Dereplication for biotechnology screening: PyMS analysis and PCR-RFLP-SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes

Brandao, P.F. and Torimura, M. and Kurane, R. and Bull, Alan T. (2002) Dereplication for biotechnology screening: PyMS analysis and PCR-RFLP-SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes. Applied Microbiology and Biotechnology, 58 (1). pp. 77-83. ISSN 0175-7598. (The full text of this publication is not available from this repository)

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Abstract

The search for exploitable biology is a major task for biotechnology-based industries. In this context, discrimination between previously tested or recovered micro-organisms (dereplication) is imperative, in order to reduce screening costs by sorting large collections of isolates, which are then subjected to further detailed evaluation. Pyrolysis mass spectrometry (PyMS) is a whole-cell fingerprinting technique that enables the rapid and reproducible sorting of micro-organisms, uses small samples and has the advantage of being fully automated. In this study, we compare chemometric fingerprinting with a ribotyping fingerprinting method, in order to investigate the extent to which pyrogroups formed by PyMS analysis relate to genetic diversity, using polymerase chain reaction-restriction fragment length polymorphism-single-strand conformational polymorphism (PRS). A mixture of environmental strains of mycolic acid containing actinomycetes was used to mimic the selection of colonies from primary isolation plates. The congruence found between the clusters defined by the chemometric and molecular fingerprinting techniques was very high and demonstrated the effectiveness of PyMS as a rapid sorting and dereplicating procedure for putatively novel strains, criteria that are critical for biotechnological screens. Moreover, PyMS analysis revealed significant variation within pyrogroups that contained strains with the same genotypic (PRS) characteristics, thus emphasising its discriminatory capacity at the infraspecies level.

Item Type: Article
Additional information: 0175-7598 (Print) Evaluation Studies Journal Article Research Support, Non-U.S. Gov't
Uncontrolled keywords: Actinomycetales/chemistry/*classification/genetics/growth & development *Bacterial Typing Techniques Biotechnology/*methods Culture Media *Genes, rRNA Mass Spectrometry/methods Polymerase Chain Reaction/methods Polymorphism, Restriction Fragment Length Polymorphism, Single-Stranded Conformational RNA, Ribosomal, 16S/*genetics Seawater/*microbiology *Soil Microbiology
Subjects: Q Science
Divisions: Faculties > Science Technology and Medical Studies > School of Biosciences > Biomedical Research Group
Depositing User: Sue Davies
Date Deposited: 17 Sep 2008 10:25
Last Modified: 22 Apr 2014 11:52
Resource URI: http://kar.kent.ac.uk/id/eprint/7352 (The current URI for this page, for reference purposes)
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