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Species' identification and microarray-based comparative genome analysis of Streptomyces species isolated from potato scab lesions in Norway.

ABSTRACT: Streptomyces strains were isolated from scab lesions on potatoes collected from different parts of Norway. Twenty-eight plant-pathogenic strains, as tested on seedlings of radish and on potato, were identified on the basis of physiological and molecular criteria. Polymerase chain reaction (PCR) analysis, using species-specific primers, and sequencing of the 16S rRNA gene identified 14 nonmelanin-producing strains to S. turgidiscabies. Fourteen melanin-producing strains were detected with primers specific to S. scabies, but whole-genome microarray analysis, based on 12 766 probes designed for 8848 predicted open reading frames (ORFs) of S. scabies, showed that the 14 strains were different from S. scabies. They were subsequently identified to be S. europaeiscabiei based on the internal transcribed spacer (ITS) sequences of the rRNA genes. This is the first report of the occurrence of S. turgidiscabies and S. europaeiscabiei in Norway. The putative 762 genes exhibiting the highest sequence differences between strains of S. europaeiscabiei and S. scabies according to microarray analysis were concentrated in relatively few gene ontology (GO) categories, including 'symbiosis and mutualism through parasitism', 'cell death' and 'responses to biotic stimulus', whereas genes related to primary metabolism appeared to be more conserved. Microarray data and 16S rRNA gene phylogeny showed, consistently, that there were two genetically distinguishable groups of S. europaeiscabiei on the basis of differences in 131 genes. The results provide novel information about the genetic variability of S. europaeiscabiei and the gene-specific variability between the genomes of S. europaeiscabiei and S. scabies. The usefulness of a custom-designed, whole-genome oligonucleotide microarray in a survey of bacterial plant pathogens was demonstrated.

SUBMITTER: Dees MW

PROVIDER: S-EPMC6638902 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

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Species' identification and microarray-based comparative genome analysis of Streptomyces species isolated from potato scab lesions in Norway.

Dees Merete W MW Somervuo Panu P Lysøe Erik E Aittamaa Marja M Valkonen Jari P T JP

Molecular plant pathology 20110901 2

Streptomyces strains were isolated from scab lesions on potatoes collected from different parts of Norway. Twenty-eight plant-pathogenic strains, as tested on seedlings of radish and on potato, were identified on the basis of physiological and molecular criteria. Polymerase chain reaction (PCR) analysis, using species-specific primers, and sequencing of the 16S rRNA gene identified 14 nonmelanin-producing strains to S. turgidiscabies. Fourteen melanin-producing strains were detected with primers ...[more]

PMID: 21880106

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Project description:Thaxtomin A is a potent phytotoxin that serves as the principle pathogenicity determinant of the common scab pathogen, Streptomyces scabiei, and is also a promising natural herbicide for agricultural applications. The biosynthesis of thaxtomin A involves the non-ribosomal peptide synthetases (NRPSs) TxtA and TxtB, and an MbtH-like protein (MLP), TxtH, which may function as a chaperone by promoting the proper folding of the two NRPS enzymes in S. scabiei. MLPs are required for the proper function of many NRPS enzymes in bacteria, and they are often capable of interacting with NRPSs from different biosynthetic pathways, though the mechanism by which this occurs is still poorly understood. To gain additional insights into MLP functional cross-talk, we conducted a broad survey of MLPs from diverse phylogenetic lineages to determine if they could functionally replace TxtH. The MLPs were assessed using a protein solubility assay to determine whether they could promote the soluble expression of the TxtA and TxtB adenylation domains. In addition, the MLPs were tested for their ability to restore thaxtomin production in a S. scabiei mutant that lacked TxtH and other endogenous MLPs. Our results showed that the MLPs investigated vary in their ability to exhibit functional cross-talk with TxtH, with two of the MLPs being unable to compensate for the loss of TxtH in the assays performed. The ability of an MLP to serve as a functional partner for the thaxtomin NRPS was not correlated with its overall amino acid similarity with TxtH, but instead with the presence of highly conserved residues. In silico structural analysis of TxtH in association with the TxtA and TxtB adenylation domains revealed that several such residues are situated at the predicted interaction interface, suggesting that they might be critical for promoting functional interactions between MLPs and the thaxtomin NRPS enzymes. Overall, our study provides additional insights into the mechanism of MLP cross-talk, and it enhances our understanding of the thaxtomin biosynthetic machinery. It is anticipated that our findings will have useful applications for both the control of common scab disease and the commercial production of thaxtomin A for agricultural use.

Dataset Information

Species' identification and microarray-based comparative genome analysis of Streptomyces species isolated from potato scab lesions in Norway.

Publications

Species' identification and microarray-based comparative genome analysis of Streptomyces species isolated from potato scab lesions in Norway.

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