Table 1.
Literature data on anaerobic growth of metabolically engineered, xylose-isomerase-based S. cerevisiae strains. The table summarises sets of targeted genetic modifications, aerobic-specific growth rates on d-xylose and any additional optimisation by laboratory evolution or mutagenesis required for anaerobic growth on d-xylose. NIA = no information available; * specific growth rate estimated from exponential increase of CO2 concentration in bioreactor off gas.
| Strain background | Strain | XI gene | Native genes overexpressed | Other targeted modifications | Aerobic growth rate (h−1) | Anaerobic growth | Reference |
|---|---|---|---|---|---|---|---|
| CEN.PK | RWB202 | Piromyces XylA (2 micron plasmid) | none | No | 0.005 | After extensive aerobic, oxygen-limited and anaerobic selection (μ = 0.03 h−1) | (Kuyper et al.2003) |
| CEN.PK | RWB217 | Piromyces XylA (2 micron plasmid) | RKI1, RPE1, TAL1, TKL1 (all pTPI1), XKS1 (pADH1) | gre3Δ | 0.22 | Anaerobic growth after ca. 35 h when inoculated at low cell densities (0.02 g biomass L−1, μ = 0.09 h−1). Immediate anaerobic growth when inoculated at high biomass concentration (0.2 g biomass L−1, μ = 0.09 h−1). | (Kuyper et al.2005), This study |
| CEN.PK | YEp-opt.XI-Clos-K | Clostridium phytofermentans, codon optimised | XKS1, RKI1, RPE1, TAL1, TKL1 | GAL2 overexpression | 0.057 | No | (Brat et al.2009) |
| CEN.PK | YEp-opt.XI-Piro | Piromyces XylA, codon-optimised | XKS1, RKI1, RPE1, TAL1, TKL1 | GAL2 overexpression | 0.056 | No | (Brat et al.2009) |
| BarraGrande (Industrial) | BWY10Xyl | Clostridium phytofermentans, codon optimised | NIA | NIA | 0.04 | Serial aerobic shake flask cultures (6) on d-xylose until anaerobic xylose consumption observed upon aerobic biomass production. | (Brat et al.2009) |
| CEN.PK | IMX696 | Piromyces XylA, codon-optimised | XKS1, RKI1, RPE1, TAL1, TKL1, NQM1, TKL2 | gre3Δ | 0.21 | After 12-day anaerobic adaptation phase (mutations in PMR1) | (Verhoeven et al.2017) |
| Ethanol Red (diploid) | HDY.GUF5 | Clostridium phytofermentans, codon-optimised | XKS1, RKI1, RPE1, TAL1, TKL1, TKL2, NQM1 | HXT7, S. stipitis AraA, B. licheniformis AraA, E. coli AraD, AraB | NIA | After extensive mutagenesis-, genome-shuffling and oxygen-limited selection experiments (no specific growth rates reported) | (Demeke et al.2013) |
| Natural isolate (banana) YB-210/GLBRCY0 | Y22–3 (haploid spore) | Clostridium phytofermentans XylA (ScTDH3p) | - | S. cerevisiae TAL1, S. stipitis XYL3 | NIA | No initial anaerobic growth observed. Aerobic selection in glucose–xylose media (34 transfers), anaerobic selection on same media (14 transfers). Evolved strain showed anaerobic growth in YPX medium (mutation in GRE3 obtained). | (Parreiras et al.2014) |
| BF264–15Dau (Sun et al.1989) | H131-A3 | Piromyces XylA, codon-optimised (2 micron plasmid) | RPE1, RKI1, TKL1 | P. stipitis XKS1& TAL1 | 0.031 ± 0.022 | Aerobic cultivation in anaerobic sequential batch reactors (SBRs) on SMX (2% xylose; ca. 70 transfers), transfer to microaerobic SBRs (YNBX, 60 transfers), transfer to anaerobic SBRs (YNBX, 60 transfers), transfer to anaerobic chemostat with increasing dilution rate over time for ca. 60 generation (YNBX, d = 0.02 h−1 to 0.12 h−1), 20 more generations with YNBX with 10% xylose until dilution rate of 0.148 h−1. | (Zhou et al.2012) |
| CEN.PK | TMB3361 | Piromyces XylA (2 micron plasmid) | TAL1, TKL1, RPE1, RKI1, XKS1 (all pPGK1) | E. coli XK (xylB), gre3Δ | 0.089 ± 0.002 | Anaerobic fermentations inoculated with very high cell densities (5 g L−1 CDW) resulting in partial conversion of the supplied xylose to ethanol (without an adaptation time) but without measurable growth (due to high initial cell densities). | (Parachin et al.2011) |
