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

Pavel Dvořák (), Barbora Burýšková, Barbora Popelářová, Birgitta E. Ebert, Tibor Botka, Dalimil Bujdoš, Alberto Sánchez-Pascuala, Hannah Schöttler, Heiko Hayen, Víctor Lorenzo, Lars M. Blank and Martin Benešík
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Pavel Dvořák: Masaryk University
Barbora Burýšková: Masaryk University
Barbora Popelářová: Masaryk University
Birgitta E. Ebert: The University of Queensland
Tibor Botka: Masaryk University
Dalimil Bujdoš: University College Cork
Alberto Sánchez-Pascuala: Max Planck Institute for Terrestrial Microbiology
Hannah Schöttler: University of Münster
Heiko Hayen: University of Münster
Víctor Lorenzo: Cantoblanco
Lars M. Blank: RWTH Aachen University
Martin Benešík: Masaryk University

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-46812-9

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