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Comparative whole genome transcriptome and metabolome analyses of five Klebsiella pneumonia strains

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Abstract

The integration of transcriptomics and metabolomics can provide precise information on gene-to-metabolite networks for identifying the function of novel genes. The goal of this study was to identify novel gene functions involved in 2,3-butanediol (2,3-BDO) biosynthesis by a comprehensive analysis of the transcriptome and metabolome of five mutated Klebsiella pneumonia strains (∆wabG = SGSB100, ∆wabG∆budA = SGSB106, ∆wabG∆budB = SGSB107, ∆wabG∆budC = SGSB108, ∆wabG∆budABC = SGSB109). First, the transcriptomes of all five mutants were analyzed and the genes exhibiting reproducible changes in expression were determined. The transcriptome was well conserved among the five strains, and differences in gene expression occurred mainly in genes coding for 2,3-BDO biosynthesis (budA, budB, and budC) and the genes involved in the degradation of reactive oxygen, biosynthesis and transport of arginine, cysteine biosynthesis, sulfur metabolism, oxidoreductase reaction, and formate dehydrogenase reaction. Second, differences in the metabolome (estimated by carbon distribution, CO2 emission, and redox balance) among the five mutant strains due to gene alteration of the 2,3-BDO operon were detected. The functional genomics approach integrating metabolomics and transcriptomics in K. Pneumonia presented here provides an innovative means of identifying novel gene functions involved in 2,3-BDO biosynthesis metabolism and whole cell metabolism.

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Acknowledgments

This work was supported by the R&D Program of MOTIE/KEIT (No. 10035578, Development of 2,3-Butanediol and Derivative Production Technology for C-Zero Bio-Platform Industry). This work was also supported by the Graduate School of Specialization for Biotechnology Program of the Ministry of Knowledge Economy.

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    Authors and Affiliations

    1. Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, 121-742, South Korea

      Soojin Lee, Borim Kim, Jeongmo Yang, Daun Jeong, Soohyun Park & Jinwon Lee

    2. Macrogen Inc., 254 Beotkkot-ro, Geumcheon-gu, Seoul, South Korea

      Sang Heum Shin, Jun Ho Kook & Kap-Seok Yang

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    1. Soojin Lee
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    2. Borim Kim
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    Correspondence to Jinwon Lee.

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    S. Lee and B. Kim contributed equally to this work.

    J. Yang and D. Jeong also contributed equally to this work.

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    Lee, S., Kim, B., Yang, J. et al. Comparative whole genome transcriptome and metabolome analyses of five Klebsiella pneumonia strains. Bioprocess Biosyst Eng 38, 2201–2219 (2015). https://doi.org/10.1007/s00449-015-1459-7

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