CRISPR/Cas9 nuclease cleavage enables marker-free genome editing in Escherichia coli : A sequential study

Development of chromosome-based T7 RNA polymerase and orthogonal T7 promoter circuit in Escherichia coli W3110 as a cell factory

Background

Orthogonal T7 RNA polymerase (T7RNAP) and T7 promoter is a powerful genetic element to mediate protein expression in different cells. Among all, Escherichia coli possess advantages of fast growth rate, easy for culture and comprehensive elements for genetic engineering. As E. coli W3110 owns the benefits of more heat shock proteins and higher tolerance to toxic chemicals, further execution of T7-based system in W3110 as cell factory is a conceivable strategy.

Results

Three novel W3110 strains, i.e., W3110:IL5, W3110::L5 and W3110::pI, were accomplished by chromosome-equipped T7RNAP. At first, the LacZ and T7RNAP with isopropyl-β-D-thiogalactopyranoside (IPTG) induction showed higher expression levels in W3110 derivatives than that in BL21(DE3). The plasmids with and without lacI/lacO repression were used to investigate the protein expression of super-fold green fluorescence protein (sfGFP), carbonic anhydrase (CA) for carbon dioxide uptake and lysine decarboxylase (CadA) to produce a toxic chemical cadaverine (DAP). All the proteins showed better expression in W3110::L5 and W3110::pI, respectively. As a result, the highest cadaverine production of 36.9 g/L, lysine consumption of 43.8 g/L and up to 100% yield were obtained in W3110::pI(−) with plasmid pSU-T7-CadA constitutively.

Conclusion

Effect of IPTG and lacI/lacO regulator has been investigated in three chromosome-based T7RNAP E. coli strains. The newly engineered W3110 strains possessed similar protein expression compared to commercial BL21(DE3). Furthermore, W3110::pI displays higher production of sfGFP, CA and CadA, due to it having the highest sensitivity to IPTG, thus it represents the greatest potential as a cell factory.

Metabolic manipulation through CRISPRi and gene deletion to enhance cadaverine production in Escherichia coli

Due to the limiting natural resources, greenhouse effect and global warming crisis, the bio-based chemicals which are environmentally friendly materials have gradually become urgent and important. Cadaverine, a 1,5-diaminopentane (DAP), is widely used as block chemicals for synthesis of biopolymer, which can be produced from lysine by lysine decarboxylase (EC 4.1.1.18) in Escherichia coli. However, the DAP will be further utilized into by-products through downstream genes of speE, puuA, speG and ygjG, which decrease the amount of product. In this study, two approaches including Lambda-Red system for gene knockout, and clustered regularly interspaced short palindromic repeats interference (CRISPRi) for gene knockdown; are explored to manipulate the metabolic flux among 26 genetic E. coli. As a result, CadA driven by inducible T7 promoter accumulated more DAP from CRISPRi targeted on single-gene repressive strains such as BT7AiE, BT7AiP, BT7AiG and BT7AiY. The highest DAP titer and productivity was obtained to 38 g/L and 2.67 g/L/h in BT7AiY (repression of ygjG). We also investigated the co-factor pyridoxal 5'-phosphate (PLP) effect on lysine consumption and DAP production from different E. coli derivatives. In contrast to CRISPRi-mediated strains, 4 genes knockout strain (BT7AdEPGY) deal with 98% lysine consumption and achieved 37.45 g/L DAP and 3.17 g/L/h DAP productivity. The metabolic regulation by CRISPRi is a simple strategy and the results are consistent with gene knockout to manipulate the pathway for DAP production.

Serine integrase recombinational engineering (SIRE): A versatile toolbox for genome editing

Chromosomal integration of biosynthetic pathways for the biotechnological production of high-value chemicals is a necessity to develop industrial strains with a high long-term stability and a low production variability. However, the introduction of multiple transcription units into the microbial genome remains a difficult task. Despite recent advances, current methodologies are either laborious or efficiencies highly fluctuate depending on the length and the type of the construct. Here we present serine integrase recombinational engineering (SIRE), a novel methodology which combines the ease of recombinase-mediated cassette exchange (RMCE) with the selectivity of orthogonal att sites of the PhiC31 integrase. As a proof of concept, this toolbox is developed for Escherichia coli. Using SIRE we were able to introduce a 10.3 kb biosynthetic gene cluster on different locations throughout the genome with an efficiency of 100% for the integrating step and without the need for selection markers on the knock-in cassette. Next to integrating large fragments, the option for multitargeting, for deleting operons, as well as for performing in vivo assemblies further expand and proof the versatility of the SIRE toolbox for E. coli. Finally, the serine integrase PhiC31 was also applied in the yeast Saccharomyces cerevisiae as a marker recovery tool, indicating the potential and portability of this toolbox.

CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art

In recent years, a variety of genetic tools have been developed and applied to various filamentous fungi, which are widely applied in agriculture and the food industry. However, the low efficiency of gene targeting has for many years hampered studies on functional genomics in this important group of microorganisms. The emergence of CRISPR/Cas9 genome-editing technology has sparked a revolution in genetic research due to its high efficiency, versatility, and easy operation and opened the door for the discovery and exploitation of many new natural products. Although the application of the CRISPR/Cas9 system in filamentous fungi is still in its infancy compared to its common use in E. coli, yeasts, and mammals, the deep development of this system will certainly drive the exploitation of fungal diversity. In this review, we summarize the research progress on CRISPR/Cas9 systems in filamentous fungi and finally highlight further prospects in this area.