Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola

• Published in: Journal of applied microbiology 2009-09, Vol.107 (3), p.717-726
• Main Authors: Li, X, Nie, J, Ward, L, Madani, M, Hsiang, T, Zhao, Y, De Boer, S.H
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - genetics; Biological and medical sciences; characterization; comparative genomics; detection; DNA Primers - genetics; Erwinia; Fundamental and applied biological sciences. Psychology; loop-mediated isothermal amplification; Microbiology; Nucleic Acid Amplification Techniques - methods; Pectobacterium; Phaseolus - virology; Phaseolus vulgaris; Polyketide Synthases - genetics; Pseudomonas aeruginosa; Pseudomonas aeruginosa - genetics; Pseudomonas fluorescens - genetics; Pseudomonas syringae; Pseudomonas syringae - genetics; Pseudomonas syringae - isolation & purification; Pseudomonas syringae pv. phaseolicola; Sensitivity and Specificity; Sequence Alignment; Sequence Analysis, DNA
• ISSN: 1364-5072; 1365-2672
• DOI: 10.1111/j.1365-2672.2009.04262.x

To design and evaluate a loop-mediated isothermal amplification (LAMP) protocol by combining comparative genomics and bioinformatics for characterization of Pseudomonas syringae pv. phaseolicola (PSP), the causal agent of halo blight disease of bean (Phaseolus vulgaris L.). Genomic sequences of Pseudomonas syringae pathovars, P. fluorescens and P. aeruginosa were analysed using multiple sequence alignment. A pathovar-specific region encoding pathogenicity-related secondary metabolites in the PSP genome was targeted for developing a LAMP assay. The final assay targeted a polyketide synthase gene, and readily differentiated PSP strains from other Pseudomonas syringae pathovars and other Pseudomonas species, as well as other plant pathogenic bacteria, e.g. species of Pectobacterium, Erwinia and Pantoea. A LAMP assay has been developed for rapid and specific characterization and identification of PSP from other pathovars of P. syringae and other plant-associated bacteria. This paper describes an approach combining a bioinformatic data mining strategy and comparative genomics with the LAMP technology for characterization and identification of a plant pathogenic bacterium. The LAMP assay could serve as a rapid protocol for microbial identification and detection with significant applications in agriculture and environmental sciences.