scholarly journals A Single Chromosome Strain of S. cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance

2020 ◽  
Author(s):  
Tyler W. Doughty ◽  
Rosemary Yu ◽  
Lucy Fang-I Chao ◽  
Zhongjun Qin ◽  
Verena Siewers ◽  
...  
Keyword(s):  
Carbon Source ◽  
Reference Strain ◽  
Biomass Concentration ◽  
Biomass Accumulation ◽  
Ethanol Metabolism ◽  
Large Chromosome ◽  
Lag Phase ◽  
Diauxic Shift ◽  
Single Chromosome ◽  
Genome Arrangement

AbstractThis study characterized the growth, metabolism, and transcriptional profile of a S. cerevisiae strain with a single large chromosome that was constructed via successive chromosomal fusions. The single chromosome strain exhibited a longer lag phase, increased doubling time, and lower final biomass concentration compared with a wildtype strain when grown on YPD. These phenotypes were amplified when ethanol was added to the medium or used as the sole carbon source. RNAseq analysis showed diminished induction of genes involved in diauxic shift, ethanol metabolism, fatty-acid ß-oxidation, and methylglyoxal catabolism during growth on ethanol compared to the reference strain. Enzyme-constrained metabolic modeling predicted that decreased flux through these poorly induced enzymes results in diminished ATP formation and decreased biomass accumulation observed. Together, these observations suggest that switch-like control of carbon source dependent gene expression in S. cerevisiae requires genome arrangement into multiple chromosomes.

scholarly journals A single chromosome strain of S. cerevisiae exhibits diminished ethanol metabolism and tolerance

2021 ◽  
Author(s):  
Tyler W Doughty ◽  
Rosemary Yu ◽  
Lucy Fang-I Chao ◽  
Zhongjun Qin ◽  
Verena Siewers ◽  
...  
Keyword(s):  
Reference Strain ◽  
Nuclear Dna ◽  
Carbon Sources ◽  
Biomass Concentration ◽  
Ethanol Metabolism ◽  
Large Chromosome ◽  
Lag Phase ◽  
Diauxic Shift ◽  
Single Chromosome ◽  
Induced Genes

Abstract Background:Eukaryotic organisms, like the model yeast S. cerevisiae, have linear chromosomes that facilitate organization and protection of nuclear DNA. A recent work described a stepwise break/repair method that enabled fusion of the sixteen chromosomes of S. cerevisiae into a single large chromosome. Construction of this strain resulted in the removal of 30 of 32 telomeres, over 300kb of subtelomeric DNA, and 107 subtelomeric ORFs. Despite these changes, characterization of the single chromosome strain uncovered modest phenotypes compared to a reference strain.Results:This study further characterized the single chromosome strain and found that it exhibited a longer lag phase, increased doubling time, and lower final biomass concentration compared with a reference strain when grown on YPD. These phenotypes were amplified when ethanol was added to the medium or used as the sole carbon source. RNAseq analysis showed poor induction of genes involved in diauxic shift, ethanol metabolism, and fatty-acid ß-oxidation during growth on ethanol compared to the reference strain. Enzyme-constrained metabolic modeling identified decreased flux through the enzymes that are encoded by these poorly induced genes as a likely cause of diminished biomass accumulation. The diminished growth on ethanol for the single chromosome strain was rescued by nicotinamide, an inhibitor of sirtuin family deacetylases, which have been shown to silence gene expression in heterochromatic regions. Conclusions:Our results indicate that sirtuin-mediated silencing in the single chromosome strain interferes with growth on non-fermentable carbon sources. We propose that the removal of subtelomeric DNA that would otherwise be bound by sirtuins leads to silencing at other loci in the single chromosome strain. Further, we hypothesize that the poorly induced genes in the single chromosome strain during ethanol growth could be silenced by sirtuins in wildtype S. cerevisiae during growth on glucose.

scholarly journals A single chromosome strain of S. cerevisiae exhibits diminished ethanol metabolism and tolerance

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tyler W. Doughty ◽  
Rosemary Yu ◽  
Lucy Fang-I Chao ◽  
Zhongjun Qin ◽  
Verena Siewers ◽  
...  
Keyword(s):  
Reference Strain ◽  
Nuclear Dna ◽  
Carbon Sources ◽  
Biomass Concentration ◽  
Ethanol Metabolism ◽  
Large Chromosome ◽  
Lag Phase ◽  
Diauxic Shift ◽  
Single Chromosome ◽  
Induced Genes

