Picrophilus torridus DSM 9790
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA10641 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Extremely thermoacidophilic Crenarchaeota belonging to the family Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. However, the pH extremes of these habitats often exceed the acid tolerance of type species and strains. Here, experimental evolution was used to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains are named super acid resistant crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance while genome and transcriptome resequencing provided insights into the underlying mechanisms responsible for evolved thermoacidophily. Transcriptomics of the evolved strains indicates that their unique phenotype may be due to an increased rate of membrane turnover under strong acid conditions.
2015-12-31 | GSE76423 | GEO
Project description:Extremely thermoacidophilic Crenarchaeota belonging to the family Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. However, the pH extremes of these habitats often exceed the acid tolerance of type species and strains. Here, experimental evolution was used to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains are named super acid resistant crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance while genome and transcriptome resequencing provided insights into the underlying mechanisms responsible for evolved thermoacidophily. Transcriptomics of the evolved strains indicates that their unique phenotype may be due to an increased rate of membrane turnover under strong acid conditions. 6 Samples were analyzed: 2 replicate control samples [SULA] and 2 replicate experimental samples [SULC and SULB]
2015-12-31 | E-GEOD-76423 | biostudies-arrayexpress
Project description:In this study, we used S. acidocaldarius adapted to two extremes, low pH and high temperature, to study its tolerance and robustness as well as its global cellular response towards organic solvents exemplified by 1-butanol. We were able to identify biofilm formation as primary cellular response to 1-butanol.
2021-03-15 | PXD023858 | Pride
Project description:Extremely thermoacidophilic members of the Archaea such as the lithoautotroph, Metallosphaera sedula, are among the most acid resistant forms of life and are of great relevance in bioleaching. Here, adaptive laboratory evolution was used to enhance the acid resistance of this organism while genomics and transcriptomics were used in an effort to understand the molecular basis for this trait. Unlike the parental strain, the evolved derivative, M. sedula SARC-M1, grew well at pH of 0.90. Enargite (Cu3AsS4) bioleaching conducted at pH 1.20 demonstrated SARC-M1 leached 23.78% more copper relative to the parental strain. Genome re-sequencing identified two mutations in SARC-M1 including a nonsynonymous mutation in Msed_0408 (an amino acid permease) and a deletion in pseudogene Msed_1517. Transcriptomic studies by RNA-seq of wild type and evolved strains at various low pH values demonstrated there was enhanced expression of genes in M. sedula SARC-M1 encoding membrane complexes and enzymes that extrude protons or that catalyze proton-consuming reactions. In addition, M. sedula SARC-M1 exhibited reduced expression of genes encoding enzymes that catalyze proton-generating reactions. These unique genomic and transcriptomic features of M. sedula SARC-M1 support a model for increased acid resistance arising from enhanced control over cytoplasmic pH.
2016-05-14 | GSE81414 | GEO
Project description:Extremely thermoacidophilic members of the Archaea such as the lithoautotroph, Metallosphaera sedula, are among the most acid resistant forms of life and are of great relevance in bioleaching. Here, adaptive laboratory evolution was used to enhance the acid resistance of this organism while genomics and transcriptomics were used in an effort to understand the molecular basis for this trait. Unlike the parental strain, the evolved derivative, M. sedula SARC-M1, grew well at pH of 0.90. Enargite (Cu3AsS4) bioleaching conducted at pH 1.20 demonstrated SARC-M1 leached 23.78% more copper relative to the parental strain. Genome re-sequencing identified two mutations in SARC-M1 including a nonsynonymous mutation in Msed_0408 (an amino acid permease) and a deletion in pseudogene Msed_1517. Transcriptomic studies by RNA-seq of wild type and evolved strains at various low pH values demonstrated there was enhanced expression of genes in M. sedula SARC-M1 encoding membrane complexes and enzymes that extrude protons or that catalyze proton-consuming reactions. In addition, M. sedula SARC-M1 exhibited reduced expression of genes encoding enzymes that catalyze proton-generating reactions. These unique genomic and transcriptomic features of M. sedula SARC-M1 support a model for increased acid resistance arising from enhanced control over cytoplasmic pH. 3 samples were analyzed: 1 control and 2 experimental samples
2016-05-14 | E-GEOD-81414 | biostudies-arrayexpress
Project description:Extreme thermoacidophilic sulfur-oxidizing archaeon
| PRJNA13935 | ENA
Project description:Clostridium thermocellum is a promising CBP candidate organism capable of directly converting lignocellulosic biomass to ethanol. Low yields, productivities and growth inhibition prevent industrial deployment of this organism for commodity fuel production. Symptoms of potential redox imbalance such as incomplete substrate utilization, and fermentation products characteristic of overflow metabolism, have been observed during growth. This perceived redox imbalance may be in part responsible for the mentioned bioproductivity limitations. Toward better understanding the redox metabolism of C. thermocellum, we analyzed gene expression, using microarrays, during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which we observed to change fermentation redox potential.
