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.

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

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 Accumulation of viruslike particles in a yeast mutant lacking a mitochondrial pore protein.

1989 ◽  
Vol 9 (3) ◽  
pp. 1100-1108 ◽  
Author(s):  
M Dihanich ◽  
E van Tuinen ◽  
J D Lambris ◽  
B Marshallsay
Keyword(s):  
Carbon Sources ◽  
Lag Phase ◽  
Cytosol Fraction ◽  
Mitochondrial Porin ◽  
Mitochondrial Functions ◽  
Microsome Fraction ◽  
Simultaneous Loss ◽  
Viruslike Particles ◽  
Mutant Cells ◽  
Pore Protein

The lack of mitochondrial porin is not lethal in Saccharomyces cerevisiae, but it impairs some respiratory functions and, therefore, growth on nonfermentable carbon sources such as glycerol. However, after a lag phase porinless mutant cells adapt to growth on glycerol, accumulating large amounts of an 86-kilodalton (kDa) protein (M. Dihanich, K. Suda, and G. Schatz, EMBO J. 6:723-728, 1987) and of a 5-kilobase RNA. Immunogold labeling localized the 86 kDa-protein exclusively to the cytosol fraction, although most of it cosedimented with the microsome fraction in earlier cell fractionations. This discrepancy was resolved when the 86-kDa protein was identified as the major coat protein in viruslike particles (VLPs) which is encoded by a double-stranded RNA (L-A RNA). Elimination of VLPs in the original porinless strain by introduction of the mak10 or the mak3 mutation increased the respiratory defect and prolonged its lag phase on nonfermentable carbon sources. The fact that the simultaneous loss of VLPs and respiratory functions are the introduction of mak10 or mak3 occurred even in some porin-containing wild-type strains suggests that there is a link between VLP and mitochondrial functions.

Biofilm formation by a biotechnologically important tropical marine yeast isolate, Yarrowia lipolytica NCIM 3589

2008 ◽  
Vol 58 (6) ◽  
pp. 1221-1229 ◽  
Author(s):  
D. H. Dusane ◽  
Y. V. Nancharaiah ◽  
V. P. Venugopalan ◽  
A. R. Kumar ◽  
S. S. Zinjarde
Keyword(s):  
Yarrowia Lipolytica ◽  
Biofilm Formation ◽  
Edible Oils ◽  
Carbon Sources ◽  
Three Dimensional ◽  
Ecological Niches ◽  
Lag Phase ◽  
Biofilm Growth ◽  
Water Media ◽  
Biofilm Development

Biofilm formation by Yarrowia lipolytica, a biotechnologically important fungus in microtitre plates, on glass slide surfaces and in flow cell was investigated. In microtitre plates, there was a short lag phase of adhesion followed by a period of rapid biofilm growth. The fungus formed extensive biofilms on glass slides, whereas in flow-cells a multicellular, three-dimensional microcolony structure was observed. The isolate formed biofilms in seawater and in fresh water media at neutral pH when grown in microtitre plates. The carbon sources differentially affected formation of biofilms in microtitre plates. Lactic acid, erythritol, glycerol, glucose and edible oils supported the formation of biofilms, while alkanes resulted in sub-optimal biofilm development. A variation in the morphology of the fungus was observed with different carbon sources. The results point to the possible existence of highly structured biofilms in varied ecological niches from where the yeast is isolated.

Accumulation of viruslike particles in a yeast mutant lacking a mitochondrial pore protein

1989 ◽  
Vol 9 (3) ◽  
pp. 1100-1108
Author(s):  
M Dihanich ◽  
E van Tuinen ◽  
J D Lambris ◽  
B Marshallsay
Keyword(s):  
Carbon Sources ◽  
Lag Phase ◽  
Cytosol Fraction ◽  
Mitochondrial Porin ◽  
Mitochondrial Functions ◽  
Microsome Fraction ◽  
Simultaneous Loss ◽  
Viruslike Particles ◽  
Mutant Cells ◽  
Pore Protein

The lack of mitochondrial porin is not lethal in Saccharomyces cerevisiae, but it impairs some respiratory functions and, therefore, growth on nonfermentable carbon sources such as glycerol. However, after a lag phase porinless mutant cells adapt to growth on glycerol, accumulating large amounts of an 86-kilodalton (kDa) protein (M. Dihanich, K. Suda, and G. Schatz, EMBO J. 6:723-728, 1987) and of a 5-kilobase RNA. Immunogold labeling localized the 86 kDa-protein exclusively to the cytosol fraction, although most of it cosedimented with the microsome fraction in earlier cell fractionations. This discrepancy was resolved when the 86-kDa protein was identified as the major coat protein in viruslike particles (VLPs) which is encoded by a double-stranded RNA (L-A RNA). Elimination of VLPs in the original porinless strain by introduction of the mak10 or the mak3 mutation increased the respiratory defect and prolonged its lag phase on nonfermentable carbon sources. The fact that the simultaneous loss of VLPs and respiratory functions are the introduction of mak10 or mak3 occurred even in some porin-containing wild-type strains suggests that there is a link between VLP and mitochondrial functions.

