risk of progression and poor outcome in CKD. The nuclear factor erythroid 2-related factor 2 (NRF2)−kelch-like erythroid cell-derived protein with CNC homology [ECH]-associated protein 1 (KEAP1) signaling pathway, the endocrine phosphate-fibroblast growth factor-23−klotho axis, increased cellular senescence, and impaired mitochondrial biogenesis are currently the most promising candidates, and different pharmaceutical compounds are already under evaluation. If studies in humans show beneficial effects, carefully phenotyped patients with CKD can benefit from them

Analyze This! A Cosmological Constraint Package for CMBEASY

We introduce a Markov Chain Monte Carlo simulation and data analysis package that extends the CMBEASY software. We have taken special care in implementing an adaptive step algorithm for the Markov Chain Monte Carlo in order to improve convergence. Data analysis routines are provided which allow to test models of the Universe against measurements of the cosmic microwave background, supernovae Ia and large scale structure. We present constraints on cosmological parameters derived from these measurements for a $\Lambda$CDM cosmology and discuss the impact of the different observational data sets on the parameters. The package is publicly available as part of the CMBEASY software at www.cmbeasy.org.Comment: Published version, JCAP style, 16 pages, 7 figures. The software is available at http://www.cmbeasy.or

Antibiotic skeletal diversification via differential enoylreductase recruitment and module iteration in trans -acyltransferase polyketide synthases

Microorganisms are remarkable chemists capable of assembling complex molecular architectures that penetrate cells and bind biomolecular targets with exquisite selectivity. Consequently, microbial natural products have wide-ranging applications in medicine and agriculture. How the “blind watchmaker” of evolution creates skeletal diversity is a key question in natural products research. Comparative analysis of biosynthetic pathways to structurally related metabolites is an insightful approach to addressing this. Here, we report comparative biosynthetic investigations of gladiolin, a polyketide antibiotic from Burkholderia gladioli with promising activity against multidrug-resistant Mycobacterium tuberculosis, and etnangien, a structurally related antibiotic produced by Sorangium cellulosum. Although these metabolites have very similar macrolide cores, their C21 side chains differ significantly in both length and degree of saturation. Surprisingly, the trans-acyltransferase polyketide synthases (PKSs) that assemble these antibiotics are almost identical, raising intriguing questions about mechanisms underlying structural diversification in this important class of biosynthetic assembly line. In vitro reconstitution of key biosynthetic transformations using simplified substrate analogues, combined with gene deletion and complementation experiments, enabled us to elucidate the origin of all the structural differences in the C21 side chains of gladiolin and etnangien. The more saturated gladiolin side chain arises from a cis-acting enoylreductase (ER) domain in module 1 and in trans recruitment of a standalone ER to module 5 of the PKS. Remarkably, module 5 of the gladiolin PKS is intrinsically iterative in the absence of the standalone ER, accounting for the longer side chain in etnangien. These findings have important implications for biosynthetic engineering approaches to the creation of novel polyketide skeletons

Insights into the Second Law of Thermodynamics from Anisotropic Gas-Surface Interactions

Thermodynamic implications of anisotropic gas-surface interactions in a closed molecular flow cavity are examined. Anisotropy at the microscopic scale, such as might be caused by reduced-dimensionality surfaces, is shown to lead to reversibility at the macroscopic scale. The possibility of a self-sustaining nonequilibrium stationary state induced by surface anisotropy is demonstrated that simultaneously satisfies flux balance, conservation of momentum, and conservation of energy. Conversely, it is also shown that the second law of thermodynamics prohibits anisotropic gas-surface interactions in "equilibrium", even for reduced dimensionality surfaces. This is particularly startling because reduced dimensionality surfaces are known to exhibit a plethora of anisotropic properties. That gas-surface interactions would be excluded from these anisotropic properties is completely counterintuitive from a causality perspective. These results provide intriguing insights into the second law of thermodynamics and its relation to gas-surface interaction physics.Comment: 28 pages, 11 figure

Corrigendum to “Environmental and life-history factors influence inter-colony multidimensional niche metrics of a breeding Arctic marine bird” [Sci. Total Environ. 796 (2021) 148935] (Science of the Total Environment (2021) 796, (S0048969721040079), (10.1016/j.scitotenv.2021.148935))

The authors regret that the printed version of the above article contained an omission of an individual deserving of co-authorship. The correct and final version follows. The authors would like to apologise for any inconvenience caused. \u3c Reyd A. Smith1⁎, David J. Yurkowski2, Kyle J.L. Parkinson1, Jérôme Fort3, Holly L. Hennin4, H. Grant Gilchrist4, Keith A. Hobson5, Mark L. Mallory6, Paco Bustamante3, Jóhannis Danielsen7, Svend E. Garbus8, Sveinn A. Hanssen9, Jón Einar Jónsson10, Christopher J. Latty11, Ellen Magnúsdóttir10, Børge Moe9, Glen J. Parsons12, Christian Sonne8, Grigori Tertitski13, and Oliver P. Love1\u3e Windsor, Windsor, Ontario, Canada, N9B 3P4 2 Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada, R3T 2N6 3 Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS – La Rochelle University, La Rochelle, France, FR-17000 4 Environment and Climate Change Canada, Ottawa, Ontario, Canada, K0A 1H0. 5 Western University, London, Ontario, Canada, N6A 3K7 6Acadia University, Wolfville, Nova Scotia, Canada, B4P 2R6 7 Faroe Marine Research Institute, Tórshavn, Faroe Islands, FO-110 8 Aarhus University, Roskilde, Denmark, DK-4000 9 Norwegian Institute for Nature Research, Tromsø, Norway, N-9296 10 University of Iceland\u27s Research Centre at Snæfellsnes, Hafnargata 3, 340, Stykkishólmur, Iceland 11 Arctic National Wildlife Refuge, U.S. Fish and Wildlife Service, Fairbanks, Alaska, United States, 99701 12 Nova Scotia Department of Lands and Forestry, Kentville, Nova Scotia, Canada, B4N 4E5 13 Institute of Geography of the Russian Academy of Sciences, Moscow, Russia, 119017\u3

Guidelines for developing optical clocks with 10−1810^{-18} fractional frequency uncertainty

There has been tremendous progress in the performance of optical frequency standards since the first proposals to carry out precision spectroscopy on trapped, single ions in the 1970s. The estimated fractional frequency uncertainty of today's leading optical standards is currently in the $10^{-18}$ range, approximately two orders of magnitude better than that of the best caesium primary frequency standards. This exceptional accuracy and stability is resulting in a growing number of research groups developing optical clocks. While good review papers covering the topic already exist, more practical guidelines are needed as a complement. The purpose of this document is therefore to provide technical guidance for researchers starting in the field of optical clocks. The target audience includes national metrology institutes (NMIs) wanting to set up optical clocks (or subsystems thereof) and PhD students and postdocs entering the field. Another potential audience is academic groups with experience in atomic physics and atom or ion trapping, but with less experience of time and frequency metrology and optical clock requirements. These guidelines have arisen from the scope of the EMPIR project "Optical clocks with $1 imes 10^{-18}$ uncertainty" (OC18). Therefore, the examples are from European laboratories even though similar work is carried out all over the world. The goal of OC18 was to push the development of optical clocks by improving each of the necessary subsystems: ultrastable lasers, neutral-atom and single-ion traps, and interrogation techniques. This document shares the knowledge acquired by the OC18 project consortium and gives practical guidance on each of these aspects