Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid

Koutinas, Michalis; Kiparissides, Alexandros; Lam, Ming-Chi; Silva‐Rocha, Rafael; Godinho, Miguel; Santos, Vítor A. P. Martins dos; Pistikopoulos, Efstratios N.; Mantalaris, Athanasios

doi:10.1016/j.bej.2011.03.012

Cited by 12 publications

(3 citation statements)

References 49 publications

(41 reference statements)

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“…Determination of transcriptional kinetics in microorganisms enables obtaining important information pertinent to the expression of catabolic genes improving the knowledge about waste streams bioconversion to high added-value chemicals and the biodegradation process triggered [28]. Moreover, future optimization of the bioprocess is enabled through the development of coupled gene expression-growth kinetic models [29,30].…”

Section: Transcriptional Kinetics Of Luh Gene In P Putida Lpk411mentioning

confidence: 99%

Resolution of alkaloid racemate: a novel microbial approach for the production of enantiopure lupanine via industrial wastewater valorization

et al. 2020

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Background: Lupanine is a plant toxin contained in the wastewater of lupine bean processing industries, which could be used for semi-synthesis of various novel high added-value compounds. This paper introduces an environmental friendly process for microbial production of enantiopure lupanine.Results: Previously isolated P. putida LPK411, R. rhodochrous LPK211 and Rhodococcus sp. LPK311, holding the capacity to utilize lupanine as single carbon source, were employed as biocatalysts for resolution of racemic lupanine. All strains achieved high enantiomeric excess (ee) of L-(−)-lupanine (> 95%), while with the use of LPK411 53% of the initial racemate content was not removed. LPK411 fed with lupanine enantiomers as single substrates achieved 92% of D-(+)-lupanine biodegradation, whereas L-(−)-lupanine was not metabolized. Monitoring the transcriptional kinetics of the luh gene in cultures supplemented with the racemate as well as each of the enantiomers supported the enantioselectivity of LPK411 for D-(+)-lupanine biotransformation, while (trans)-6-oxooctahydro-1H-quinolizine-3-carboxylic acid was detected as final biodegradation product from D-(+)-lupanine use. Ecotoxicological assessment demonstrated that lupanine enantiomers were less toxic to A. fischeri compared to the racemate exhibiting synergistic interaction. Conclusions:The biological chiral separation process of lupanine presented here constitutes an eco-friendly and low-cost alternative to widely used chemical methods for chiral separation.

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Section: Transcriptional Kinetics Of Luh Gene In P Putida Lpk411mentioning

confidence: 99%

Resolution of alkaloid racemate: a novel microbial approach for the production of enantiopure lupanine via industrial wastewater valorization

et al. 2020

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“…Therefore, the Monod model, which is perhaps the best classical description of growth kinetics, is based on the assumption that culture growth is limited by a single rate-limiting enzyme reaction following the well-known Michaelis-Menten kinetics [ 23 ]. However, although traditional models can be in some cases very accurate, they are apparently not capable of capturing the regulatory effects controlling upstream the production of catabolic enzymes, providing a rather simplified and idealised view of complex biological processes [ 58 ]. The current progress in molecular biology can be used to unravel the underlying biological mechanisms that regulate gene expression and cellular function.…”

Section: Bioprocess Systems Engineeringmentioning

confidence: 99%

Bioprocess Systems Engineering: Transferring Traditional Process Engineering Principles to Industrial Biotechnology

Koutinas

Kiparissides

Pistikopoulos

et al. 2012

Computational and Structural Biotechnology Journal

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The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

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“…E. coli continues to serve as a popular host for new circuit applications, such as a synthetic modular electron transfer circuit which facilitated hydrogen production [35], and a synthetic reporter protein specific for copper ions has transformed the bacterium into an automatic copper remover [36]. Other bacterial hosts have gradually gained applicability in circuit design, including a hybrid genetic circuit for investigating protein secretion in Salmonella typhimurium SL1344 [37]; and the TOL circuit in P. putida mt2 which has been modelled as a set of logic gates to understand the growth patterns in mixed carbon sources [38,39] and a metabolic amplifier motif has been revealed from logic modelling of the circuit [40]. Circuits involving RNAs are also becoming popular in synthetic bacterial circuits [41,42].…”

Section: Designing Biological Circuits and Metabolic Pathwaysmentioning

confidence: 99%

Programmable bacterial catalysis – designing cells for biosynthesis of value‐added compounds

Lam¹,

Diez²,

Godinho³

et al. 2012

FEBS Letters

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Bacteria have long been used for the synthesis of a wide range of useful proteins and compounds. The developments of new bioprocesses and improvements of existing strategies for syntheses of valuable products in various bacterial cell hosts have their own challenges and limitations. The field of synthetic biology has combined knowledge from different science and engineering disciplines and facilitated the advancement of novel biological components which has inspired the design of targeted biosynthesis. Here we discuss recent advances in synthetic biology with relevance to biosynthesis in bacteria and the applications of computational algorithms and tools for manipulation of cellular components. Continuous improvements are necessary to keep up with increasing demands in terms of complexity, scale, and predictability of biosynthesis products.

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Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid

Cited by 12 publications

References 49 publications

Resolution of alkaloid racemate: a novel microbial approach for the production of enantiopure lupanine via industrial wastewater valorization

Resolution of alkaloid racemate: a novel microbial approach for the production of enantiopure lupanine via industrial wastewater valorization

Bioprocess Systems Engineering: Transferring Traditional Process Engineering Principles to Industrial Biotechnology

Programmable bacterial catalysis – designing cells for biosynthesis of value‐added compounds

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