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McCaughey, C. S.

Publications and source records attributed to McCaughey, C. S..

2 recordsLinked to original sources

Vanadium-dependent haloperoxidases from diverse microbes halogenate exogenous alkyl quinolone quorum sensing signals

Site-selective vanadium-dependent haloperoxidases (VHPOs) are a unique enzyme family that catalyze selective halogenation reactions previously characterized within bacterial natural product biosynthetic pathways. However, the broader chemical roles and biological distribution of these halogenases remains to be explored. Using bioinformatic methods, we have defined a VHPO subfamily that regioselectively brominates alkyl quinolone (AQ) quorum sensing molecules. In vitro AQ halogenation activity was demonstrated from phylogenetically distinct bacteria lacking established AQ biosynthetic pathways and sourced from diverse environments. AQ-VHPOs show high sequence and biochemical similarities with negligible genomic synteny or biosynthetic gene cluster co-localization. Exposure of VHPO-containing microbes to synthetic AQs or established bacterial producers identifies the chemical and spatial response to subvert their bacteriostatic effects. The characterization of novel homologs from bacterial taxa without previously demonstrated vanadium enzymology suggests VHPO-mediated AQ bromination is a niche to manipulate the chemical ecology of microbial communities. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/606109v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@17a6b2aorg.highwire.dtl.DTLVardef@119f77org.highwire.dtl.DTLVardef@fc5855org.highwire.dtl.DTLVardef@10b6e66_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisA broadly distributed subfamily of bacterial site-selective VHPOs provides protection against exogenously encountered bacteriostatic alkyl quinolone quorum sensing signals.

biochemistry↗

TIMSCONVERT: A workflow to convert trapped ion mobility data to open data formats

SummaryAdvances in mass spectrometry instrumentation have led to the development of mass spectrometers with ion mobility separation (IMS) capabilities and dual source instrumentation, but the current software ecosystem lacks interoperability with downstream data analysis using open-source software/pipelines. Here, we present TIMSCONVERT, a data conversion workflow from timsTOF fleX MS raw data files to size conscious mzML and imzML formats with minimal preprocessing to allow for compatibility with downstream data analysis tools, which we showcase with several examples using data acquired across different experiments and acquisition modalities on the timsTOF fleX. Availability and ImplementationTIMSCONVERT and its documentation can be found at https://github.com/gtluu/timsconvert and is available as a standalone command line interface, Nextflow workflow, and online in the Global Natural Products Social (GNPS) platform (https://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params={%22workflow%22%3A%20%22TIMSCONVERT%22}). ContactMingxun Wang, miw023@ucsd.edu Supplementary InformationSupplementary data are available at Bioinformatics online.

bioinformatics↗