Abstract Background Eukaryotic organisms, like the model yeast S. cerevisiae, have linear chromosomes that facilitate organization and protection of nuclear DNA. A recent work described a stepwise break/repair method that enabled fusion of the 16 chromosomes of S. cerevisiae into a single large chromosome. Construction of this strain resulted in the removal of 30 of 32 telomeres, over 300 kb of subtelomeric DNA, and 107 subtelomeric ORFs. Despite these changes, characterization of the single chromosome strain uncovered modest phenotypes compared to a reference strain. Results This study further characterized the single chromosome strain and found that it exhibited a longer lag phase, increased doubling time, and lower final biomass concentration compared with a reference strain when grown on YPD. These phenotypes were amplified when ethanol was added to the medium or used as the sole carbon source. RNAseq analysis showed poor induction of genes involved in diauxic shift, ethanol metabolism, and fatty-acid ß-oxidation during growth on ethanol compared to the reference strain. Enzyme-constrained metabolic modeling identified decreased flux through the enzymes that are encoded by these poorly induced genes as a likely cause of diminished biomass accumulation. The diminished growth on ethanol for the single chromosome strain was rescued by nicotinamide, an inhibitor of sirtuin family deacetylases, which have been shown to silence gene expression in heterochromatic regions. Conclusions Our results indicate that sirtuin-mediated silencing in the single chromosome strain interferes with growth on non-fermentable carbon sources. We propose that the removal of subtelomeric DNA that would otherwise be bound by sirtuins leads to silencing at other loci in the single chromosome strain. Further, we hypothesize that the poorly induced genes in the single chromosome strain during ethanol growth could be silenced by sirtuins in wildtype S. cerevisiae during growth on glucose.

The circulating floating bed reactor: effect of particle size distribution of the carrier on ammonia conversion

2000 ◽  
Vol 41 (4-5) ◽  
pp. 393-400 ◽  
Author(s):  
J.M. Garrido-Fernandez ◽  
R. Méndez ◽  
J.M. Lema ◽  
V. Lazarova
Keyword(s):  
Particle Size ◽  
Size Distribution ◽  
G Protein ◽  
Biomass Concentration ◽  
Biomass Accumulation ◽  
Ammonia Removal ◽  
Operating Conditions ◽  
Nitrification Rate ◽  
Ammonia Conversion ◽  
Biomass Activity

Three Circulating Floating Bed Reactors (CFBR) R1, R2 and R3 with 20% v/v of a plastic carrier with different size distribution were operated to study the effect of the particles size of the carrier on biomass accumulation and nitrification performance. Operating conditions were similar in the three systems: ammonia concentrations around 50 mg-N–NH4+/ L, ammonia loading rates up to 1.2 kg N–NH4+/m3·d and temperatures between 14 and 27°C. Accumulation of nitrite was observed until day 65th. This w as result both of the inhibition of nitrite oxidation by free ammonia until day 20th and the insignificant accumulation of a biomass with low nitrite oxidising capacity between days 20 and 65th. Ammonia conversion rate and removal efficiency were higher in the reactor with lower particle size, R3 (nitrification rate of 1.1 kg N–NH4+/m3·d and ammonia removal of 97% at 16°C), than in R2 or R1 (nitrification rate of 1.0 kg N–NH4+/m3·d and ammonia removal of 90% at 16°C). The better efficiency in R3 was obtained as a result of the higher specific surface of the biofilm developed. Biomass activity was similar in the three reactors (2.2 and 1.12 g N/g protein · d at 30 and 15°C, respectively). Both the biomass evolution with time and biomass retention in the systems was practically not influenced by the size of particle. Biomass concentration of 1.2 g protein/L was retained in the carrier and up to 20% of the newly produced biomass was retained in the CFBRs.

scholarly journals Bioproduction of succinic acid from xylose by engineered Yarrowia lipolytica without pH control

2020 ◽  
Author(s):  
Ashish Prabhu ◽  
Rodrigo Ledesma- Amaro ◽  
Carol Sze Ki Lin ◽  
Frederic Coulon ◽  
Vijay kumar Thakur ◽  
...  
Keyword(s):  
Cell Growth ◽  
Carbon Source ◽  
Succinic Acid ◽  
Yarrowia Lipolytica ◽  
Recombinant Strain ◽  
Sole Carbon Source ◽  
Substrate Inhibition ◽  
Biomass Concentration ◽  
Value Added ◽  
Green Economy

Abstract Background Xylose is a most prevalent sugar available in hemicellulose fraction of lignocellulosic biomass (LCB) and of great interest for the green economy. Unfortunately, most of the cell factories cannot inherently metabolize xylose as sole carbon source. Yarrowia lipolytica is a non-conventional yeast to produce industrially important metabolites, and it is able to metabolize a large variety of substrates including both hydrophilic and hydrophobic carbon sources. However, Y. lipolytica lacks effective metabolic pathway for xylose uptake and only scarce information is available on utilization of xylose. For the economically feasible of LCB-based biorefineries, effective utilization of both pentose and hexose sugars is obligatory. Results In the present study, succinic acid (SA) production from xylose by Y. lipolytica was examined. To this end, Y. lipolytica PSA02004 strain was engineered by overexpressing pentose pathway cassette comprising of xylose reductase ( XR ), xylitol dehydrogenase ( XDH ) and xylulose kinase ( XK ) gene. The recombinant strain exhibited a robust growth on xylose as sole carbon source and accumulated SA (3.8 g/L) with a yield of 0.19 g/g in shake flask studies. Substrate inhibition studies revealed a marked negative impact on cell growth and product formation above 60 g/L xylose concentration. The modelling based on inhibition kinetics revealed that Aiba model showed better fit with experimental data, which resulted the correlation coefficient (R 2 ) of 0.82 and inhibition constant (K I ) 88.9 g/L. The batch cultivation of recombinant strain in bioreactor resulted in a maximum biomass concentration of 7.3 g/L and SA titer of 11.2 g/L with the yield of 0.18 g/g. Similar results in term of cell growth and SA production were obtained with xylose-rich hydrolysate derived from sugarcane bagasse. The fed-batch fermentation yielded biomass concentration of 11.8 g/L (OD 600 : 56.1) and SA titer of 22.3 g/L with a gradual decrease in pH below 4.0. Acetic acid was obtained as a main byproduct in all the fermentations. Conclusion The recombinant strain displayed potential bioconversion of xylose to succinic acid. Further this study provided a new insight on conversion of LCB into value-added products. To the best of our knowledge, this is the first study on SA production by Y. lipolytica using xylose as a sole carbon source.

Lag, adaptation and ageing in a micro-organism ( Bact. lactis aerogenes )

1961 ◽  
Vol 155 (959) ◽  
pp. 195-201 ◽  
Keyword(s):  
Carbon Source ◽  
Generation Time ◽  
Sole Carbon Source ◽  
The Other ◽  
Lag Phase ◽  
Glucose Medium ◽  
Galactosidase Activity ◽  
Aerobacter Aerogenes ◽  
Isomerase Activity

The lag preceding growth of Bact. lactis aerogenes (Aerobacter aerogenes) after a first transfer to a medium containing D-arabinose as sole carbon source increases with the age and decreases with the size of the inoculum. During the long lag phase the β -galactosidase activity declines steeply. In contrast with this (and with a control ageing in a glucose medium) the D-ribulose isomerase activity is maintained, although no detectable consumption of D-arabinose occurs. If the long lag of unadapted cells in D-arabinose is divided into parts by intermediate passages in glucose or lactose media, the sum of the partial lags is nearly constant and equal to that observed when there is no interruption. But the periodic passages in the other media increase the rate at which growth eventually occurs in the D-arabinose. It is concluded that during the lag a decay of the enzymes in general occurs concomitantly with the development of the specific mechanisms concerned in the utilization of the new substrate. The balance of these processes (together with varying loss or retention of diffusible metabolites) is largely responsible for the observed variations in lag and mean generation time.

Research on the Isolation, Identification and Degradation Characteristics of a Diesel Oil Degrading Strain

2013 ◽  
Vol 641-642 ◽  
pp. 206-210 ◽  
Author(s):  
Lei Huang ◽  
Jing Xie ◽  
Xiao Feng Shi ◽  
Jing Yan Lian
Keyword(s):  
Carbon Source ◽  
Yeast Extract ◽  
Contaminated Soils ◽  
Biomass Concentration ◽  
Diesel Oil ◽  
Artificial Seawater ◽  
Oil Field ◽  
Optimal Concentration ◽  
Optimal Temperature

A hydrocarbon-degrading strain ZRS was isolated from petroleum-contaminated soils sampled from Xinjiang oil field and identified as Acinetobacter beijerinckii, which could use diesel oil as solo carbon source. The optimal temperature and pH for strain utilizing ethanol was 25°C and 7.2; the optimal concentration of ethanol and the biomass concentration was 4.5% and 109 CFU/mL, respectively. Inoculated to artificial seawater which added (NH4)2SO4 2.64g/L、Na2HPO4 1.5 g/L and yeast extract 13 mg/L after 7 days of culture at temperature 25°C, the rate of degradation was 73.9％.

scholarly journals Bioproduction of succinic acid from xylose by engineered Yarrowia lipolytica without pH control

2020 ◽  
Author(s):  
Ashish Prabhu ◽  
Rodrigo Ledesma- Amaro ◽  
Carol Sze Ki Lin ◽  
Frederic Coulon ◽  
Vijay kumar Thakur ◽  
...  
Keyword(s):  
Cell Growth ◽  
Carbon Source ◽  
Succinic Acid ◽  
Lignocellulosic Biomass ◽  
Yarrowia Lipolytica ◽  
Recombinant Strain ◽  
Sole Carbon Source ◽  
Biomass Concentration ◽  
Value Added ◽  
Green Economy

Abstract Background : Xylose is a most prevalent sugar available in hemicellulose fraction of lignocellulosic biomass (LCB) and of great interest for the green economy. Unfortunately, most of the cell factories cannot inherently metabolize xylose as sole carbon source. Yarrowia lipolytica is a non-conventional yeast to produce industrially important metabolites. The yeast is able to metabolize a large variety of substrates including both hydrophilic and hydrophobic carbon sources. However, Y. lipolytica lacks effective metabolic pathway for xylose uptake and only scarce information is available on utilization of xylose. For the economically feasibility of LCB-based biorefineries, effective utilization of both pentose and hexose sugars is obligatory. Results : In the present study, succinic acid (SA) production from xylose by Y. lipolytica was examined. To this end, Y. lipolytica PSA02004 strain was engineered by overexpressing pentose pathway cassette comprising of xylose reductase ( XR ), xylitol dehydrogenase ( XDH ) and xylulose kinase ( XK ) gene. The recombinant strain exhibited a robust growth on xylose as sole carbon source and produced substantial amount of SA. The inhibition of cell growth and SA formation was observed above 60 g/L xylose concentration. The batch cultivation of recombinant strain in bioreactor resulted in a maximum biomass concentration of 7.3 g/L and SA titer of 11.2 g/L with the yield of 0.19 g/g. Similar results in term of cell growth and SA production were obtained with xylose-rich hydrolysate derived from sugarcane bagasse. The fed-batch fermentation yielded biomass concentration of 11.8 g/L (OD 600 : 56.1) and SA titer of 22.3 g/L with a gradual decrease in pH below 4.0. Acetic acid was obtained as a main byproduct in all the fermentations. Conclusion : The recombinant strain displayed potential for bioconversion of xylose to SA. Further, this study provided a new insight on conversion of lignocellulosic biomass into value-added products. To the best of our knowledge, this is the first study on SA production by Y. lipolytica using xylose as a sole carbon source.

The role of mutation in the adaptation of a yeast to galactose

1954 ◽  
Vol 142 (907) ◽  
pp. 267-287 ◽  
Keyword(s):  
Carbon Source ◽  
Genetic Factor ◽  
Synthetic Medium ◽  
Lag Phase ◽  
Phase 3 ◽  
Gradual Development ◽  
Visible Growth ◽  
Cell Processes ◽  
The Stability

