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PMID: 23084938 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Phylogenetic approaches to natural product structure prediction.

Methods in enzymology ·Vol. 517 ·2012-00-00 ·Pages 161-82

Ziemert N, Jensen PR

Abstract

Phylogenetics is the study of the evolutionary relatedness among groups of organisms. Molecular phylogenetics uses sequence data to infer these relationships for both organisms and the genes they maintain. With the large amount of publicly available sequence data, phylogenetic inference has become increasingly important in all fields of biology. In the case of natural product research, phylogenetic relationships are proving to be highly informative in terms of delineating the architecture and function of the genes involved in secondary metabolite biosynthesis. Polyketide synthases and nonribosomal peptide synthetases provide model examples in which individual domain phylogenies display different predictive capacities, resolving features ranging from substrate specificity to structural motifs associated with the final metabolic product. This chapter provides examples in which phylogeny has proven effective in terms of predicting functional or structural aspects of secondary metabolism. The basics of how to build a reliable phylogenetic tree are explained along with information about programs and tools that can be used for this purpose. Furthermore, it introduces the Natural Product Domain Seeker, a recently developed Web tool that employs phylogenetic logic to classify ketosynthase and condensation domains based on established enzyme architecture and biochemical function.

MeSH Terms
Amino Acid Sequence Bacteria/classification,genetics,metabolism Bacterial Proteins/genetics,metabolism Bayes Theorem Biological Products/metabolism Computational Biology/methods Databases, Genetic Evolution, Molecular Genes, Bacterial Peptide Biosynthesis, Nucleic Acid-Independent Peptide Synthases/biosynthesis,classification,genetics Phylogeny Polyketide Synthases/biosynthesis,classification,genetics Sequence Alignment Sequence Homology, Amino Acid Software Substrate Specificity
Chemicals
Bacterial Proteins Biological Products Polyketide Synthases Peptide Synthases non-ribosomal peptide synthase
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Ziemert Nadine
Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.
Jensen Paul R
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Article Info
Journal
Methods in enzymology
Abbr.
Methods Enzymol
ISSN
1557-7988
DOI
10.1016/B978-0-12-404634-4.00008-5
Published
2012-00-00
Pages
161-82
Language
English
Region
United States
NLM ID
0212271
PMCID
PMC4504231
Subset
IM
Grants
NIGMS NIH HHS · R01 GM086261 · United States
NIGMS NIH HHS · 1R01GM086261-01 · United States
External Links
PubMed source DOI: 10.1016/B978-0-12-404634-4.00008-5 PMC Full Text
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