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

J 2024

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

DVOŘÁK, Pavel, Barbora BURÝŠKOVÁ, Barbora POPELÁŘOVÁ, Birgitta E. EBERT, Tibor BOTKA et. al.

Basic information

Original name

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

Authors

DVOŘÁK, Pavel (203 Czech Republic, guarantor, belonging to the institution), Barbora BURÝŠKOVÁ (203 Czech Republic, belonging to the institution), Barbora POPELÁŘOVÁ (203 Czech Republic, belonging to the institution), Birgitta E. EBERT, Tibor BOTKA (203 Czech Republic, belonging to the institution), Dalimil BUJDOŠ, Alberto SÁNCHEZ-PASCUALA, Hannah SCHÖTTLER, Heiko HAYEN, Víctor DE LORENZO, Lars M. BLANK and Martin BENEŠÍK (203 Czech Republic, belonging to the institution)

Edition

Nature Communications, Nature Portfolio, 2024, 2041-1723

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

20801 Environmental biotechnology

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 16.600 in 2022

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1038/s41467-024-46812-9

UT WoS

001191874200006

Keywords in English

Applied microbiology; Bacterial evolution; Experimental evolution; Metabolic engineering

Abstract

V originále

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.

Links

GA22-12505S, research and development project

Name: Syntetické konsorcium kmenů Pseudomonas putida pro biodegradaci a ko-utilizaci (hemi)celulózových polymerů

Investor: Czech Science Foundation, Synthetic consortium of Pseudomonas putida strains for biodegradation and co-utilisation of (hemi)cellulosic polymers.

LM2023042, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii

Investor: Ministry of Education, Youth and Sports of the CR, CIISB - Czech Infrastructure for Integrative Structural Biology

LX22NPO5103, research and development project

Name: Národní institut virologie a bakteriologie (Acronym: NIVB)

Investor: Ministry of Education, Youth and Sports of the CR, National Institute of Virology and Bacteriology, 5.1 EXCELES

MUNI/J/0003/2021, interní kód MU

Name: A new generation bacterial platform for lignocellulose biotechnology (Acronym: NEWGEN)

Investor: Masaryk University, MASH JUNIOR - MUNI Award In Science and Humanities JUNIOR

90254, large research infrastructures

Name: e-INFRA CZ II

Files attached

2388277.pdf

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Citovat

DVOŘÁK, Pavel, Barbora BURÝŠKOVÁ, Barbora POPELÁŘOVÁ, Birgitta E. EBERT, Tibor BOTKA, Dalimil BUJDOŠ, Alberto SÁNCHEZ-PASCUALA, Hannah SCHÖTTLER, Heiko HAYEN, Víctor DE LORENZO, Lars M. BLANK and Martin BENEŠÍK. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nature Communications. Nature Portfolio, 2024, vol. 15, March 2024, p. 1-18. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-024-46812-9.

@article{2388277,
   author = {Dvořák, Pavel and Burýšková, Barbora and Popelářová, Barbora and Ebert, Birgitta E. and Botka, Tibor and Bujdoš, Dalimil and SánchezandPascuala, Alberto and Schöttler, Hannah and Hayen, Heiko and de Lorenzo, Víctor and Blank, Lars M. and Benešík, Martin},
   article_number = {March 2024},
   doi = {http://dx.doi.org/10.1038/s41467-024-46812-9},
   keywords = {Applied microbiology; Bacterial evolution; Experimental evolution; Metabolic engineering},
   language = {eng},
   issn = {2041-1723},
   journal = {Nature Communications},
   title = {Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose},
   url = {https://www.nature.com/articles/s41467-024-46812-9},
   volume = {15},
   year = {2024}
}

TY  - JOUR
ID  - 2388277
AU  - 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
PY  - 2024
TI  - Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
JF  - Nature Communications
VL  - 15
IS  - March 2024
SP  - 1-18
EP  - 1-18
PB  - Nature Portfolio
SN  - 20411723
KW  - Applied microbiology
KW  - Bacterial evolution
KW  - Experimental evolution
KW  - Metabolic engineering
UR  - https://www.nature.com/articles/s41467-024-46812-9
N2  - 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.
ER  -

DVOŘÁK, Pavel, Barbora BURÝŠKOVÁ, Barbora POPELÁŘOVÁ, Birgitta E. EBERT, Tibor BOTKA, Dalimil BUJDOŠ, Alberto SÁNCHEZ-PASCUALA, Hannah SCHÖTTLER, Heiko HAYEN, Víctor DE LORENZO, Lars M. BLANK and Martin BENEŠÍK. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. \textit{Nature Communications}. Nature Portfolio, 2024, vol.~15, March 2024, p.~1-18. ISSN~2041-1723. Available from: https://dx.doi.org/10.1038/s41467-024-46812-9.

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