2015-07-29 | GSE71465 | GEO
Project description:This study provides novel insights into archaeal stress response. The effect of nutrient limitation on the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius was monitored over time on transcriptomic, proteomic and metabolic level. To our knowledge, this linkage of transcriptome, proteome, metabolome analysis makes this study a pioneer study to elucidate cellular stress response triggered by nutrient limitation. We further connect previously identified pH and salt stress responsive genes (1) with genes regulated in starvation and suggest that they constitute the core of stress responsive genes active under multiple stress sources.
2018-12-21 | GSE113716 | GEO
Project description:Morris2009 - α-Synuclein aggregation
variable temperature and pH
This model is described in the article:
Alpha-synuclein aggregation
variable temperature and variable pH kinetic data: a
re-analysis using the Finke-Watzky 2-step model of nucleation
and autocatalytic growth.
Morris AM, Finke RG.
Biophys. Chem. 2009 Mar; 140(1-3):
9-15
Abstract:
The aggregation of proteins is believed to be intimately
connected to many neurodegenerative disorders. We recently
reported an "Ockham's razor"/minimalistic approach to analyze
the kinetic data of protein aggregation using the Finke-Watzky
(F-W) 2-step model of nucleation (A-->B, rate constant k(1))
and autocatalytic growth (A+B-->2B, rate constant k(2)).
With that kinetic model we have analyzed 41 representative
protein aggregation data sets in two recent publications,
including amyloid beta, alpha-synuclein, polyglutamine, and
prion proteins (Morris, A. M., et al. (2008) Biochemistry 47,
2413-2427; Watzky, M. A., et al. (2008) Biochemistry 47,
10790-10800). Herein we use the F-W model to reanalyze protein
aggregation kinetic data obtained under the experimental
conditions of variable temperature or pH 2.0 to 8.5. We provide
the average nucleation (k(1)) and growth (k(2)) rate constants
and correlations with variable temperature or varying pH for
the protein alpha-synuclein. From the variable temperature
data, activation parameters DeltaG(double dagger),
DeltaH(double dagger), and DeltaS(double dagger) are provided
for nucleation and growth, and those values are compared to the
available parameters reported in the previous literature
determined using an empirical method. Our activation parameters
suggest that nucleation and growth are energetically similar
for alpha-synuclein aggregation (DeltaG(double
dagger)(nucleation)=23(3) kcal/mol; DeltaG(double
dagger)(growth)=22(1) kcal/mol at 37 degrees C). From the
variable pH data, the F-W analyses show a maximal k(1) value at
pH approximately 3, as well as minimal k(1) near the
isoelectric point (pI) of alpha-synuclein. Since solubility and
net charge are minimized at the pI, either or both of these
factors may be important in determining the kinetics of the
nucleation step. On the other hand, the k(2) values increase
with decreasing pH (i.e., do not appear to have a minimum or
maximum near the pI) which, when combined with the k(1) vs. pH
(and pI) data, suggest that solubility and charge are less
important factors for growth, and that charge is important in
the k(1), nucleation step of alpha-synuclein. The chemically
well-defined nucleation (k(1)) rate constants obtained from the
F-W analysis are, as expected, different than the 1/lag-time
empirical constants previously obtained. However, k(2)x[A](0)
(where k(2) is the rate constant for autocatalytic growth and
[A](0) is the initial protein concentration) is related to the
empirical constant, k(app) obtained previously. Overall, the
average nucleation and average growth rate constants for
alpha-synuclein aggregation as a function of pH and variable
temperature have been quantitated. Those values support the
previously suggested formation of a partially folded
intermediate that promotes aggregation under high temperature
or acidic conditions.
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2024-09-02 | BIOMD0000000566 | BioModels