Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate 
D-xylose

Dvořák, Pavel; Burýšková, Barbora; Popelářová, Barbora; Ebert, Birgitta E.; Botka, Tibor; Bujdoš, Dalimil; Sánchez-Pascuala, Alberto; Schöttler, Hannah; Hayen, Heiko; de Lorenzo, Víctor; Blank, Lars M.; Benešík, Martin

doi:10.1038/s41467-024-46812-9

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Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose

Dvořák, P., Burýšková, B., Popelářová, B., Ebert, B. E., Botka, T., Bujdoš, D., et al. (2024). Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nature Communications, 15: 2666. doi:10.1038/s41467-024-46812-9.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000F-26E6-3 Version Permalink: https://hdl.handle.net/21.11116/0000-000F-26E7-2

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https://doi.org/10.1038/s41467-024-46812-9 (Publisher version) Open Access Gold

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Creators:
Dvořák, Pavel¹, Author
Burýšková, Barbora¹, Author
Popelářová, Barbora¹, Author
Ebert, Birgitta E.¹, Author
Botka, Tibor¹, Author
Bujdoš, Dalimil¹, Author
Sánchez-Pascuala, Alberto², Author
Schöttler, Hannah¹, Author
Hayen, Heiko¹, Author
de Lorenzo, Víctor¹, Author
Blank, Lars M.¹, Author
Benešík, Martin¹, Author

Affiliations:
1external, ou_persistent22
2Max Planck Institute for Terrestrial Microbiology_others, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, Karl-von Frisch Str. 10, 35043 Marburg, Germany, ou_3556424

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Abstract: To broaden the substrate scope of microbial cell factories towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by rational metabolic engineering remain scarce. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous xylose isomerase pathway remained unresolved. Here, we elucidate the xylose metabolism and establish a foundation for further engineering followed by ALE. First, native glycolysis is derepressed by deleting the local transcriptional regulator gene hexR. We then enhance the pentose phosphate pathway by implanting exogenous transketolase and transaldolase into two lag-shortened strains and allow ALE to finetune the rewired metabolism. Subsequent multilevel analysis and reverse engineering provide detailed insights into the parallel paths of bacterial adaptation to the non-native carbon source, highlighting the enhanced expression of transaldolase and xylose isomerase along with derepressed glycolysis as key events during the process.

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Language(s): eng - English

Dates: Date issued: 2024-03-26

Publication Status: Issued

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Rev. Type: Peer

Identifiers: URI: https://doi.org/10.1038/s41467-024-46812-9
Other: Dvořák2024
DOI: 10.1038/s41467-024-46812-9

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Title: Nature Communications

Abbreviation : Nat. Commun.

Source Genre: Journal

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Publ. Info: London : Nature Publishing Group

Pages: - Volume / Issue: 15 Sequence Number: 2666 Start / End Page: - Identifier: ISSN: 2041-1723
CoNE: https://pure.mpg.de/cone/journals/resource/2041-1723