Table 2.
Applications of systems biology tools on improving strains tolerance.
| Strategy | Stress | Strains | Omics tools | Tolerance-related genes/enzymes | Reference |
|---|---|---|---|---|---|
| Identifying tolerance-related genes from strains under different stresses | furfural | Clostridium beijerinckii | transcriptomics | two enzymes encoded by Cbei_3974 and Cbei_3904 belonging to aldo/keto reductase (AKR) and short-chain dehydrogenase/reductase (SDR families) | [54] |
| phenolic aldehydes | Z. mobilis | transcriptomics | genes encoding key reductases: ZMO1696, ZMO1116, and ZMO1885 | [55] | |
| p-benzoq-uinone | Z. mobilis | transcriptomics | Zinc-binding alcohol dehydrogenase ZMO1696, NAD(P)H dehydrogenase ZMO1949, short-chain dehydrogenase/reductase ZMO1576, aldo-keto reductase ZMO1984, fatty acid hydroxylase ZMO1399 | [56] | |
| formate, acetate | S. cerevisiae | transcriptomics | transcriptional/translational machinery-related genes: RTC3 and ANB1 | [57] | |
| butanol | Cyanobacteria | transcriptomics | the small heat shock protein HspA | [58] | |
| isopen-tanol | E. coli | transcriptomics | genes related to oxidative stress response (fpr), general stress response (metR, yqhD, and gidB), heat shock-related response (ibpA), and transport (mdlB) | [59] | |
| butanol | Chlamydomonas reinhardti | proteomics | Cre.770 peroxidase | [60] | |
| limonene | Y. lipolytica | transcriptomics | YALI0F19492g gene encoding a 169 amino acid protein YALI0F19492p | [61] | |
| acetic acid | S. cerevisiae | metabolomics | key genes of pentose phosphate pathway: transketolase gene TKL1 and transaldolase gene TAL1 | [62] | |
| Identifying tolerance-related genes from mutant strains | ethanol | Cyanobacterium synechocystis | metabolomics | two transcriptional regulators (TR) and one eukaryotic-like protein phosphatases (PP) | [63] |
| 1-butanol | S. cerevisiae | metabolomics | genes related to accumulation of threonine and reduction of citric acid | [64] | |
| ethanol | S. cerevisiae | metabolomics | LEU4 and LEU9 genes (related to accumulation of valine) or INM1 and INM2 genes (related to reduction of inositol) | [65] | |
| butanol | C. acetobutylicum | proteomics | chaperones and solvent formation related genes | [66] | |
| sabinene | E. coli | transcriptomics | ybcK gene of the DLP12 family, inner membrane protein gene ygiZ, methylmalonyl-CoA mutase gene scpA | [67] | |
| ferulic acid | Y. lipolytica | transcriptomics | YALI0_E25201g, YALI0_B18854g, YALI0_F16731g | [68] | |
| salt | Z. mobilis | metabolomics | gene ZZ6_1149 encoding carboxyl-terminal protease | [69] | |
| methanol | O. polymorpha | genomics | gene LPL1 (encoding a putative lipase) and gene IZH3 (encoding a membrane protein related to zinc metabolism) | [70] |