A navigation guide of synthetic biology tools for Pseudomonas putida

Martín-Pascual, María; Batianis, Christos; Bruinsma, Lyon; Asin-Garcia, Enrique; Garcia-Morales, Luis J.; Weusthuis, Ruud A.; Kranenburg, Richard van; Santos, Vítor A. P. Martins dos

doi:10.1016/j.biotechadv.2021.107732

Cited by 61 publications

(50 citation statements)

References 242 publications

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“…Counterselection strategies for genomic modifications including gene deletions have also been successfully adapted to Pseudomonas (e.g. by use of sacB, CRISPR-Cas9, or I-SceI) [142]. This array of tools, together with an increasing understanding of tolerance traits, will facilitate the generation of chassis with specifically adapted tolerance features in the near future.…”

Section: Identification and Implementation Of Tolerance-related Genesmentioning

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: Identification and Implementation Of Tolerance-related Genesmentioning

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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“…Moreover, a variety of native (P m , P sal , P alkB , P u , and P xylA ) and heterologous (P araB , P rhaB , P trc , P lac , P tac , P tet , P T7-lac and P lacUV5 , P mekA , P mtlE , P chnB , and P DB3 ) inducible expression systems have been demonstrated in P. putida strains 9 – 11 . These induction systems use a wide range of inducing chemicals such as 3-methylbenzoate, 3-methylbenzyl alcohol, dicyclopropylketone, methyl ethyl ketone, m -toluate, salicylate, n -octane, 3-chloro-4-hydroxyphenylacetic acid, cyclohexanone, rhamnose, arabinose, xylose, mannitol, p -cumate, anhydrotetracycline, and isopropyl-β-D-1-thiogalactopyranoside (IPTG) with varying degrees of success 9 – 13 . In addition, temperature inducible 14 and quorum sensing promoter systems 15 , 16 were employed in P. putida strains.…”

Section: Introductionmentioning

confidence: 99%

Inducible and tunable gene expression systems for Pseudomonas putida KT2440

Sathesh‐Prabu

Tiwari

Kim

et al. 2021

Sci Rep

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Inducible and tunable expression systems are essential for the microbial production of biochemicals. Five different carbon source- and substrate-inducible promoter systems were developed and further evaluated in Pseudomonas putida KT2440 by analyzing the expression of green fluorescent protein (GFP) as a reporter protein. These systems can be induced by low-cost compounds such as glucose, 3-hydroxypropionic acid (3HP), levulinic acid (LA), and xylose. 3HP-inducible HpdR/PhpdH was also efficiently induced by LA. LvaR/PlvaA and XutR/PxutA systems were induced even at low concentrations of LA (0.1 mM) and xylose (0.5 mM), respectively. Glucose-inducible HexR/Pzwf1 showed weak GFP expression. These inducer agents can be used as potent starting materials for both cell growth and the production of a wide range of biochemicals. The efficiency of the reported systems was comparable to that of conventional chemical-inducible systems. Hence, the newly investigated promoter systems are highly useful for the expression of target genes in the widely used synthetic biology chassis P. putida KT2440 for industrial and medical applications.

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“…It is unclear how exactly termination-reinitiation works mechanistically in bacteria; however, overlapping stop and start codons are prevalent throughout all prokaryotes (Huber et al, 2019). The bicistronic design approach has been used in several studies to modulate gene expression and enable expression of difficult-to-produce proteins such as membrane proteins (Mutalik et al, 2013a;Zhao et al, 2016;Jang et al, 2018;Claassens et al, 2019;Nieuwkoop et al, 2019;Sun et al, 2020b;Martin-Pascual et al, 2021;Torres-Bacete et al, 2021). For instance, Claassens et al (2019) used bicistronic design to constitutively express 'difficult-to-produce' membrane proteins such as AraH, which is the membrane integral part of the arabinose ABC transporter in E. coli.…”

Section: Tackling Context Dependency: Bicistronic Operon Design and Translational Couplingmentioning

confidence: 99%

Importance of the 5′ regulatory region to bacterial synthetic biology applications

Tietze

Lale

2021

Microbial Biotechnology

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The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of precharacterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5 0 regulatory regionspromoters, untranslated regions and 5 0 -end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.

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A navigation guide of synthetic biology tools for Pseudomonas putida

Cited by 61 publications

References 242 publications

Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways

Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways

Inducible and tunable gene expression systems for Pseudomonas putida KT2440

Importance of the 5′ regulatory region to bacterial synthetic biology applications

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