Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose.
Pavel DvořákBarbora BurýškováBarbora PopelářováBirgitta E EbertTibor BotkaDalimil BujdošAlberto Sánchez-PascualaHannah SchöttlerHeiko HayenVictor de LorenzoLars Mathias BlankMartin BenešíkPublished in: Nature communications (2024)
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.
Keyphrases
- saccharomyces cerevisiae
- genome wide
- transcription factor
- poor prognosis
- copy number
- physical activity
- escherichia coli
- microbial community
- stem cells
- heavy metals
- amino acid
- mesenchymal stem cells
- staphylococcus aureus
- oxidative stress
- wastewater treatment
- bone marrow
- case control
- pseudomonas aeruginosa
- candida albicans
- network analysis