CRISPR/Cas Technologies and Their Applications in Escherichia coli

Increasing the efficiency of gene editing with CRISPR-Cas9 via concurrent expression of the Beta protein

Escherichia coli has emerged as an important host for the production of biopharmaceuticals or other industrially relevant molecules. An efficient gene editing tool is indispensable for ensuring high production levels and optimal release of target products. However, in Escherichia coli, the CRISPR-Cas9 system has been shown to achieve gene modifications with relatively low frequency. Large-scale PCR screening is required, hindering the identification of positive clones. The beta protein, which weakly binds to single-stranded DNA but tightly associates with complementary strand annealing products, offers a promising solution to this issue. In the present study, we describe a targeted and continuous gene editing strategy for the Escherichia coli genome. This strategy involves the coexpression of the beta protein alongside the CRISPR-Cas9 system, enabling a variety of genome modifications such as gene deletion and insertion with an efficiency exceeding 80 %. The integrity of beta proteins is essential for the CRISPR-Cas9/Beta-based gene editing system. In this work, the deletion of either the N- or C-terminal domain significantly impaired system efficiency. Overall, our findings established the CRISPR-Cas9/Beta system as a suitable gene editing tool for various applications in Escherichia coli.

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.

Vaccines to Control Salmonella in Poultry

This review is focused on describing and analyzing means by which Salmonella enterica serotype strains have been genetically modified with the purpose of developing safe, efficacious vaccines to present Salmonella-induced disease in poultry and to prevent Salmonella colonization of poultry to reduce transmission through the food chain in and on eggs and poultry meat. Emphasis is on use of recently developed means to generate defined deletion mutations to eliminate genetic sequences conferring antimicrobial resistance or residual elements that might lead to genetic instability. Problems associated with prior means to develop vaccines are discussed with presentation of various means by which these problems have been lessened, if not eliminated. Practical considerations are also discussed in hope of facilitating means to move lab-proven successful vaccination procedures and vaccine candidates to the marketplace to benefit the poultry industry.

Multiplex gene knockout raises Ala-Gln production by Escherichia coli expressing amino acid ester acyltransferase

L-Alanyl-L-Glutamine (Ala-Gln) is a common parenteral nutritional supplement. In our previous study, the recombinant whole-cell catalyst Escherichia coli BL21(DE3) overexpressing α-amino acid ester acyltransferase (BPA) to produce Ala-Gln has high activity and has been applied to large-scale production experiments. However, the degradation of Ala-Gln is detected under prolonged incubation, and endogenous broad-spectrum dipeptidase may be the primary cause. In this study, a CRISPR-Cas9 method was used to target pepA, pepB, pepD, pepN, dpp, and dtp to knock out one or more target genes. The deletion combination was optimized, and a triple knockout strain BL21(DE3)-ΔpepADN was constructed. The degradation performance of the knockout chassis was measured, and the results showed that the degradation rate of Ala-Gln was alleviated by 48% compared with the control. On this basis, B_pADNPA (BPA-ΔpepADN) was built, and the production of Ala-Gln was 129% of the BPA's accumulation, proving that the ΔpepADN knockout conducive to the accumulation of dipeptide. This study will push forward the industrialization process of Ala-Gln production by whole-cell catalyst Escherichia coli expressing α-amino acid ester acyltransferase. KEY POINTS: • Endogenous dipeptidase knockout alleviates the degradation of Ala-Gln by the chassis • The balanced gene knockout combination is pepA, pepD, and pepN • The accumulation of Ala-Gln with B_pADNPA was 129% of the control.

Effect of chromosomal integration on catalytic performance of a multi-component P450 system in Escherichia coli

Cytochromes P450 are useful biocatalysts in synthetic chemistry and important bio-bricks in synthetic biology. Almost all bacterial P450s require separate redox partners for their activity, which are often expressed in recombinant Escherichia coli using multiple plasmids. However, the application of CRISPR/Cas recombineering facilitated chromosomal integration of heterologous genes which enables more stable and tunable expression of multi-component P450 systems for whole-cell biotransformations. Herein, we compared three E. coli strains W3110, JM109, and BL21(DE3) harboring three heterologous genes encoding a P450 and two redox partners either on plasmids or after chromosomal integration in two genomic loci. Both loci proved to be reliable and comparable for the model regio- and stereoselective two-step oxidation of (S)-ketamine. Furthermore, the CRISPR/Cas-assisted integration of the T7 RNA polymerase gene enabled an easy extension of T7 expression strains. Higher titers of soluble active P450 were achieved in E. coli harboring a single chromosomal copy of the P450 gene compared to E. coli carrying a medium copy pET plasmid. In addition, improved expression of both redox partners after chromosomal integration resulted in up to 80% higher (S)-ketamine conversion and more than fourfold increase in total turnover numbers.

Bioinformatic survey of CRISPR loci across 15 Serratia species

The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR‐associated proteins (CRISPR–Cas) system of prokaryotes is an adaptative immune defense mechanism to protect themselves from invading genetic elements (e.g., phages and plasmids). Studies that describe the genetic organization of these prokaryotic systems have mainly reported on the Enterobacteriaceae family (now reorganized within the order of Enterobacterales). For some genera, data on CRISPR–Cas systems remain poor, as in the case of Serratia (now part of the Yersiniaceae family) where data are limited to a few genomes of the species marcescens. This study describes the detection, in silico, of CRISPR loci in 146 Serratia complete genomes and 336 high‐quality assemblies available for the species ficaria, fonticola, grimesii, inhibens, liquefaciens, marcescens, nematodiphila, odorifera, oryzae, plymuthica, proteomaculans, quinivorans, rubidaea, symbiotica, and ureilytica. Apart from subtypes I‐E and I‐F1 which had previously been identified in marcescens, we report that of I‐C and the I‐E unique locus 1, I‐E*, and I‐F1 unique locus 1. Analysis of the genomic contexts for CRISPR loci revealed mdtN‐phnP as the region mostly shared (grimesii, inhibens, marcescens, nematodiphila, plymuthica, rubidaea, and Serratia sp.). Three new contexts detected in genomes of rubidaea and fonticola (puu genes‐mnmA) and rubidaea (osmE‐soxG and ampC‐yebZ) were also found. The plasmid and/or phage origin of spacers was also established.

Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research

Herpesviruses are major pathogens that infect humans and animals. Manipulating the large genome is critical for exploring the function of specific genes and studying the pathogenesis of herpesviruses and developing novel anti-viral vaccines and therapeutics. Bacterial artificial chromosome (BAC) technology significantly advanced the capacity of herpesviruses researchers to manipulate the virus genomes. In the past years, advancements in BAC-based genome manipulating and screening strategies of recombinant BACs have been achieved, which has promoted the study of the herpes virus. This review summarizes the advances in BAC-based gene editing technology and selection strategies. The merits and drawbacks of BAC-based herpesvirus genome editing methods and the application of BAC-based genome manipulation in viral research are also discussed. This review provides references relevant for researchers in selecting gene editing methods in herpes virus research. Despite the achievements in the genome manipulation of the herpes viruses, the efficiency of BAC-based genome manipulation is still not satisfactory. This review also highlights the need for developing more efficient genome-manipulating methods for herpes viruses.

Striving for sustainable biosynthesis: discovery, diversification, and production of antimicrobial drugs in Escherichia coli

New antimicrobials need to be discovered to fight the advance of multidrug-resistant pathogens. A promising approach is the screening for antimicrobial agents naturally produced by living organisms. As an alternative to studying the native producer, it is possible to use genetically tractable microbes as heterologous hosts to aid the discovery process, facilitate product diversification through genetic engineering, and ultimately enable environmentally friendly production. In this mini-review, we summarize the literature from 2017 to 2022 on the application of Escherichia coli and E. coli-based platforms as versatile and powerful systems for the discovery, characterization, and sustainable production of antimicrobials. We highlight recent developments in high-throughput screening methods and genetic engineering approaches that build on the strengths of E. coli as an expression host and that led to the production of antimicrobial compounds. In the last section, we briefly discuss new techniques that have not been applied to discover or engineer antimicrobials yet, but that may be useful for this application in the future.

Past, Present, and Future of Genome Modification in Escherichia coli

Escherichia coli K-12 is one of the most well-studied species of bacteria. This species, however, is much more difficult to modify by homologous recombination (HR) than other model microorganisms. Research on HR in E. coli has led to a better understanding of the molecular mechanisms of HR, resulting in technical improvements and rapid progress in genome research, and allowing whole-genome mutagenesis and large-scale genome modifications. Developments using λ Red (exo, bet, and gam) and CRISPR-Cas have made E. coli as amenable to genome modification as other model microorganisms, such as Saccharomyces cerevisiae and Bacillus subtilis. This review describes the history of recombination research in E. coli, as well as improvements in techniques for genome modification by HR. This review also describes the results of large-scale genome modification of E. coli using these technologies, including DNA synthesis and assembly. In addition, this article reviews recent advances in genome modification, considers future directions, and describes problems associated with the creation of cells by design.