Mining the genomes of gliding bacteria with emphasis on Herpetosiphon aurantiacus
Mining the genomes of gliding bacteria with emphasis on Herpetosiphon aurantiacus
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DissertationDate of Exam
20.11.2012Date of Publication
29.11.2012Advisor
König, Gabriele M.Co-Referee
Kostenis, EviMetadata
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Abstract
The advancement in the computational tools and comprehensive knowledge in nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modular genes has been instrumental in the identification of new biosynthetic gene clusters from genomes. These biosynthetic clusters are often cryptic, i.e. associated with as yet unknown compounds. Thus, this approach called “genome mining” can be applied for the discovery of natural products useful for drug development.
Gliding bacteria, which are known for their complex life style, include the chemically prolific myxobacteria and cyanobacteria. Other bacterial taxa in this group are hardly investigated for their chemistry. Therefore, the first part of this project aimed to evaluate 18 completely sequenced gliding bacterial genomes from the phyla Chloroflexi, Firmicutes, Bacteroidetes, Planctomycetes, Chlorobi and Proteobacteria for the presence of PKS and NRPS genes.
The focus of the second part of the study was a detailed investigation of the complete genome sequence of the chemically unexplored Herpetosiphon aurantiacus DSM 785 for PKS and NRPS gene clusters. Information on sequences of cryptic gene clusters and their encoded putative structures were to be used to optimize the conditions for the isolation of secondary metabolites from this bacterium.
In the last part of this study, PKS/NRPS gene locus-1 from H. aurantiacus was to be characterized in detail. Emphasis was to be put on the adenylation domains, an integral component of NRPS, which control the entry of amino acid building blocks.
Gliding bacteria, which are known for their complex life style, include the chemically prolific myxobacteria and cyanobacteria. Other bacterial taxa in this group are hardly investigated for their chemistry. Therefore, the first part of this project aimed to evaluate 18 completely sequenced gliding bacterial genomes from the phyla Chloroflexi, Firmicutes, Bacteroidetes, Planctomycetes, Chlorobi and Proteobacteria for the presence of PKS and NRPS genes.
The focus of the second part of the study was a detailed investigation of the complete genome sequence of the chemically unexplored Herpetosiphon aurantiacus DSM 785 for PKS and NRPS gene clusters. Information on sequences of cryptic gene clusters and their encoded putative structures were to be used to optimize the conditions for the isolation of secondary metabolites from this bacterium.
In the last part of this study, PKS/NRPS gene locus-1 from H. aurantiacus was to be characterized in detail. Emphasis was to be put on the adenylation domains, an integral component of NRPS, which control the entry of amino acid building blocks.
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570 Biowissenschaften, BiologieNatesan, Lavanya: Mining the genomes of gliding bacteria with emphasis on Herpetosiphon aurantiacus. - Bonn, 2012. - Dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn.
Online-Ausgabe in bonndoc: https://nbn-resolving.org/urn:nbn:de:hbz:5n-30714
Online-Ausgabe in bonndoc: https://nbn-resolving.org/urn:nbn:de:hbz:5n-30714
@phdthesis{handle:20.500.11811/5422,
urn: https://nbn-resolving.org/urn:nbn:de:hbz:5n-30714,
author = {{Lavanya Natesan}},
title = {Mining the genomes of gliding bacteria with emphasis on Herpetosiphon aurantiacus},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2012,
month = nov,
note = {The advancement in the computational tools and comprehensive knowledge in nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modular genes has been instrumental in the identification of new biosynthetic gene clusters from genomes. These biosynthetic clusters are often cryptic, i.e. associated with as yet unknown compounds. Thus, this approach called “genome mining” can be applied for the discovery of natural products useful for drug development.
Gliding bacteria, which are known for their complex life style, include the chemically prolific myxobacteria and cyanobacteria. Other bacterial taxa in this group are hardly investigated for their chemistry. Therefore, the first part of this project aimed to evaluate 18 completely sequenced gliding bacterial genomes from the phyla Chloroflexi, Firmicutes, Bacteroidetes, Planctomycetes, Chlorobi and Proteobacteria for the presence of PKS and NRPS genes.
The focus of the second part of the study was a detailed investigation of the complete genome sequence of the chemically unexplored Herpetosiphon aurantiacus DSM 785 for PKS and NRPS gene clusters. Information on sequences of cryptic gene clusters and their encoded putative structures were to be used to optimize the conditions for the isolation of secondary metabolites from this bacterium.
In the last part of this study, PKS/NRPS gene locus-1 from H. aurantiacus was to be characterized in detail. Emphasis was to be put on the adenylation domains, an integral component of NRPS, which control the entry of amino acid building blocks.},
url = {https://hdl.handle.net/20.500.11811/5422}
}
urn: https://nbn-resolving.org/urn:nbn:de:hbz:5n-30714,
author = {{Lavanya Natesan}},
title = {Mining the genomes of gliding bacteria with emphasis on Herpetosiphon aurantiacus},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2012,
month = nov,
note = {The advancement in the computational tools and comprehensive knowledge in nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modular genes has been instrumental in the identification of new biosynthetic gene clusters from genomes. These biosynthetic clusters are often cryptic, i.e. associated with as yet unknown compounds. Thus, this approach called “genome mining” can be applied for the discovery of natural products useful for drug development.
Gliding bacteria, which are known for their complex life style, include the chemically prolific myxobacteria and cyanobacteria. Other bacterial taxa in this group are hardly investigated for their chemistry. Therefore, the first part of this project aimed to evaluate 18 completely sequenced gliding bacterial genomes from the phyla Chloroflexi, Firmicutes, Bacteroidetes, Planctomycetes, Chlorobi and Proteobacteria for the presence of PKS and NRPS genes.
The focus of the second part of the study was a detailed investigation of the complete genome sequence of the chemically unexplored Herpetosiphon aurantiacus DSM 785 for PKS and NRPS gene clusters. Information on sequences of cryptic gene clusters and their encoded putative structures were to be used to optimize the conditions for the isolation of secondary metabolites from this bacterium.
In the last part of this study, PKS/NRPS gene locus-1 from H. aurantiacus was to be characterized in detail. Emphasis was to be put on the adenylation domains, an integral component of NRPS, which control the entry of amino acid building blocks.},
url = {https://hdl.handle.net/20.500.11811/5422}
}
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