Nonribosomal Peptide and Polyketide Biosynthesis, 1st ed. 2016 Methods and Protocols Methods in Molecular Biology Series, Vol. 1401

This volume presents an overview of nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) structure and function.  It then continues with methods for the analysis of these pathways including conventional enzymological assays, contemporary mass spectrometric analysis techniques, specialized molecular biological approaches applicable to NRPSs and PKSs, and small molecule analysis tools tailored to this very special class of natural products, and concludes by examining bioinformatics tools for the analysis of these enzymes, pathways, and molecules. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Nonribosomal Peptide and Polyketide Biosynthesis: Methods and Protocols serves as a valuable reference for those experienced in studying NRPS and PKS enzymes, pathways, and natural products as well as a gateway for those just entering the field.

Part I: Background and Overview

1. Structural Biology of Nonribosomal Peptide Synthetases

            Bradley R. Miller and Andrew M. Gulick

2. The Assembly Line Enzymology of Polyketide Biosynthesis

            Marisa Till and Paul R. Race

Part II: In Vitro Methods

3. Measurement of Nonribosomal Peptide Synthetase Adenylation Domain Activity Using a Continuous Hydroxylamine Release Assay

            Benjamin P. Duckworth, Daniel J. Wilson, and Courtney C. Aldrich

4. Affinity Purification Method for the Identification of Nonribosomal Peptide Biosynthetic Enzymes Using a Synthetic Probe for Adenylation Domains

            Fumihiro Ishikawa and Hideaki Kakeya

5. Colorimetric Detection of the Adenylation Activity in Nonribosomal Peptide Synthetases

            Chitose Maruyama, Haruka Niikura, Masahiro Takakuwa, Hajime Katano, and Yoshimitsu Hamano

6. Facile Synthetic Access to Glycopeptide Antibiotic Precursor Peptides for the Investigation of Cytochrome P450 Action in Glycopeptide Antibiotic Biosynthesis

            Clara Brieke, Veronika Kratzig, Madeleine Peschke, and Max J. Cryle

7. Reconstitution of Fungal Nonribosomal Peptide Synthetases in Yeast and In Vitro

            Ralph A. Cacho and Yi Tang

8. The Continuing Development of E. coli as a Heterologous Host for Complex Natural Product Biosynthesis

            Haoran Zhang, Lei Fang, Marcia S. Osburne, and Blaine A. Pfeifer

9. Screening for Expressed Non

            Yunqiu Chen, Ryan A. McClure, and Neil L. Kelleher

10. Enhancing Nonribosomal Peptide Biosynthesis in Filamentous Fungi

            Alexandra A. Soukup, Nancy P. Keller, and Philipp Wiemann

11. In Situ Analysis of Bacterial Lipopeptide Antibiotics by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

            Delphine Debois, Marc Ongena, Hélène Cawoy, and Edwin De Pauw

12. Secondary Metabolic Pathway-Targeted Metabolomics

            Maria I. Vizcaino and Jason M. Crawford

Part III: Bioinformatic Methods

13. Annotating and Interpreting Linear and Cyclic Peptide Tandem Mass Spectra

14. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

            Valérie Leclère, Tilmann Weber, Philippe Jacques, and Maude Pupin

15. The Use of ClusterMine360 for the Analysis of Polyketide and Nonribosomal Peptide Biosynthetic Pathways

            Nicolas Tremblay, Patrick Hill, Kyle R. Conway, and Christopher N. Boddy

16. Alignment-Free Methods for the Detection and Specificity Prediction of Adenylation Domains

            Guillermin Agüero-Chapin, Gisselle Pérez-Machado, Aminael Sánchez-Rodríguez, Miguel Machado Santos, and Agostinho Antunes

17. Characterization of Nonribosomal Peptide Synthetases with NRPSsp

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Includes cutting-edge methods and protocols for NPRS and PKS research

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras