Construction of an easy-to-use CRISPR-Cas9 system by patching a newly designed EXIT circuit

Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing

Covering: up to the end of 2023Type I CRISPR-Cas systems are widely distributed, found in over 40% of bacteria and 80% of archaea. Among genome-sequenced actinomycetes (particularly Streptomyces spp.), 45.54% possess type I CRISPR-Cas systems. In comparison to widely used CRISPR systems like Cas9 or Cas12a, these endogenous CRISPR-Cas systems have significant advantages, including better compatibility, wide distribution, and ease of operation (since no exogenous Cas gene delivery is needed). Furthermore, type I CRISPR-Cas systems can simultaneously edit and regulate genes by adjusting the crRNA spacer length. Meanwhile, most actinomycetes are recalcitrant to genetic manipulation, hindering the discovery and engineering of natural products (NPs). The endogenous type I CRISPR-Cas systems in actinomycetes may offer a promising alternative to overcome these barriers. This review summarizes the challenges and recent advances in CRISPR-based genome engineering technologies for actinomycetes. It also presents and discusses how to establish and develop genome editing tools based on type I CRISPR-Cas systems in actinomycetes, with the aim of their future application in gene editing and the discovery of NPs in actinomycetes.

CRISPR-Cas9-assisted genome editing in E. coli elevates the frequency of unintended mutations

Cas-assisted lambda Red recombineering techniques have rapidly become a mainstay of bacterial genome editing. Such techniques have been used to construct both individual mutants and massive libraries to assess the effects of genomic changes. We have found that a commonly used Cas9-assisted editing method results in unintended mutations elsewhere in the genome in 26% of edited clones. The unintended mutations are frequently found over 200 kb from the intended edit site and even over 10 kb from potential off-target sites. We attribute the high frequency of unintended mutations to error-prone polymerases expressed in response to dsDNA breaks introduced at the edit site. Most unintended mutations occur in regulatory or coding regions and thus may have phenotypic effects. Our findings highlight the risks associated with genome editing techniques involving dsDNA breaks in E. coli and likely other bacteria and emphasize the importance of sequencing the genomes of edited cells to ensure the absence of unintended mutations.

Retron-mediated multiplex genome editing and continuous evolution in Escherichia coli

While there are several genome editing techniques available, few are suitable for dynamic and simultaneous mutagenesis of arbitrary targeted sequences in prokaryotes. Here, to address these limitations, we present a versatile and multiplex retron-mediated genome editing system (REGES). First, through systematic optimization of REGES, we achieve efficiency of ∼100%, 85 ± 3%, 69 ± 14% and 25 ± 14% for single-, double-, triple- and quadruple-locus genome editing, respectively. In addition, we employ REGES to generate pooled and barcoded variant libraries with degenerate RBS sequences to fine-tune the expression level of endogenous and exogenous genes, such as transcriptional factors to improve ethanol tolerance and biotin biosynthesis. Finally, we demonstrate REGES-mediated continuous in vivo protein evolution, by combining retron, polymerase-mediated base editing and error-prone transcription. By these case studies, we demonstrate REGES as a powerful multiplex genome editing and continuous evolution tool with broad applications in synthetic biology and metabolic engineering.

Enhanced Bioreduction of Radionuclides by Driving Microbial Extracellular Electron Pumping with an Engineered CRISPR Platform

Dissimilatory metal-reducing bacteria (DMRB) with extracellular electron transfer (EET) capability show great potential in bioremediating the subsurface environments contaminated by uranium through bioreduction and precipitation of hexavalent uranium [U(VI)]. However, the low EET efficiency of DMRB remains a bottleneck for their applications. Herein, we develop an engineered CRISPR platform to drive the extracellular electron pumping of Shewanella oneidensis, a representative DMRB species widely present in aquatic environments. The CRISPR platform allows for highly efficient and multiplex genome editing and rapid platform elimination post-editing in S. oneidensis. Enabled by such a platform, a genomic promoter engineering strategy (GPS) for genome-widely engineering the EET-encoding gene network was established. The production of electron conductive Mtr complex, synthesis of electron shuttle flavin, and generation of NADH as intracellular electron carrier are globally optimized and promoted, leading to a significantly enhanced EET ability. Applied to U(VI) bioreduction, the edited strains achieve up to 3.62-fold higher reduction capacity over the control. Our work endows DMRB with an enhanced ability to remediate the radionuclides-contaminated environments and provides a gene editing approach to handle the growing environmental challenges of radionuclide contaminations.

Roles of cation efflux pump in biomineralization of cadmium into quantum dots in Escherichia coli

Cadmium (Cd) is a typical and widely present toxic heavy metals in environments. Biomineralization of Cd ions could alleviate the toxicity and produce valuable products in certain waste streams containing selenite. However, the impact of the intrinsic Cd(II) efflux system on the biotransformation process remains unrevealed. In this work, the significance of the efflux system on Cd biomineralization was evaluated by constructing engineered Escherichia coli strains, including ΔzntA with suppressed Cd(II) efflux system and pYYDT-zntA with strengthened Cd(II) efflux system. Compared to the wild type (WT), 20% more Cd ions were accumulated in ΔzntA and 17% less were observed in pYYDT-zntA in the presence of selenite as determined by inductively coupled plasma atomic emission spectrometer. Through combination with X-ray absorption fine structure analysis, it was discovered that 50% higher production of CdS_xSe_1-x quantum dots (QDs) was achieved in the ΔzntA cells than that in the WT cells. Moreover, the ΔzntA cells exhibited the same viability as the WT cells and the pYYDT-zntA cells because accumulated Cd ions were transformed into biocompatible QDs. In addition, the biosynthesized QDs had a uniform particle size (3.82 ± 0.53 nm) and a long fluorescence lifetime (45.6 ns), which could potentially be utilized for bio-imaging. These results not only elucidate the significance of Cd(II) efflux system in the biotransformation of Cd ions and selenite, but also provide a promising way to recover Cd and Se as valuable products in certain waste streams.

Rapid and highly efficient genomic engineering with a novel iEditing device for programming versatile extracellular electron transfer of electroactive bacteria

The advances in synthetic biology bring exciting new opportunities to reprogram microorganisms with novel functionalities for environmental applications. For real-world applications, a genetic tool that enables genetic engineering in a stably genomic inherited manner is greatly desired. In this work, we design a novel genetic device for rapid and efficient genome engineering based on the intron-encoded homing-endonuclease empowered genome editing (iEditing). The iEditing device enables rapid and efficient genome engineering in Shewanella oneidensis MR-1, the representative strain of the electroactive bacteria group. Moreover, combining with the Red or RecET recombination system, the genome-editing efficiency was greatly improved, up to approximately 100%. Significantly, the iEditing device itself is eliminated simultaneously when genome editing occurs, thereby requiring no follow-up to remove the encoding system. Then, we develop a new extracellular electron transfer (EET) engineering strategy by programming the parallel EET systems to enhance versatile EET. The engineered strains exhibit sufficiently enhanced electron output and pollutant reduction ability. Furthermore, this device has demonstrated its great potential to be extended for genome editing in other important microbes. This work provides a useful and efficient tool for the rapid generation of synthetic microorganisms for various environmental applications.

Phosphate-Suppressed Selenite Biotransformation by Escherichia coli

Biotransformation of selenite to valuable elemental selenium nanoparticles (Se⁰) is a promising avenue to remediate seleniferous environments and simultaneously recover selenium (Se). However, the underlying oxyanion competition and selenite transformation mechanism in prokaryotes are poorly understood. In this work, the impacts of phosphate on selenite uptake and transformation were elucidated with Escherichia coli and its mutant deficient in phosphate transport as model microbial strains. Selenite uptake was inhibited by phosphate in E. coli. Moreover, the transformation of internalized Se was shifted from Se⁰ to toxic organo-Se with elevated phosphate levels, as evidenced by the linear combination fit analysis of the Se K-edge X-ray absorption near-edge structure. Such a phosphate-regulated selenite biotransformation process was mainly assigned to the competitive uptake of phosphate and selenite, which was primarily mediated by a low affinity phosphate transporter (PitA). Under phosphate-deficient conditions, the cells not only produced abundant Se⁰ nanoparticles but also maintained good cell viability. These findings provide new insights into the phosphate-regulated selenite biotransformation by prokaryotes and contribute to the development of new processes for bioremediating Se-contaminated environments, as well as bioassembly of Se⁰.

Developing a Synthetic Biology Toolkit for Comamonas testosteroni, an Emerging Cellular Chassis for Bioremediation

Synthetic biology is rapidly evolving into a new phase that emphasizes real-world applications such as environmental remediation. Recently, Comamonas testosteroni has become a promising chassis for bioremediation due to its natural pollutant-degrading capacity; however, its application is hindered by the lack of fundamental gene expression tools. Here, we present a synthetic biology toolkit that enables rapid creation of functional gene circuits in C. testosteroni. We first built a shuttle system that allows efficient circuit construction in E. coli and necessary phenotypic testing in C. testosteroni. Then, we tested a set of wildtype inducible promoters, and further used a hybrid strategy to create engineered promoters to expand expression strength and dynamics. Additionally, we tested the T7 RNA Polymerase-P_T7 promoter system and reduced its leaky expression through promoter mutation for gene expression. By coupling random library construction with FACS screening, we further developed a synthetic T7 promoter library to confer a wider range of expression strength and dynamic characteristics. This study provides a set of valuable tools to engineer gene circuits in C. testosteroni, facilitating the establishment of the organism as a useful microbial chassis for bioremediation purposes.