A CRISPR/Cas9-based genome editing system for Rhodococcus ruber TH

Liang, Youxiang; Song, Jiao; Wang, Miaomiao; Yu, Huimin; Shen, Zhongyao

doi:10.1016/j.ymben.2019.10.003

Cited by 62 publications

(51 citation statements)

References 51 publications

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“…In particular, more extensive multi-omic studies and metabolic engineering strategies of Rhodococcus strains are needed to delve into the major gene clusters involved in the anabolic pathways of interest and to identify specific genetic traits to be targeted for synthetic biology approaches. In this regard, novel genetic toolkits based on CRISPR/Cas9 system and recombineering have been recently applied for metabolic engineering of model strains of this genus (De Lorenzo et al 2018 ; Liang et al 2020 ), but they are mostly at the proof-of-concept stage and need to be further implemented to be used for the development of Rhodococcus -based microbial cell factories for efficient biotechnology applications. The extension of metabolic and genetic analyses of non-model Rhodococcus spp.…”

Section: Discussionmentioning

confidence: 99%

“…Genome-based manipulation strategies based on CRISPR-Cas9 and recombineering, were successfully applied in Rhodococcus spp. strains, opening new frontiers for genetic and metabolic engineering of members of this genus aimed at optimizing biofuel production from lignocellulose bioconversion (DeLorenzo et al 2018 ; Liang et al 2020 ). In order to implement metabolic engineering strategies for waste bioconversion into valuable compounds, a genome-scale model was also developed in R. jostii RHA1 to describe and predict the accumulation rate of three types of carbon storage compounds (i.e., glycogen, polyhydroxyalkanoate, and triacyloglycerols) using different carbon sources (glucose or acetate) and under growth conditions typically occurring in activated sludge bioreactor systems for wastewater recovery (Tajparast and Frigon 2015 , 2018 ).…”

Section: Intracellular Accumulation Of Storage Compoundsmentioning

confidence: 99%

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Biotechnology of Rhodococcus for the production of valuable compounds

Cappelletti

Presentato

Piacenza

et al. 2020

Appl Microbiol Biotechnol

106

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Bacteria belonging to Rhodococcus genus represent ideal candidates for microbial biotechnology applications because of their metabolic versatility, ability to degrade a wide range of organic compounds, and resistance to various stress conditions, such as metal toxicity, desiccation, and high concentration of organic solvents. Rhodococcus spp. strains have also peculiar biosynthetic activities that contribute to their strong persistence in harsh and contaminated environments and provide them a competitive advantage over other microorganisms. This review is focused on the metabolic features of Rhodococcus genus and their potential use in biotechnology strategies for the production of compounds with environmental, industrial, and medical relevance such as biosurfactants, bioflocculants, carotenoids, triacylglycerols, polyhydroxyalkanoate, siderophores, antimicrobials, and metal-based nanostructures. These biosynthetic capacities can also be exploited to obtain high value-added products from low-cost substrates (industrial wastes and contaminants), offering the possibility to efficiently recover valuable resources and providing possible waste disposal solutions. Rhodococcus spp. strains have also recently been pointed out as a source of novel bioactive molecules highlighting the need to extend the knowledge on biosynthetic capacities of members of this genus and their potential utilization in the framework of bioeconomy. Key points • Rhodococcus possesses promising biosynthetic and bioconversion capacities. • Rhodococcus bioconversion capacities can provide waste disposal solutions. • Rhodococcus bioproducts have environmental, industrial, and medical relevance.

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Section: Discussionmentioning

confidence: 99%

Section: Intracellular Accumulation Of Storage Compoundsmentioning

confidence: 99%

Biotechnology of Rhodococcus for the production of valuable compounds

Cappelletti

Presentato

Piacenza

et al. 2020

Appl Microbiol Biotechnol

106

View full text Add to dashboard Cite

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“…Nowadays, the new insights toward CRISPR tool kits and designing gRNA for expression of function-specific genes related to remediation in nonmodel organisms (i.e., Rhodococcus ruber TH, Comamonas testosteroni and Achromobacter sp. HZ01) are also suggested in the field of bioremediation (Mougiakos et al, 2016;Jusiak et al, 2016;Hong et al, 2017;Stein et al, 2018;Tang et al, 2018;Liang et al, 2020). For gene editing and metabolic engineering, the contaminant-inhabited bacteria are the most suitable candidates because they are used to survive and harbor in stress conditions of various toxic, recalcitrant and non-degradable xenobiotics, as discussed above.…”

Section: Genetic and Metabolic Engineeringmentioning

confidence: 99%

Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

2020

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Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.

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“…Recombinases Che9c60 and Che9c61 from mycobacteriophage together with double-stranded linear DNA was used for recombineering in Rhodococcus [18]. Recently, a CRISPR/cas9-mediated genome modification system has been reported [19]. This involved use of triple plasmids and the applicability of this system was demonstrated in R.…”

Section: Introductionmentioning

confidence: 99%

Genomic deletions in Rhodococcus based on transformation of linear heterologous DNA

2021

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Several genome engineering methods have been developed for Rhodococcus . However, they suffer from limitations such as extensive cloning, multiple steps, successful expression of heterologous genes via plasmid etc. Here, we report a rapid method for performing genomic deletions/disruptions in Rhodococcus spp. using heterologous linear DNA. The method is cost effective and less labour intensive. The applicability of the method was demonstrated by successful disruption of rodA and orphan parA. None of the disrupted genes were found to be essential for the viability of the cell. Disruption of orphan parA and rodA resulted in elongated cells and short rods, respectively. This is the first report demonstrating disruption of rodA and orphan parA genes by electroporation of heterologous linear DNA in Rhodococcus spp.

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A CRISPR/Cas9-based genome editing system for Rhodococcus ruber TH

Cited by 62 publications

References 51 publications

Biotechnology of Rhodococcus for the production of valuable compounds

Biotechnology of Rhodococcus for the production of valuable compounds

Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

Genomic deletions in Rhodococcus based on transformation of linear heterologous DNA

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