| CEN.PK | YRH631 (naive), YRH1114 (evolved) | Prevotella ruminicola TC2–24 XI (codon-optimised) | XKS1 | No | 0.06 (naive) 0.23 (evolved) | Six transfers in microaerobic conditions (μ unknown). | (Hector et al.2013) |
| INVSc1 (Invitrogen, USA) | INVSc1/pRS406XKS/pILSUT1/pWOXYLA (XKS, Sut1, XylA) | Orpinomyces xylA (2 μm plasmid) | XKS1 | P. stipitis SUT1 over-expression | NIA | CO2-flushed bottles inoculated with 5 g biomass L−1 showed consumption of 15.5 g L−1 xylose from a total of 50 g L−1 within 140 h. | (Madhavan et al.2009) |
| CEN.PK | TMB3066 | Piromyces XylA (2 μm plasmid) | TAL1, TKL1, RPE1, RKI1, XKS1 (all pPGK1 | gre3Δ | 0.02 | Anaerobic cultures resulting in partial conversion of the supplied xylose to ethanol (16.8 g of 50 g L−1 within 100 h, without an adaptation time) at high biomass density, no anaerobic growth reported. | (Karhumaa et al.2007) |
| CEN.PK | IMU078 | Piromyces XylA (2 μm plasmid) | TAL1, TKL1, RPE1, RKI1, NQM1, TKL2, XKS1 | gre3Δ | NIA | Anaerobic growth after ca. 7–8 d when inoculated at low biomass concentration (0.02 g biomass L−1), μ = ca. 0.09 h−1*. Immediate anaerobic growth when (i) inoculated at high biomass density (0.2 g biomass L−1, μ = 0.05 h−1*), (ii) upon supplementation with 0.1% CO2 in N2 used from sparging of bioreactors (μ = 0.05 h−1) or (iii) when l-aspartate is supplied as nitrogen source (μ = 0.05 h−1). | This study |
| CEN.PK | IMU079 | Piromyces XylA (2 μm plasmid) | TAL1, TKL1, RPE1, RKI1, XKS1 | gre3Δ | NIA | Anaerobic growth after ca. 40 h when inoculated at low cell densities (0.02 g biomass L−1, μ = 0.08 h−1). Immediate anaerobic growth when inoculated at high biomass concentration (0.2 g biomass L−1, μ = 0.07 h−1*). | This study |
| PE-2 | LVY27 LVY34.4 (evolved) LVY41.5 (evolved) | Orpinomyces sp. xylA (codon-optimised; flanked with δ LTR sequences for high copy integration) | XKS1*2, TAL1, RKI1, TKL1, RPE1 | gre3Δ | Very slow growth with 1 copy of XylA. Evolved: μ = 0.23 and 0.129 h−1 | No anaerobic growth upon integration of one copy of xylA. Selection in semi-anaerobic conditions with 5 g L−1 glucose and 40 g L−1 xylose (12 transfers). Faster growth upon selection for increased xylA copy numbers, resulting in 36 and 26 copies. | (dos Santos et al.2016) |
| BY4741 | BY4741-S2A3K | Mutated Piromyces xylA3* (2 μm plasmid) | XKS1 | gre3Δ, S. stipitis TAL1 over-expression | 0.061 h−1 | Xylose fermentation possible in high cell density, micro-aerobic conditions (no growth rates available). | (Lee et al.2012) |
| BY4741 | SXA-R2P | Mutated Piromyces xylA3* (2 copies; Lee et al.2012) | XKS1 | gre3Δ, pho13 Δ, S. stipitis TAL1 over-expression (2 copies) | 0.105 h−1 and 0.128 h−1 (evolved) | Naïve strain slowly consumed xylose in microaerobic conditions. Adaptive evolution in closed falcon tubes with media containing 20 g L−1 xylose (12 transfers). Evolved strain was capable of fast xylose consumption when inoculated at high biomass concentration in non-purged anaerobic bioreactors where initial oxygen was consumed within 12 h (no growth rates available). | (Lee et al.2014) |
| CEN.PK | BSPC095 | Piromyces xylA (2 μm plasmid) | TAL1, TKL1, RPE1, RKI1, XKS1 | gre3Δ, cox4Δ, | No initial aerobic growth | Weak aerobic growth observed in liquid xylose medium upon 10 days of aerobic incubation. Serial transfers of aerobic cultures with xylose during 1000 h resulted in aerobic growth rate of, μ = 0.11 h−1. | (Shen et al.2012) |