Czajka2024 - Lipomyces genome scale model
Ontology highlight
ABSTRACT:
SUBMITTER: 
Jeffery Czajka
PROVIDER: MODEL2403190001 | BioModels | 2024-03-20
REPOSITORIES: BioModels
Similar Datasets
Project description:The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit the genotypic and phenotypic diversity to boost yeast’s industrial value is still urgently needed. Here, we analyzed 5400 growth curves obtained from 36 S. cerevisiae strains and comprehensively profiled their resistances against 13 industrially relevant stresses. We observed that bioethanol and brewing strains exhibit higher resistance against acidic conditions, however, plant isolates tend to have wider range of resistance, which may be associated with their metabolome and fluxome signatures in TCA cycle and fatty acid metabolism. By deep genomic sequencing we found that industrial strains have more genomic duplications especially affecting transcription factors, presenting disparate evolutionary paths in comparison to the environmental strains which have more InDels, gene deletions and strain-specific genes. Genome-wide association studies coupled with protein-protein interaction networks uncovered novel genetic determinants of stress resistances. These resistance-related engineering targets and strain rankings provide a valuable source for engineering significantly improved industrial platform strains.</br></br> This metabolomic study of 36 yeast strains measured intra- and extracellular metabolome under standard glucose medium, profiled by GS-MS. This is part of a multi-omic study on yeast strain collection.
2019-01-16 | MTBLS780 | MetaboLights
Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
| 2140168 | ecrin-mdr-crc
Project description:Schizosaccharomyces pombe is a model unicellular eukaryote with ties to the basic research, oenology and industrial biotechnology sectors. While most investigations into S. pombe cell biology utilize Leupold’s 972h- laboratory strain background, recent studies have described a wealth of genetic and phenotypic diversity within wild populations of S. pombe including stress resistance phenotypes which may be of interest to industry. Here we describe the genomic and transcriptomic characterization of Wilmar-P, an S. pombe isolate used for bioethanol production from sugarcane molasses at industrial scale. Novel sequences present in Wilmar-P but not in the laboratory S. pombe genome included multiple coding sequences with near-perfect nucleotide identity to Schizosaccharomyces octosporus sequences. Wilmar-P also contained a ~100kb duplication in the right arm of chromosome III, a region harboring ght5+, the predominant hexose transporter encoding gene. Transcriptomic analysis of Wilmar-P grown in molasses revealed strong downregulation of core environmental stress response genes and upregulation of hexose transporters and drug efflux pumps compared to laboratory S. pombe. Finally, examination of the regulatory network of Scr1, which is involved in the regulation of several genes differentially expressed on molasses revealed expanded binding of this transcription factor in Wilmar-P compared to laboratory S. pombe in the molasses condition. Together our results point to both genomic plasticity and transcriptomic adaptation as mechanisms driving phenotypic adaptation of Wilmar-P to the molasses environment and therefore adds to our understanding of genetic diversity within industrial fission yeast strains and the capacity of this strain for commercial scale bioethanol production.
2020-01-23 | GSE141744 | GEO
Project description:Schizosaccharomyces pombe is a model unicellular eukaryote with ties to the basic research, oenology and industrial biotechnology sectors. While most investigations into S. pombe cell biology utilize Leupold’s 972h- laboratory strain background, recent studies have described a wealth of genetic and phenotypic diversity within wild populations of S. pombe including stress resistance phenotypes which may be of interest to industry. Here we describe the genomic and transcriptomic characterization of Wilmar-P, an S. pombe isolate used for bioethanol production from sugarcane molasses at industrial scale. Novel sequences present in Wilmar-P but not in the laboratory S. pombe genome included multiple coding sequences with near-perfect nucleotide identity to Schizosaccharomyces octosporus sequences. Wilmar-P also contained a ~100kb duplication in the right arm of chromosome III, a region harboring ght5+, the predominant hexose transporter encoding gene. Transcriptomic analysis of Wilmar-P grown in molasses revealed strong downregulation of core environmental stress response genes and upregulation of hexose transporters and drug efflux pumps compared to laboratory S. pombe. Finally, examination of the regulatory network of Scr1, which is involved in the regulation of several genes differentially expressed on molasses revealed expanded binding of this transcription factor in Wilmar-P compared to laboratory S. pombe in the molasses condition. Together our results point to both genomic plasticity and transcriptomic adaptation as mechanisms driving phenotypic adaptation of Wilmar-P to the molasses environment and therefore adds to our understanding of genetic diversity within industrial fission yeast strains and the capacity of this strain for commercial scale bioethanol production.
2019-12-11 | GSE141715 | GEO
Project description:Saccahromycopsis schoenii belongs to a genus of yeasts that have the ability to attack and kill other yeast and fungi. De novo genomic sequencing and genome assembly suggests that S. schoenii might belong to the CTG clade. To examine whether it translated CTG codons to leucine (standard codon usage) or serine (alternative codon usage), we analysed its proteome during growth on full media. To see if translation is changed during nutritional stress or during predation on a prey cell (Saccharomyces cerevisiae), we analysed and quantified its proteome during these conditions compared to its proteomic expression in full media.
2019-03-18 | PXD008453 | Pride
Project description:Archer2011 - Genome-scale metabolic model of
Escherichia coli (iCA1273)
This model is described in the article:
The genome sequence of E.
coli W (ATCC 9637): comparative genome analysis and an improved
genome-scale reconstruction of E. coli.
Archer CT, Kim JF, Jeong H, Park JH,
Vickers CE, Lee SY, Nielsen LK.
