Table 3.
Cellular engineering strategies used to enhance the cell factory productivities
| Strain | Product | Description | Outcome | Refs. |
|---|---|---|---|---|
| Cellular tolerance | ||||
| E. coli | Amorphadiene and kaurene | Overexpression of native AcrAB-TolC, MdtEF-TolC and the exogenous pump mexAB-OprM | 118% and 104% improvement, respectively | Wang et al. (2013) |
| E. coli | Amorphadiene | Overexpression of lipopolysaccharide transport system | N. A | Zhang et al. (2016) |
| E. coli | α-Pinene | Overexpression of AcrB, AcrAB, and TtgB | 1.9-fold | Niu et al. (2018) |
| E. coli | Sabinene | Overexpression of the genes scpA, ygiZ and ybcK via ALE | 191.76 mg/L | Wu et al. (2020a) |
| E. coli | Isoprenol | Genome-wide knockout was employed to identify enzymes associated with isoprenol transport | NA | Wang et al. (2015) |
| E. coli | β-carotene | Development of an artificial membrane vesicle transport system | 24-fold improvement | Wu et al. (2019) |
| E. coli | β-carotene | Engineering membrane bending proteins and membrane synthesis pathway | 44.2 mg/g DCW | Wu et al. (2017) |
| E. coli | Lycopene | Membrane engineering via exogenous of and endogenous expression of almgs, plsB, plsC and dgka, respectively | 36.4 mg/g DCW | Wu et al. (2018) |
| E. coli | Rainbow colorant | Membrane engineering via inner- and outer-membrane vesicle formation and cell morphology engineering | Varying | Yang et al. (2021) |
| E. coli | Squalene | Membrane engineering via membrane proteins overexpression | 612 mg/L | Meng et al. (2020b) |
| S. cerevisiae | Astaxanthin | Atmospheric and room-temperature plasma as well as UV for strain improvement | 404.78 mg/L | Jiang et al. (2020a) |
| S. cerevisiae | Crocetin | Development of a temperature-responsive strain coupled with chromosomal integration of pathway genes | 139.64 ± 2.24 µg/g DCW | Liu et al. (2020e) |
| S. cerevisiae | β-carotene | Comparative proteomic and transcriptional analysis of ABC transporters | 4.04-fold (secretion), 1.33-fold (intracellular) | Bu et al. (2020) |
| S. cerevisiae | Alkane | Exogenous expression of ABC transporters from Y. lipolytica | 80-fold improvement | Chen et al. (2013a) |
| S. cerevisiae | Triterpenoids | Deletion of phosphatidic acid phosphatase (PAH1) for endoplasmic reticulum expansion | 6-, 8-, 16-folds | Arendt et al. (2017) |
| S. cerevisiae | Geraniol | Immobilization of MVA pathway enzymes on yeast surface for in vitro fermentation | 7.55 mg/L | Luo et al. (2021) |
| Y. lipolytica | α-, β-, γ-bisabolene | Exogenously expressing AcrB of the AcrAB-TolC system from E. coli and ABC-G1 from Grosmania clavigera under the constitutive promoter | 2.7-, 8.5-, 1.2-fold, respectively | Zhao et al. (2021) |
| Y. lipolytica | β-carotene | Morphological engineering by deletion of CLA4 and MHY1 genes to convert mycelium form to the yeast form in addition with chromosomal integration | 139% improvement | Liu et al. (2021c) |
| Phaffia rhodozyma | Astaxanthin | Combined atmospheric and room-temperature and UV mutagenesis | 88.57 mg/L | (Zhuang et al. 2020) |
| Phaffia rhodozyma | Carotenoid | Application of magnetic field for improved cellular concentration | 1146.39 ± 26.18 µg/L | (Silva et al. 2020) |
| Chromosomal integration | ||||
| E. coli | Astaxanthin | A plasmid-free strain | 1.4 mg/g CDW | Lemuth et al. (2011) |
| E. coli | β-carotene | Integration of pathway genes | 2.0 g/L | Li et al. (2015) |
| E. coli | β-carotene | Integration of two modules of MVA into the chromosome | 26% improvement | Ye et al. (2016) |
| E. coli | Salvianic acid A | A plasmid-free strain | 5.6 g/L | Zhou et al. (2017) |
| E. coli | Mevalonate | Integration of atoB, mvaS, and mvaE at adhE and ldhA loci | 30 g/L | Wang et al. (2016) |
