Highlights d A genetic circuit designed to functionally select anti-CRISPR genes from metagenomes d Four protein families, AcrIIA7-10, that inhibit Cas9 in vivo and in vitro were identified d AcrIIA7-10 are widely distributed across seven bacterial phyla d Dissemination patterns of AcrIIA7-10 suggest interphylum horizontal gene transfer

Butyrate pathway was constructed in recombinant Escherichia coli using the genes from Clostridium acetobutylicum and Treponema denticola. However, the pathway constructed from exogenous enzymes did not efficiently convert carbon flux to butyrate. Three steps of the productivity enhancement were attempted in this study. First, pathway engineering to delete metabolic pathways to by-products successfully improved the butyrate production. Second, synthetic scaffold protein that spatially co-localizes enzymes was introduced to improve the efficiency of the heterologous pathway enzymes, resulting in threefold improvement in butyrate production. Finally, further optimizations of inducer concentrations and pH adjustment were tried. The final titer of butyrate was 4.3 and 7.2 g/L under batch and fed-batch cultivation, respectively. This study demonstrated the importance of synthetic scaffold protein as a useful tool for optimization of heterologous butyrate pathway in E. coli.

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Genome editing using CRISPR/Cas9 was successfully demonstrated in Esherichia coli to effectively produce n-butanol in a defined medium under microaerobic condition. The butanol synthetic pathway genes including those encoding oxygen-tolerant alcohol dehydrogenase were overexpressed in metabolically engineered E. coli, resulting in 0.82 g/L butanol production. To increase butanol production, carbon flux from acetyl-CoA to citric acid cycle should be redirected to acetoacetyl-CoA. For this purpose, the 5'-untranslated region sequence of gltA encoding citrate synthase was designed using an expression prediction program, UTR designer, and modified using the CRISPR/Cas9 genome editing method to reduce its expression level. E. coli strains with decreased citrate synthase expression produced more butanol and the citrate synthase activity was correlated with butanol production. These results demonstrate that redistributing carbon flux using genome editing is an efficient engineering tool for metabolite overproduction.

Glucosamine and its derivatives are utilized in the food and biomedical industries. However, current production relies on hydrolysis of natural sources, making it difficult to maintain quality and eliminate allergenic risk. Therefore, microbial production with aid of metabolic engineering is required. We previously demonstrated production of N-acetylglucosamine (GlcNAc) in Saccharomyces cerevisiae by overexpressing an allosteric regulation-free Gfa1p mutant and the haloacid dehalogenase-like phosphatase YqaB. In this study, we further improved GlcNAc production by reducing glycolytic flux. Eukaryotic phosphofructokinase 1 (PFK-1) is allosterically activated by fructose 2,6-bisphosphate (F26BP). Disruption of PFK-2, which synthesizes F26BP, resulted in a slight decrease of GlcNAc production and no significant change of glucose consumption and ethanol production. However, when galactose was used as a sole carbon source to the strain without PFK-2, GlcNAc production was significantly increased and ethanol production was reduced, suggesting that further reduction of glycolytic flux can be used to further improve GlcNAc production. The methodology used in this study can be applied to improve production of carbohydrate derivatives in S. cerevisiae. Biotechnol. Bioeng. Biotechnol. Bioeng. 2016;113: 2524-2528. © 2016 Wiley Periodicals, Inc.

S. cerevisiae sake K6 was the firstly isolated industrial strain to overproduce S-adenosyl-L-methionine (SAM). Although the strain has advantages over other strains, such as GRAS (generally recognized as safe) property, the S. cerevisiae K6 has not been further developed with DNA recombinant technology due to the lack of a proper genetic marker. In this study, UV mutagenesis was conducted with S. cerevisiae sake K6. With the method, a mutant of sake yeast with leucine auxotroph, K6-1, was isolated. The mutant showed comparable growth rate and SAM productivity with its wild type. Using the auxotroph as a genetic marker, a SAM synthase in S. cerevisiae, SAM2, was overexpressed in the mutant strain. This recombinant DNA technology successfully increased SAM productivity in sake yeast.

Engineered microbes often suffer from reduced fitness resulting from metabolic burden and various stresses. The productive lifetime of a bioreactor with engineered microbes is therefore susceptible to the rise of nonproductive mutants with better fitness. Synthetic addiction is emerging as a concept to artificially couple the growth rate of the microbe to production to tackle this problem. However, only a few successful cases of synthetic addiction systems have been reported to date. To understand the limitations and design constraints in long-term cultivations, we designed and studied conditional synthetic addiction circuits in Saccharomyces cerevisiae. This allowed us to probe a range of selective pressure strengths and identify the optimal balance between circuit stability and production-to-growth coupling. In the optimal balance, the productive lifetime was greatly extended compared with suboptimal circuit tuning. With a too-high or -low pressure, we found that production declines mainly through homologous recombination. These principles of trade-off in the design of synthetic addition systems should lead to the better control of bioprocess performance.