bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.

Autor: Guerrero-Egido G; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.; Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.; Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain., Pintado A; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.; Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.; Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain., Bretscher KM; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.; Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.; Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain., Arias-Giraldo LM; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands., Paulson JN; Department of Data Sciences, N-Power Medicine, Redwood City, CA, 94063, USA., Spaink HP; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands., Claessen D; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands., Ramos C; Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain.; Área de Genética, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain., Cazorla FM; Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.; Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain., Medema MH; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.; Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands., Raaijmakers JM; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands., Carrión VJ; Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. vcarrion@uma.es.; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands. vcarrion@uma.es.; Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain. vcarrion@uma.es.; Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain. vcarrion@uma.es.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Mar 07; Vol. 15 (1), pp. 2072. Date of Electronic Publication: 2024 Mar 07.
DOI: 10.1038/s41467-024-46302-y
Abstrakt: Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.com/Carrion-lab/bacLIFE ) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.
(© 2024. The Author(s).)
Databáze: MEDLINE
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