A modular toolkit for environmental Rhodococcus , Gordonia , and Nocardia enables complex metabolic manipulation

• Published in: Applied and environmental microbiology 2024-08, Vol.90 (8), p.e0034024
• Main Authors: Jansen, Zachary, Alameri, Abdulaziz, Wei, Qiyao, Kulhanek, Devon L, Gilmour, Andrew R, Halper, Sean, Schwalm, 3rd, Nathan D, Thyer, Ross
• Format: Article
• Language: English
• Subjects: Actinomycetes; Antibiotic resistance; Biosynthesis; Biotechnology; Carotenoids; E coli; Fluorescence; Genetic control; Genetic diversity; Genetic engineering; Genetics and Molecular Biology; Gordonia; Gordonia Bacterium - genetics; Gordonia Bacterium - metabolism; Metabolic Engineering; Microbiomes; Molecular and Cellular Biology; Nocardia; Nocardia - genetics; Nocardia - metabolism; Plasmids - genetics; Pseudomonas putida; Replication origins; Rhodococcus; Rhodococcus - genetics; Rhodococcus - metabolism; Spotlight Selection; Toolkits
• ISSN: 0099-2240; 1098-5336; 1098-5336
• DOI: 10.1128/aem.00340-24

Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as or , posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate C208, and demonstrate conserved functionality in 11 additional environmental isolates of , , and . This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. , , and are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, C208 was shown to degrade polyethylene; can assimilate carbon from solid hydrocarbons; and (and many other spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.