scholarly journals High-Affinity Transporters for NAD+ Precursors in Candida glabrata Are Regulated by Hst1 and Induced in Response to Niacin Limitation

2009 ◽  
Vol 29 (15) ◽  
pp. 4067-4079 ◽  
Author(s):  
Biao Ma ◽  
Shih-Jung Pan ◽  
Renee Domergue ◽  
Tracey Rigby ◽  
Malcolm Whiteway ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Candida Glabrata ◽  
Transcriptional Response ◽  
Opportunistic Pathogen ◽  
Lag Phase ◽  
High Affinity ◽  
Induced Genes ◽  
Necessary And Sufficient ◽  
Transcriptional Induction

ABSTRACT The yeast Candida glabrata is an opportunistic pathogen of humans. C. glabrata is a NAD+ auxotroph, and its growth depends on the availability of niacin (environmental vitamin precursors of NAD+). We have previously shown that a virulence-associated adhesin, encoded by EPA6, is transcriptionally induced in response to niacin limitation. Here we used transcript profiling to characterize the transcriptional response to niacin limitation and the roles of the sirtuins Hst1, Hst2, and Sir2 in mediating this response. The majority of genes transcriptionally induced by niacin limitation are regulated by Hst1, suggesting that it is the primary sensor of niacin limitation in C. glabrata. We show that three highly induced genes, TNA1, TNR1, and TNR2, encode transporters which are necessary and sufficient for high-affinity uptake of NAD+ precursors. Strikingly, if a tna1 tnr1 tnr2 mutant is starved for niacin, it exhibits an extended lag phase, suggesting a central role for the transporters in restoring NAD+ homeostasis after niacin limitation. Lastly, we had previously shown that the adhesin encoded by EPA6 is induced during experimental urinary tract infection (UTI); we show here that EPA6 transcriptional induction during UTI is strongly enhanced in the tna1 tnr1 tnr2 mutant strain, implicating the transporters in the growth of C. glabrata during infection.

scholarly journals Mevalonate production from ethanol by direct conversion through acetyl-CoA using recombinant Pseudomonas putida, a novel biocatalyst for terpenoid production

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Jeongmo Yang ◽  
Ji Hee Son ◽  
Hyeonsoo Kim ◽  
Sukhyeong Cho ◽  
Jeong-geol Na ◽  
...  
Keyword(s):  
Pseudomonas Putida ◽  
Batch Fermentation ◽  
Fossil Fuels ◽  
Fatty Acid Biosynthesis ◽  
Carbon Sources ◽  
Value Added ◽  
Product Yield ◽  
Cellulosic Biomass ◽  
Ethanol Metabolism ◽  
Acetyl Coa

Abstract Background Bioethanol is one of the most representative eco-friendly fuels developed to replace the non-renewable fossil fuels and is the most successful commercially available bio-conversion technology till date. With the availability of inexpensive carbon sources, such as cellulosic biomass, bioethanol production has become cheaper and easier to perform, which can facilitate the development of methods for converting ethanol into higher value-added biochemicals. In this study, a bioconversion process using Pseudomonas putida as a biocatalyst was established, wherein ethanol was converted to mevalonate. Since ethanol can be converted directly to acetyl-CoA, bypassing its conversion to pyruvate, there is a possibility that ethanol can be converted to mevalonate without producing pyruvate-derived by-products. Furthermore, P. putida seems to be highly resistant to the toxicity caused by terpenoids, and thus can be useful in conducting terpenoid production research. Results In this study, we first expressed the core genes responsible for mevalonate production (atoB, mvaS, and mvaE) in P. putida and mevalonate production was confirmed. Thereafter, through an improvement in genetic stability and ethanol metabolism manipulation, mevalonate production was enhanced up to 2.39-fold (1.70 g/L vs. 4.07 g/L) from 200 mM ethanol with an enhancement in reproducibility of mevalonate production. Following this, the metabolic characteristics related to ethanol catabolism and mevalonate production were revealed by manipulations to reduce fatty acid biosynthesis and optimize pH by batch fermentation. Finally, we reached a product yield of 0.41 g mevalonate/g ethanol in flask scale culture and 0.32 g mevalonate/g ethanol in batch fermentation. This is the highest experimental yield obtained from using carbon sources other than carbohydrates till date and it is expected that further improvements will be made through the development of fermentation methods. Conclusion Pseudomonas putida was investigated as a biocatalyst that can efficiently convert ethanol to mevalonate, the major precursor for terpenoid production, and this research is expected to open new avenues for the production of terpenoids using microorganisms that have not yet reached the stage of mass production.

