Planta Med 2012; 78 - IL8
DOI: 10.1055/s-0032-1320195

Imabing mass spectrometry and molecular network guided genome mining of microbial systems

PC Dorrestein 1
  • 1Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, USA, Center for Marine Biotechnology and Biomedicine, Bruker Therapeutic Discovery Mass Spectrometry Center, UC San Diego, CA

In this lecture I will describe the latest mass spectrometry based tools and genome mining approaches we have developed to study the metabolic exchange of microbes.1–8 The goal for visualizing molecules microbes and bridging this with genome mining is to enable the functional translation to understand their molecular language. The presentation will highlight microbial imaging mass spectrometry, the development of mass spectrometry based genome mining tools, including the utility of peptidogenomics and glycogenomics tools that will be explained by Brad Moore in the next talk, in conjunction with live colony mass spectrometry, molecular networking, molecular dendrograms, and ambient mass microscopy to study metabolic exchange and ecology of microbial communities for applications in agriculture, diagnostics and therapeutic discovery. Finally, perhaps most significantly, this lecture will introduce the development of a molecular “Genbank” and its search engines that are being co-developed with the Bandeira laboratory at the NIH Center for Computational Mass Spectrometry that will merge natural product analysis with modern genome mining.

References

1. Yang, Y.L., Xu, Y., Straight, P., Dorrestein, P.C., Translating metabolic exchange with imaging mass spectrometry. Nature Chemical Biology (2009) 5,885–7.

2. Wei-Ting Liu, Yu-Liang Yang, Yuquan Xu, Anne Lamsa, Nina M Haste, Jane Y. Yang, Julio Ng, David Gonzalez, Craig D. Ellermeier, Paul D. Straight, Pavel A. Pevzner, Joe Pogliano, Victor Nizet, Kit Pogliano, Pieter C. Dorrestein. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis Proc. Natl. Acad. Sci. USA. (2010) 107,16286–90.

3. Jeramie D. Watrous, Pieter C. Dorrestein, Imaging mass spectrometry in microbiology Nature Reviews Microbiology (2011), 9, 683–694.

4. Yu-Liang Yang, Yuquan Xu, Roland Kersten, Wei-Ting Liu, Michael J. Meehan, Bradley S. Moore, Nuno Bandeira, Pieter C. Dorrestein, Connecting chemotypes and phenotypes of cultured marine microbial assemblages using imaging mass spectrometry. Angewandte Chemie (2011), 50, 5839–42.

6. Roland D Kersten, Yu-Liang Yang, Yuquan Xu, Peter Cimermancic, Sang-Jip Nam, William Fenical, Michael A Fischbach, Bradley S Moore, Pieter C Dorrestein, A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nature Chemical Biology (2011), 7, 794–802.

7. Vanessa V Phelan, Wei-Ting Liu, Kit Pogliano, Pieter C Dorrestein Microbial metabolic exchange-the chemotype-phenotype link. Nature Chemical Biology (2012), 8, 26–35.

8. Jeramie Watrous, Patrick Roach, Theodore Alexandrov, Brandi Heath, Jane Y. Yang, Roland D. Kersten, Menno van der voort, Kit Pogliano, Harald Gross, Jos Raaijmakers, Bradley S. Moore, Julia Laskin, Nuno Bandeirac, Pieter C. Dorrestein, Mass spectral molecular networking of living microbial colonies. Proc. Natl. Acad. Sci. USA., (2012), in press.