Adaptation of a diploid yeast strain of Saccharomyces cerevisiae to a synthetic medium containing galactose as carbon source is shown to involve selective growth of a few cells that have mutated to a condition enabling this sugar to be utilized readily, rather than gradual development in the majority of cells of the ability to utilize galactose. That the first mechanism is the correct one is shown by: ( а ) the ability of 1 cell in 10 5 of the unadapted strain to utilize galactose more or less immediately and form large colonies in 2 days on a galactose-agar growth medium, under circumstances in which all the cells of the fully adapted strain can grow at once; ( b ) the identical rates of multiplication in the liquid galactose medium of the adapted strain and of the small number of variant cells, the measurement in the latter case being made during the lag phase before visible growth has started; ( c ) the length of this lag phase (3 days), which is consistent with the initial proportion of variant cells; ( d ) the hereditary difference between the adapted and unadapted diploid strains which seems to depend on a single genetic factor. Two haploid cultures from a four-spored ascus of the adapted strain grow with a short lag in the liquid galactose medium, and two grow with a long lag, being similar in this respect to the four haploids from the unadapted strain. This difference between the two types is preserved through subsequent matings. Exceptional properties are shown by spore cultures from two out of twenty-two asci both in the glucose and the galactose medium. This may be due to extra-chromosomal material being partitioned in unusual proportions at meiosis. The adapted strain does not revert during 500 generations in a medium containing glucose as carbon source. To account for the stability relationships between the adapted and unadapted strain, it is proposed that the co-ordination of cell processes is disturbed while adjustments conditioned by a mutation are taking place. Thus the growth rate may be reduced and, for this reason alone, accumulation of mutated cells in a population retarded.

scholarly journals Optimization of Carbon Source for Hairy Root Growth and Withaferin A and Withanone Production in Withania somnifera

2012 ◽  
Vol 7 (10) ◽  
pp. 1934578X1200701 ◽  
Author(s):  
Ganeshan Sivanandhan ◽  
Manoharan Rajesh ◽  
Muthukrishnan Arun ◽  
Murugaraj Jeyaraj ◽  
Gnanajothi Kapil Dev ◽  
...  
Keyword(s):  
Carbon Source ◽  
Liquid Medium ◽  
Hairy Root ◽  
Root Biomass ◽  
Withania Somnifera ◽  
Carbon Sources ◽  
Root Culture ◽  
Biomass Accumulation ◽  
Hairy Root Culture ◽  
Withaferin A

This study optimized carbon sources in half MS liquid medium for maximum biomass accumulation and withanolides production in hairy root culture of Withania somnifera. The highest production of withaferin A and withanone was achieved when sucrose and sucrose+glucose were used individually as carbon sources. The hairy root suspension culture supplemented with a lower level of sucrose (2%) favored hairy root biomass accumulation (1.41 g DW) followed by sucrose+glucose (2+1) when compared with other carbon sources in half MS liquid medium after 40 days of culture. The hairy roots grown on sucrose (4%) enriched half MS liquid medium stimulated higher production of withaferin A (2.21 mg/g DW) and withanone (2.41 mg/g DW) on the 40th day of culture, followed by sucrose+glucose (4+1%) compared with glucose, fructose, maltose and other combinations tested.

Growth of a Methane-Utilizing Mixed Culture HD6T on Methanol and Poly-β-Hydroxybutyrate Biosynthesis

2010 ◽  
Vol 160-162 ◽  
pp. 171-175 ◽  
Author(s):  
Jing Dong ◽  
Jia Ying Xin ◽  
Ying Xin Zhang ◽  
Lin Lin Chen ◽  
Hong Ye Liang ◽  
...  
Keyword(s):  
Mixed Culture ◽  
Mineral Salt Medium ◽  
Biomass Concentration ◽  
Dry Weight ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Production Costs ◽  
Lag Phase ◽  
Phase Duration ◽  
Phb Production

Methane-utilizing mixed culture HD6T was successfully cultivated in a brief non-sterile process using methanol as a sole carbon and energy source for the production of poly-β-hydroxybutyrate(PHB). Shake-flask experiments showed HD6T could grow well in the mineral salt medium with the addition of methanol exposed to the air directly. This non-sterile process and the use of cheap substrates (methanol) can reduce the production costs of PHB. It was found that HD6T grew better and PHB production in a more effective way with an initial liquid methanol concentration of 0.15%(v/v).The lag phase duration, the maximum growth rate, the biomass concentration and the PHB yield, for the optimal conditions were, respectively, 12.03h, 0.04h-1(OD600), 1.54g/l(dry weight), 0.424g/l(dry weight). Methane-utilizing mixed culture HD6T appears to be a promising organism for PHB production.

Sign in / Sign up

Export Citation Format

Share Document