KS seq Analysis description

Over ten thousands of bioactive compounds were discovered from actinomycetes,1 in which polyketide (PK) and nonribosomal peptide (NRP) compounds are especially important for pharmaceutical industries. Recently, type-I PKS and NRPS genes of isolated strains are often analyzed to assess their potential to produce novel PK and NRP compounds.2-4 In such studies, PCR assays are conventionally used, which target ketosynthase (KS) domain and adenylation (A) domain regions in type-I PKS and NRPS genes, respectively. The novelties of detected genes are usually assessed according to similarities of the amplicon sequences to already reported biosynthetic genes. However, even if a sequence showed low similarity to reported genes, it is not always suggested that a novel compound is produced, because only limited numbers of biosynthetic genes corresponding to known PK and NRP compounds have been identified. Thus, we have to consider the possibility that the gene seems to be novel but its product is already reported.

In order to minimize such cases, we have extensively determined KS and A domain sequences in our collections including 333 antibiotic-producers and 464 type strains of Streptomyces preserved at NBRC, and registered them here. If you enter your isolates KS and/or A domain DNA sequences as queries, this program replies the Blast results searched for our database, and you can check the novelty of your strain's gene based on the similarity to the huge numbers of sequences we registered. As the results, advanced dereplication will be achieved., and you can check the novelty of your strain's gene based on the similarity to the huge numbers of sequences we registered. As the results, advanced dereplication will be achieved.


References

  1. Bérdy J.: Bioactive microbial metabolites. J Antibiot 58, 1-26, 2005

  2. Komaki H. et al: Discovery of a pimaricin analog JBIR-13, from Streptomyces bicolor NBRC 12746 as predicted by sequence analysis of type I polyketide synthase gene. Appl Microbiol Biotechnol 83, 127-133, 2009

  3. Khan ST. et al: Streptomyces associated with a marine sponge Haliclona sp.; biosynthetic genes for secondary metabolites and products. Environ Microbiol 13, 391-403, 2011

  4. Enkh-Amgalan J. et al: Diversity of nonribosomal peptide synthetase and polyketide synthase genes in the genus Actinoplanes found in Mongolia. J Antibiot 65, 103-108, 2012


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