scholarly journals Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Rafael Wesley Bastos ◽  
Clara Valero ◽  
Lilian Pereira Silva ◽  
Taylor Schoen ◽  
Milton Drott ◽  
...  
Keyword(s):  
Cell Wall ◽  
Reference Strain ◽  
Carbon Sources ◽  
Neutrophil Function ◽  
Clinical Isolates ◽  
Biological Characterization ◽  
Content Type ◽  
Virulence Traits ◽  
Opportunistic Fungal Pathogen

ABSTRACT Aspergillus nidulans is an opportunistic fungal pathogen in patients with immunodeficiency, and virulence of A. nidulans isolates has mainly been studied in the context of chronic granulomatous disease (CGD), with characterization of clinical isolates obtained from non-CGD patients remaining elusive. This study therefore carried out a detailed biological characterization of two A. nidulans clinical isolates (CIs), obtained from a patient with breast carcinoma and pneumonia and from a patient with cystic fibrosis that underwent lung transplantation, and compared them to the reference, nonclinical FGSC A4 strain. Both CIs presented increased growth in comparison to that of the reference strain in the presence of physiologically relevant carbon sources. Metabolomic analyses showed that the three strains are metabolically very different from each other in these carbon sources. Furthermore, the CIs were highly susceptible to cell wall-perturbing agents but not to other physiologically relevant stresses. Genome analyses identified several frameshift variants in genes encoding cell wall integrity (CWI) signaling components. Significant differences in CWI signaling were confirmed by Western blotting among the three strains. In vivo virulence studies using several different models revealed that strain MO80069 had significantly higher virulence in hosts with impaired neutrophil function than the other strains. In summary, this study presents detailed biological characterization of two A. nidulans sensu stricto clinical isolates. Just as in Aspergillus fumigatus, strain heterogeneity exists in A. nidulans clinical strains that can define virulence traits. Further studies are required to fully characterize A. nidulans strain-specific virulence traits and pathogenicity. IMPORTANCE Immunocompromised patients are susceptible to infections with opportunistic filamentous fungi from the genus Aspergillus. Although A. fumigatus is the main etiological agent of Aspergillus species-related infections, other species, such as A. nidulans, are prevalent in a condition-specific manner. A. nidulans is a predominant infective agent in patients suffering from chronic granulomatous disease (CGD). A. nidulans isolates have mainly been studied in the context of CGD although infection with A. nidulans also occurs in non-CGD patients. This study carried out a detailed biological characterization of two non-CGD A. nidulans clinical isolates and compared the results to those with a reference strain. Phenotypic, metabolomic, and genomic analyses highlight fundamental differences in carbon source utilization, stress responses, and maintenance of cell wall integrity among the strains. One clinical strain had increased virulence in models with impaired neutrophil function. Just as in A. fumigatus, strain heterogeneity exists in A. nidulans clinical strains that can define virulence traits.

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.

Gordonia (nocardia) amarae foaming due to biosurfactant production

2002 ◽  
Vol 46 (1-2) ◽  
pp. 519-524 ◽  
Author(s):  
K.R. Pagilla ◽  
A. Sood ◽  
H. Kim
Keyword(s):  
Surface Tension ◽  
Carbon Source ◽  
Stationary Phase ◽  
Activated Sludge ◽  
Sole Carbon Source ◽  
Wastewater Treatment Plants ◽  
Carbon Sources ◽  
Biomass Concentration ◽  
Culture Broth ◽  
Biosurfactant Production

Gordonia amarae, a filamentous actinomycete, commonly found in foaming activated sludge wastewater treatment plants was investigated for its biosurfactant production capability. Soluble acetate and sparingly soluble hexadecane were used as carbon sources for G. amarae growth and biosurfactant production in laboratory scale batch reactors. The lowest surface tension (critical micelle concentration, CMC) of the cell-free culture broth was 55 dynes/cm when 1,900 mg/L acetate was used as the sole carbon source. The lowest surface tension was less than 40 dynes/cm when either 1% (v/v) hexadecane or a mixture of 1% (v/v) hexadecane and 0.5% (w/v) acetate was used as the carbon source. The maximum biomass concentration (the stationary phase) was achieved after 4 days when acetate was used along with hexadecane, whereas it took about 8 days to achieve the stationary phase with hexadecane alone. The maximum biosurfactant production was 3 × CMC with hexadecane as the sole carbon source, and it was 5 × CMC with the mixture of hexadecane and acetate. Longer term growth studies (∼ 35 days of culture growth) indicated that G. amarae produces biosurfactant in order to solubilize hexadecane, and that adding acetate improves its biosurfactant production by providing readily degradable substrate for initial biomass growth. This research confirms that the foaming problems in activated sludge containing G. amarae in the activated sludge are due to the biosurfactant production by G. amarae when hydrophobic substrates such as hexadecane are present.

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