Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life

Nieto-Domínguez, Manuel; Nikel, Pablo I.

doi:10.1002/cbic.202000091

Cited by 23 publications

(21 citation statements)

References 340 publications

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“…Another emerging strategy to achieve a higher and more balanced flux is to spatially organise enzymes within synthetic scaffolds [164,165] to create high local concentrations of metabolites and enzymes, with well-defined stoichiometry to support immediate conversion without diffusion of intermediates. All these strategies (Figure 3) together with an increasing understanding of tolerance traits will be instrumental for effective production applications and expanding the catalytic landscape of Pseudomonas towards novel chemistries [12,166].…”

Section: Engineering Of Optimal Flux In Cell Factories With Novel Pathwaysmentioning

confidence: 99%

Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways

Bitzenhofer

Kruse

Thies

et al. 2021

Essays in Biochemistry

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Biotechnological production in bacteria enables access to numerous valuable chemical compounds. Nowadays, advanced molecular genetic toolsets, enzyme engineering as well as the combinatorial use of biocatalysts, pathways, and circuits even bring new-to-nature compounds within reach. However, the associated substrates and biosynthetic products often cause severe chemical stress to the bacterial hosts. Species of the Pseudomonas clade thus represent especially valuable chassis as they are endowed with multiple stress response mechanisms, which allow them to cope with a variety of harmful chemicals. A built-in cell envelope stress response enables fast adaptations that sustain membrane integrity under adverse conditions. Further, effective export machineries can prevent intracellular accumulation of diverse harmful compounds. Finally, toxic chemicals such as reactive aldehydes can be eliminated by oxidation and stress-induced damage can be recovered. Exploiting and engineering these features will be essential to support an effective production of natural compounds and new chemicals. In this article, we therefore discuss major resistance strategies of Pseudomonads along with approaches pursued for their targeted exploitation and engineering in a biotechnological context. We further highlight strategies for the identification of yet unknown tolerance-associated genes and their utilisation for engineering next-generation chassis and finally discuss effective measures for pathway fine-tuning to establish stable cell factories for the effective production of natural compounds and novel biochemicals.

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Section: Engineering Of Optimal Flux In Cell Factories With Novel Pathwaysmentioning

confidence: 99%

Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways

Bitzenhofer

Kruse

Thies

et al. 2021

Essays in Biochemistry

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“…Interestingly, 5′-FDA was not converted to 5′-FDRP (or any other fluorinated derivative) in the absence of a FluoroBrick-encoded PNP, indicating that the endogenous phosphorylase activities of strain KT2440 are largely unreactive toward 5′-FDA. This circumstance can be exploited for the design of neo-metabolism 48 , where metabolic nodes based on fluorometabolites, orthogonal to the extant biochemistry of the host, are exploited to drive biosynthesis of organofluorines (e.g. fluoro-amino acids, which can be incorporated into proteins 49,50 ).…”

Section: Discussionmentioning

confidence: 99%

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

et al. 2020

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Fluorine is a key element in the synthesis of molecules broadly used in medicine, agriculture and materials. Addition of fluorine to organic structures represents a unique strategy for tuning molecular properties, yet this atom is rarely found in Nature and approaches to integrate fluorometabolites into the biochemistry of living cells are scarce. In this work, synthetic gene circuits for organofluorine biosynthesis are implemented in the platform bacterium Pseudomonas putida. By harnessing fluoride-responsive riboswitches and the orthogonal T7 RNA polymerase, biochemical reactions needed for in vivo biofluorination are wired to the presence of fluoride (i.e. circumventing the need of feeding expensive additives). Biosynthesis of fluoronucleotides and fluorosugars in engineered P. putida is demonstrated with mineral fluoride both as only fluorine source (i.e. substrate of the pathway) and as inducer of the synthetic circuit. This approach expands the chemical landscape of cell factories by providing alternative biosynthetic strategies towards fluorinated building-blocks.

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“…First published in 2002 and revisited in 2016, the full genome sequence of P. putida KT2440 has shed light on the diverse transport and metabolic systems (Belda et al 2016;Nelson et al 2002). Moreover, the pangenome of P. putida has been studied and revealed 3386 conserved genes belonging to the core genome and comprising genes related to ED and pentose phosphate (PP) pathway, proline and arginine metabolism, aromatic compound degradation, as well as a vast collection of nutrient transporters (Udaondo et al 2016).…”

Section: Genomics and Metabolic Reconstructionsmentioning

confidence: 99%

“…Initiated by the discovery of the potential of P. putida in biodegradation of xenobiotics in the 1960s (Nakazawa 2002), the acquisition of knowledge about the genetics, biochemistry, and physiology of this microbe has been continuously progressing over the last five decades. This led, inter alia, to the decryption of the complete genomic repertoire (Belda et al 2016;Nelson et al 2002) (Fig. 2) and the construction of genome-scale metabolic models for in silico simulations and data mapping (Nogales et al 2020;Puchałka et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Industrial biotechnology of Pseudomonas putida: advances and prospects

Weimer

Kohlstedt

Volke

et al. 2020

Appl Microbiol Biotechnol

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154

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Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. Key points • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs. Electronic supplementary material The online version of this article (10.1007/s00253-020-10811-9) contains supplementary material, which is available to authorized users.

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Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life

Cited by 23 publications

References 340 publications

Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways

Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

Industrial biotechnology of Pseudomonas putida: advances and prospects

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