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.

Základní údaje

Originální název

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

Autoři

Vydání

Nature Communications, Nature Portfolio, 2024, 2041-1723

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

20801 Environmental biotechnology

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 15.700

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/24:00135743

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

Applied microbiology; Bacterial evolution; Experimental evolution; Metabolic engineering

Štítky

14314010, CF PROT, NIVB_PřF, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 4. 2025 12:56, Mgr. Marie Novosadová Šípková, DiS.

Anotace

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.

Návaznosti

GA22-12505S, projekt VaV

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

Investor: Grantová agentura ČR, Syntetické konsorcium kmenů Pseudomonas putida pro biodegradaci a ko-utilizaci (hemi)celulózových polymerů

LX22NPO5103, projekt VaV

Název: Národní institut virologie a bakteriologie (Akronym: NIVB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Národní institut virologie a bakteriologie, 5.1 EXCELES

MUNI/J/0003/2021, interní kód MU

Název: A new generation bacterial platform for lignocellulose biotechnology (Akronym: NEWGEN)

Investor: Masarykova univerzita, A new generation bacterial platform for lignocellulose biotechnology, MASH JUNIOR - MUNI Award In Science and Humanities JUNIOR

90242, velká výzkumná infrastruktura

Název: CIISB III

90254, velká výzkumná infrastruktura

Název: e-INFRA CZ II

Přiložené soubory

2388277.pdf

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 a Martin BENEŠÍK. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nature Communications. Nature Portfolio, 2024, roč. 15, č. 1, s. 1-18. ISSN 2041-1723. Dostupné z: https://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 = {1},
   doi = {https://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  - 1
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 a Martin BENEŠÍK. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. \textit{Nature Communications}. Nature Portfolio, 2024, roč.~15, č.~1, s.~1-18. ISSN~2041-1723. Dostupné z: https://doi.org/10.1038/s41467-024-46812-9.

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