Journal article
Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling
Section for Microbial and Chemical Ecology, Department of Biotechnology and Biomedicine, Technical University of Denmark1
Antimicrobial Agents and microbial ecology, Section for Microbial and Chemical Ecology, Department of Biotechnology and Biomedicine, Technical University of Denmark2
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark3
Microbial Evolution and Synthetic Biology, Research Groups, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark4
Research Groups, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark5
iLoop, Translational Management, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark6
Technical University of Denmark7
Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modeling.
Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. The OpdH and BenF-like porins were involved in citrate and ferulic acid uptake, respectively.
The citrate transporter (encoded by PP_0147) and the TctABC system were important for supporting cell growth in citrate; PcaT and VanK were associated with ferulic acid uptake; and the ABC transporter AapJPQM was involved in serine transport. A genome-scale metabolic model of P. putida KT2440 was used to integrate and analyze the transcriptomic data, identifying and confirming the active catabolic pathways for each carbon source.
This study reveals novel information about transporters that are essential for understanding bacterial adaptation to different environments.
Language: | English |
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Publisher: | John Wiley & Sons, Inc. |
Year: | 2019 |
Pages: | 87-97 |
ISSN: | 17582229 |
Types: | Journal article |
DOI: | 10.1111/1758-2229.12704 |
ORCIDs: | 0000-0003-4347-2203 , D'Arrigo, Isotta , Cardoso, João G. R. , Rennig, Maja and Sonnenschein, Nikolaus |