Browsing by Author "Monteil, Caroline L."
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- Ice nucleation in a Gram-positive bacterium isolated from precipitation depends on a polyketide synthase and non-ribosomal peptide synthetaseFailor, Kevin C.; Liu, Haijie; Llontop, Marco E. Mechan; LeBlanc, Sophie; Eckshtain-Levi, Noam; Sharma, Parul; Reed, Austin; Yang, Shu; Tian, Long; Lefevre, Christopher; Menguy, Nicolas; Du, Liangcheng; Monteil, Caroline L.; Vinatzer, Boris A. (2021-10-23)Earth's radiation budget and frequency and intensity of precipitation are influenced by aerosols with ice nucleation activity (INA), i.e., particles that catalyze the formation of ice. Some bacteria, fungi, and pollen are among the most efficient ice nucleators but the molecular basis of INA is poorly understood in most of them. Lysinibacillus parviboronicapiens (Lp) was previously identified as the first Gram-positive bacterium with INA. INA of Lp is associated with a secreted, nanometer-sized, non-proteinaceous macromolecule or particle. Here a combination of comparative genomics, transcriptomics, and a mutant screen showed that INA in Lp depends on a type I iterative polyketide synthase and a non-ribosomal peptide synthetase (PKS-NRPS). Differential filtration in combination with gradient ultracentrifugation revealed that the product of the PKS-NRPS is associated with secreted particles of a density typical of extracellular vesicles and electron microscopy showed that these particles consist in "pearl chain"-like structures not resembling any other known bacterial structures. These findings expand our knowledge of biological INA, may be a model for INA in other organisms for which the molecular basis of INA is unknown, and present another step towards unraveling the role of microbes in atmospheric processes.
- Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogensMonteil, Caroline L.; Yahara, Koji; Studholme, David J.; Mageiros, Leonardos; Méric, Guillaume; Swingle, Bryan; Morris, Cindy E.; Vinatzer, Boris A.; Sheppard, Samuel K. (2016-10)Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1, to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae.
- A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and NomenclatureMarakeby, Haitham; Badr, Eman; Torkey, Hanaa; Song, Yuhyun; Leman, Scotland C.; Monteil, Caroline L.; Heath, Lenwood S.; Vinatzer, Boris A. (PLOS, 2014-02-21)A broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. The current system is thus inadequate to classify and name the immense genetic diversity within species that is now being revealed by genome sequencing on a daily basis. To address this lack of a general intra-species classification and naming system adequate for today’s speed of discovery of new diversity, we propose a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis. We provide examples demonstrating that genome similarity-based codes largely align with current taxonomic groups at many different levels in bacteria, animals, humans, plants, and viruses. Importantly, the proposed approach is only slightly affected by the order of code assignment and can thus provide codes that reflect similarity between organisms and that do not need to be revised upon discovery of new diversity. We envision genome similarity-based codes to complement current biological nomenclature and to provide a universal means to communicate unambiguously about any genome-sequenced organism in fields as diverse as biodiversity research, infectious disease control, human and microbial forensics, animal breed and plant cultivar certification, and human ancestry research.