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Study of the complete genome sequence of Streptomyces scabies (or scabiei) 87.22
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Yaxley, Alice M. (2009) Study of the complete genome sequence of Streptomyces scabies (or scabiei) 87.22. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b2340081~S15
Abstract
A study of the complete genome sequence of Streptomyces scabies 87.22, a common
causative agent of scab disease of tubers including potato (Solanum tuberosum), is
described. This work includes annotation of the genome and in-depth description of
gene clusters likely to encode biosynthetic pathways for complex natural products
and not also found in either “Streptomyces coelicolor” A3(2) or Streptomyces
avermitilis MA-4680.
Twenty-eight gene clusters were identified as likely to encode enzymes for the
biosynthesis of complex natural products. Substances predicted by this work, not
previously known to be made by S. scabies 87.22, were confirmed by collaborators
as products - desferrioxamines, germicidins, and hopene. Of the clusters identified,
fourteen gene clusters are not conserved in the other two streptomycete genome
sequences for which comparisons have been undertaken. The Streptomyces genus is
a reservoir of producer organisms from which many complex natural products of
therapeutic importance have been isolated. These findings suggest that the cargo of
cryptic and silent gene clusters amongst other members of this genus may add
significantly to previous estimates of undiscovered bioactive natural products.
Methods developed in this work could enable other researchers to rapidly identify
gene clusters likely to encode enzymes involved in biosynthesis of complex natural
products from complete genome sequences. De-replication is a problem for
approaches to drug discovery based on activity screening and isolation of wild
producer organisms. Computational methods in this work allow rapid de-replication
of gene clusters following sequencing which may lead to discovery of many new
natural products with therapeutic benefit.
Sequences predicted to be involved in scab disease pathogenicity are not found in
only one ‘pathogenicity island’ location as expected, but at several loci. Two
possible mechanisms were identified from sequence data which it is suggested could
be involved in regulation of pathogenicity traits: an MbtH-like protein family and an
iron box sequence likely to be triggered response to low iron conditions.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QR Microbiology | ||||
Library of Congress Subject Headings (LCSH): | Streptomyces scabies -- Genome mapping, Biosynthesis | ||||
Official Date: | June 2009 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | Department of Biological Sciences | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Wellington, E. M. H. (Elizabeth M. H.), 1954- ; Allaby, Robin | ||||
Extent: | xviii, 1, 223 leaves : ill., charts | ||||
Language: | eng |
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