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@PHDTHESIS{Schito:976519,
author = {Schito, Simone},
othercontributors = {Wiechert, Wolfgang and Büchs, Jochen},
title = {{C}ommunity of niche-optimized strains : a novel concept
for the biotechnological production of small molecules},
school = {Rheinisch-Westfälische Technische Hochschule Aachen},
type = {Dissertation},
address = {Aachen},
publisher = {RWTH Aachen University},
reportid = {RWTH-2024-00279},
pages = {1 Online-Ressource : Illustrationen},
year = {2023},
note = {Veröffentlicht auf dem Publikationsserver der RWTH Aachen
University 2024; Dissertation, Rheinisch-Westfälische
Technische Hochschule Aachen, 2023},
abstract = {Nowadays, most fermentation processes for the production of
platform and fine chemicals utilize pure cultures of highly
engineered model microorganisms with flexible metabolic
capacities. However, in a bioreactor environment, these
strains are characterized by high expression of unused
enzymes resulting in carbon and energy waste, thereby
affecting process efficiency. In contrast, microorganisms in
nature have evolved in communities and are often
characterized by auxotrophies. This suggests that
co-cultures with leaner genomes and interactions via
cross-feeding must have significant advantages over pure
cultures of organisms with naturally larger genomes.To
explore this hypothesis and demonstrate its potential for
establishing new bioprocesses, the concept of Communities of
Niche-optimized Strains (CoNoS) was developed and
investigated. A model-based approach was used to create
multiple CoNoS composed of co-cultures of at least two
strains of the same species, each carrying a different
auxotrophy. While the auxotrophies provide some carbon and
energy savings due to the deletion of highly expressed
genes, cross-feeding compensates for the auxotrophies and
helps create a defined ecological niche in which the CoNoS
can use available resources more efficiently. To establish
the CoNoS, auxotrophic strains of Corynebacterium glutamicum
were constructed, and rational metabolic engineering was
applied to enhance amino acid exchange among community
members. In this way, a fast-growing co-culture was
established that exhibited a growth rate of $83\%$ of the
corresponding reference monoculture. Moreover, after an
initial growth phase, this CoNoS was able to accumulate one
of the exchanged amino acids. This demonstrated the general
suitability for bio-based production. In parallel, an
automated adaptive laboratory evolution approach was applied
to improve the growth of selected CoNoS. In this experiment,
a previously uncharacterized transporter for L-arginine was
discovered and annotated with ArgTUV. In addition, the
deletion of ArgTUV in an L-arginine-producing strain
increased the final concentration of this target product.
Finally, a modular coculture was constructed with a strain
carrying a synthetic switch to regulate relative community
composition and more efficiently direct carbon sources into
the assimilation of the desired product. The advanced CoNoS
was then compared to a monoculture-based production process
under well-controlled bioreactor conditions. Here, the CoNoS
process outperformed the monoculture showing a more than
doubled L-arginine titer, highlighting its potential and
applicability for the development of more efficient
bioprocesses.In summary, this work demonstrated that the
CoNoS approach is universally applicable to establishing
genome-reduced co-cultures. In this way, not only can energy
and carbon sources be more efficiently channeled into the
biosynthesis of desired products, but also new knowledge
about platform organisms can be generated using
evolution-guided metabolic engineering.},
cin = {420410},
ddc = {620},
cid = {$I:(DE-82)420410_20140620$},
pnm = {DFG project 402205663 - SPP 2170: Neuartige
Produktionsverfahren durch skalenübergreifende Analyse,
Modellierung und Gestaltung von Zell-Zell- und
Zell-Bioreaktor-Interaktionen (InterZell) (402205663) / DFG
project 427904493 - Communities of niche-optimized strains
(CoNoS) – Ein neues Konzept zur Verbesserung der
biotechnologischen Produktion von kleinen Molekülen
(427904493) / DFG project 428038451 - SiMBal 2.0:
Quantifizierung der Co-Kultur-Leistung und der
intrazellulären Interaktionen in Abhängigkeit der Umgebung
(428038451)},
pid = {G:(GEPRIS)402205663 / G:(GEPRIS)427904493 /
G:(GEPRIS)428038451},
typ = {PUB:(DE-HGF)11},
doi = {10.18154/RWTH-2024-00279},
url = {https://publications.rwth-aachen.de/record/976519},
}
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