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Systems Biology Tools for Methylotrophs

  • Marina G. Kalyuzhnaya
  • Song Yang
  • David A. C. Beck
  • Ludmila ChistoserdovaEmail author
Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

The methylotrophy field is currently experiencing a renaissance. Innovative cultivation techniques are resulting in discovery of novel types of methylotrophs, the growing genomic databases are providing blueprints for metabolic reconstruction in traditional as well as newly discovered methylotrophs, and the concepts and dogmas formed during the pre-omics era are changing, sometimes dramatically. The emerging approach in characterizing methylotrophs, as well as other metabolic specialists, is a combination of systems biology approaches, with availability of the genomic sequence being a prerequisite. We here describe a series of omics approaches to characterizing methylotrophs, which, in their combination, provide comprehensive outlook at how methylotrophy metabolism is enabled in specific methylotroph guilds and how it is regulated.

Keywords:

Community dynamics Genomics Metabolic modeling Metabolomics Methanotroph Methylotroph Proteomics Transcriptomics 

Notes

Acknowledgements

This material is based upon the work supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC-0010556, and the Joint Fund of National Natural Science Foundation of China (Grant Number U1462109).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Marina G. Kalyuzhnaya
    • 1
  • Song Yang
    • 2
  • David A. C. Beck
    • 3
    • 4
  • Ludmila Chistoserdova
    • 3
    Email author
  1. 1.Biology DepartmentSan Diego State UniversitySan DiegoUSA
  2. 2.School of Life SciencesQingdao Agricultural University and Qingdao International Center on Microbes Utilizing BiogasShandong ProvincePeople’s Republic of China
  3. 3.Department of Chemical EngineeringUniversity of WashingtonSeattleUSA
  4. 4.eScience Institute, University of WashingtonSeattleUSA

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