| E. coli | Bisabolene | Integration of sucrose utilizing operon and MVA pathway | Fivefold improvement | Alonso-Gutierrez et al. (2018) |
| S. cerevisiae | Geraniol | Integration of truncated geraniol synthase | 236.34 mg/L | Jiang et al. (2017) |
| S. cerevisiae | Abscisic acid | Integration of the abscisic gene cluster coupled with plasmid expression | 4.1-fold | Otto et al. (2019) |
| S. cerevisiae | Zerumbone | A multicopy integration of pathway genes | 40 mg/L | Zhang et al. (2018a) |
| S. cerevisiae | Lycopene | Chromosomal integration of engineered crtEB | 41.8 mg/g DCW | Hong et al. (2019) |
| S. cerevisiae | β-carotene | Chromosomal integration of β-carotene biosynthetic pathway genes from Xanthophylomyces dendrorhous | 46.5 mg/g DCW | Fathi et al. (2021) |
| S. cerevisiae | 8-hydroxygeraniol | Development of a plasmid-free strain | 227 mg/L | Yee et al. (2019) |
| S. cerevisiae | Glycyrrhetinic acid and 11-oxo-β-amyrin | Chromosomal integration of glycyrrhetinic acid biosynthetic pathway in two representative strains, haploid and diploid | 18.9 ± 2.0 mg/L and 108.1 ± 4.6 mg/L, respectively | Zhu et al. (2018) |
| S. cerevisiae | (−)-eremophilene | Genomic integration of an Ocimum sanctum sesquiterpene synthase | 34.6 g/L | Deng et al. (2022) |
| Y. lipolytica | β-carotene | Integration of codon-optimized carRA and carB coupled with pathway optimization | 1.7 g/L | Liu et al. (2021b) |
| Y. lipolytica | β-carotene | Multiple chromosomal integration of pathway enzymes under strong promoters | 4 g/L | Gao et al. (2017) |
| Y. lipolytica | Isoprene | Genomic integration of codon-optimized isoprene synthase from Pueraria montana coupled with overexpression of pathway enzymes | ~ 500 µg/L | Shaikh and Odaneth (2021) |
| Bacillus subtilis | Amorphadiene | Chromosomal integration of a fused amorphadiene synthase and green fluorescent protein | 416 ± 15 mg/L | Pramastya et al. (2021) |
| Modularization | ||||
| E. coli | Isoprene | An inter- and intra-module of pathway | 4.7-fold increment | Lv et al. (2016a) |
| E. coli | Taxadiene-5α-ol and Taxadiene | A multivariate-modular pathway | 2400- and 15,000-fold increment, respectively | Ajikumar et al. (2010) |
| E. coli | Pinene | Modular co-culture of MVA pathway and a TIGR-mediated gene cluster | 166.5 mg/L | Niu et al. (2018) |
| S. cerevisiae | Squalene and protopanaxadiol | Engineering of the endoplasmic reticulum as a special compartment triggered a global rewiring of metabolic pathway | 71- and 8-fold, respectively | Kim et al. (2019) |
| S. cerevisiae | Isoprene | Dual regulation of the mitochondrial and endoplasmic reticulum compartments | 2527 mg/L | Lv et al. (2016b) |
| S. cerevisiae | Ginsenoside compound K | Localization of pathway enzymes and metabolic intermediates to lipid droplets | 5 g/L | Shi et al. (2021b) |
| S. cerevisiae | Squalene | Peroxisomal and cytoplasmic engineering | 11 g/L | Liu et al. (2020a) |
| S. cerevisiae | Squalene | A combinatorial engineering of both cytoplasm and mitochondria to alleviate MVA pathway-related toxicity | 21.1 g/L | Zhu et al. (2021) |
| Y. lipolytica | β-ionone | Enhancing cytosolic acetyl-CoA and MVA flux supply via modular engineering and fed-batch fermentation | 0.98 g/L | Lu et al. (2020) |
| Y. lipolytica | Astaxanthin | Subcellular organelle compartmentalization of fused β-carotene ketolase and hydroxylase | 858 mg/L | Ma et al. (2021) |
| Pichia pastoris X33 | α-farnesene | Peroxisomal and cytoplasmic engineering | 2.56 ± 0.04 g/L | Liu et al. (2021a) |
| Bacillus subtilis | Amorphadiene | Modularization of amorphadiene biosynthesis pathway including terpene synthase module, branch pathway module and central metabolic pathway module | 116 mg/L | Song et al. (2021) |