BMC Genomics 2011; 12: 9
Abstract:
BACKGROUND: Escherichia coli is a model prokaryote, an
important pathogen, and a key organism for industrial
biotechnology. E. coli W (ATCC 9637), one of four strains
designated as safe for laboratory purposes, has not been
sequenced. E. coli W is a fast-growing strain and is the only
safe strain that can utilize sucrose as a carbon source.
Lifecycle analysis has demonstrated that sucrose from sugarcane
is a preferred carbon source for industrial bioprocesses.
RESULTS: We have sequenced and annotated the genome of E. coli
W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two
plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also
present. W has unique features relative to other sequenced
laboratory strains (K-12, B and Crooks): it has a larger genome
and belongs to phylogroup B1 rather than A. W also grows on a
much broader range of carbon sources than does K-12. A
genome-scale reconstruction was developed and validated in
order to interrogate metabolic properties. CONCLUSIONS: The
genome of W is more similar to commensal and pathogenic B1
strains than phylogroup A strains, and therefore has greater
utility for comparative analyses with these strains. W should
therefore be the strain of choice, or 'type strain' for group
B1 comparative analyses. The genome annotation and tools
created here are expected to allow further utilization and
development of E. coli W as an industrial organism for
sucrose-based bioprocesses. Refinements in our E. coli
metabolic reconstruction allow it to more accurately define E.
coli metabolism relative to previous models.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180010.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180010 | BioModels
Project description:A continuous culture of Bifidobacterium longum NCC2705 was carried out in a 2.5-l reactor (Bioengineering AG, Wald, Switzerland), equipped with a Biospectra control system (Biospectra AG, Schlieren, Switzerland) and containing 2 l of MRS, added of 0.05% cysteine, inoculated with 2 % (v/v) preculture. The temperature was maintained at 37°C and the pH at 6.0 by addition of 5 M NaOH. The culture was stirred constantly at 250 rpm using two rushton type propellers. Anaerobic conditions were maintained by flushing the headspace of the reactor with CO2. After 8 h in batch mode the culture was run in continuous mode at a dilution rate of 0.1 h-1. Fresh medium was added using a peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland), and fermented broth harvested with a second peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland) set at a slightly higher flow rate. A stabilization period of 90 h (corresponding to nine reactor volume changes) was operated prior culture monitoring (t=0). Aliquots of 2 ml taken at t=31, 134 and 211 h were centrifuged (4,000 g, 1 min, room temperature) for transcriptomic analysis. Supernatants were discarded and cell pellets snap frozen in liquid nitrogen and stored at -80ºC until RNA-extraction. Keywords: Time course of Bifidobacterium longum in continuous culture Bifidobacterium longum NCC2705 at time 31 versus time 134 h and versus time 211 h in continuous culture. Two technical replicares with dyes swaps
2010-05-19 | E-GEOD-14896 | biostudies-arrayexpress
Project description:Nogales2008 - Genome-scale metabolic network
of Pseudomonas putida (iJN746)
This model is described in the article:
A genome-scale metabolic
reconstruction of Pseudomonas putida KT2440: iJN746 as a cell
factory.
Nogales J, Palsson BØ, Thiele
I.
BMC Syst Biol 2008; 2: 79
Abstract:
BACKGROUND: Pseudomonas putida is the best studied pollutant
degradative bacteria and is harnessed by industrial
biotechnology to synthesize fine chemicals. Since the
publication of P. putida KT2440's genome, some in silico
analyses of its metabolic and biotechnology capacities have
been published. However, global understanding of the
capabilities of P. putida KT2440 requires the construction of a
metabolic model that enables the integration of classical
experimental data along with genomic and high-throughput data.
The constraint-based reconstruction and analysis (COBRA)
approach has been successfully used to build and analyze in
silico genome-scale metabolic reconstructions. RESULTS: We
present a genome-scale reconstruction of P. putida KT2440's
metabolism, iJN746, which was constructed based on genomic,
biochemical, and physiological information. This
manually-curated reconstruction accounts for 746 genes, 950
reactions, and 911 metabolites. iJN746 captures
biotechnologically relevant pathways, including
polyhydroxyalkanoate synthesis and catabolic pathways of
aromatic compounds (e.g., toluene, benzoate, phenylacetate,
nicotinate), not described in other metabolic reconstructions
or biochemical databases. The predictive potential of iJN746
was validated using experimental data including growth
performance and gene deletion studies. Furthermore, in silico
growth on toluene was found to be oxygen-limited, suggesting
the existence of oxygen-efficient pathways not yet annotated in
P. putida's genome. Moreover, we evaluated the production
efficiency of polyhydroxyalkanoates from various carbon sources
and found fatty acids as the most prominent candidates, as
expected. CONCLUSION: Here we presented the first genome-scale
reconstruction of P. putida, a biotechnologically interesting
all-surrounder. Taken together, this work illustrates the
utility of iJN746 as i) a knowledge-base, ii) a discovery tool,
and iii) an engineering platform to explore P. putida's
potential in bioremediation and bioplastic production.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180068.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180068 | BioModels
Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
| 2643590 | ecrin-mdr-crc
Project description:Most proteogenomic approaches for mapping single amino acid polymorphisms (SAPs) require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. We present a new strategy for direct SAP detection without relying on NGS data. Among the 348 putative SAP peptides identified in an industrial yeast strain, 85.6% of SAP sites were validated by genomic sequencing.
2018-04-18 | PXD003101 | Pride