Ontology highlight
ABSTRACT:
PROVIDER: PRJNA740357 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. Our analysis reveals that naturally relevant light conditions drastically modify gene expression dynamics in cyanobacteria Notably, the expression of circadian clock-controlled genes is responsive to changes in light intensity, showing modulated dynamics that can allow cyanobacteria to adapt their metabolism to changing environmental conditions
2017-12-16 | GSE104203 | GEO
Project description:Many cyanobacteria can form nitrogen-fixing symbioses with a broad range of plant species. Unlike other plant-bacteria symbioses, little is understood about the immunological responses induced by plant cyanobionts (symbiotic cyanobacteria). Here, we used Arabidopsis thaliana suspension cell cultures as a model system to demonstrate that the model plant-symbiotic cyanobacteria, Nostoc punctiforme is capable of protecting against plant programmed cell death (PCD). We also profiled the early transcriptomic changes that were induced in response to conditioned medium (CM) from N. punctiforme cell cultures. Interestingly, the PCD reduction was preceded by the induction of genes associated with defence and immunity, the most striking of which were a number of WRKY-family transcription factors. Down-regulated included genes involved in the regulation of cell growth and differentiation. This work is the first to show that a cyanobacteria can regulate plant PCD and provides a useful transcriptome resource for studying early plant cell responses to symbiotic cyanobacteria.
2020-12-10 | GSE155980 | GEO
Project description:INTERACTIONS BETWEEN CYANOBACTERIA AND HETEROTROPHS UNDER DIFFERENT TROPHIC CONDITIONS
| PRJNA231839 | ENA
Project description:To characterize how symbiotic bacteria affect the lolecular and cellular mechanisms of epithelial homeostasis, human colonic Caco-2 cells were co-culture with Lactobacillus casei and Bifidobacterium breve.
2013-04-09 | GSE37369 | GEO
Project description:Cyanobacteria are phototrophic prokaryotes that can convert inorganic carbon as CO2 into organic carbon compounds at the expense of light energy. In addition, they need only a few inorganic nutrients and can be cultivated in high densities using non-arable land and seawater. This features qualified cyanobacteria as attractive organisms for the production of third generation biofuels as part of the development of future CO2-neutral energy production. Synechocystis sp. PCC 6803 represents one of the most widely used cyanobacterial model strains. On the basis of its available genome sequence and genetic tools, many strains of Synechocystis have been generated that produce different biotechnological products. Efficient isoprene production is an attractive goal, since this compound represents not only an energy-rich biofuel but is also used as chemical feedstock. Here, we report on our attempts to generate isoprene-producing strains of Synechocystis. The cDNA of a codon-optimized plant isoprene synthase (IspS) was cloned under the control of different Synechocystis promoters, which ensure strong constitutive or light-regulated ispS expression. The expression of the ispS gene was quantified by qPCR, whereas the amount of isoprene was quantified using GC-MS. Incubation of our strains at different salt conditions had marked impact on the isoprene production rates. Under low salt conditions, a good correlation was found between ispS expression and isoprene production rate. However, the cultivation of isoprene production strains under salt-supplemented conditions decreased isoprene production despite the fact that ispS expression was salt-stimulated. The characterization of the metabolome of isoprene producing strains indicated that isoprene production might be limited by insufficient precursor levels. Our isoprene production rates under low salt conditions were 2 - 6.5times higher compared to the previous report of Lindberg et al. (2010). These results can be used to guide future attempts establishing the isoprene production with cyanobacterial host systems.
2015-11-13 | GSE74940 | GEO
Project description:We compared changes, induced by the addition of 100 nM and 5 mM glucose in the proteome and metabolome complements in several strains of Synechococcus and Prochlorococcus, growing either under standard light conditions or darkness. Our results demonstrate that glucose is being metabolized by these cyanobacteria, using mainly the oxidative pentoses pathway, while no evidence was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the metabolic strategies for glucose utilization, both between genera, and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. Our results also suggest that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness.
2023-01-05 | PXD035483 | Pride
Project description:We compared changes, induced by the addition of 100 nM and 5 mM glucose in the proteome and metabolome complements in several strains of Synechococcus and Prochlorococcus, growing either under standard light conditions or darkness. Our results demonstrate that glucose is being metabolized by these cyanobacteria, using mainly the oxidative pentoses pathway, while no evidence was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the metabolic strategies for glucose utilization, both between genera, and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. Our results suggest that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness.
2023-01-05 | PXD035660 | Pride
Project description:We compared changes, induced by the addition of 100 nM and 5 mM glucose in the proteome and metabolome complements in several strains of Synechococcus and Prochlorococcus, growing either under standard light conditions or darkness. Our results demonstrate that glucose is being metabolized by these cyanobacteria, using mainly the oxidative pentoses pathway, while no evidence was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the metabolic strategies for glucose utilization, both between genera, and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. Our results also suggest that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness.
2023-01-05 | PXD035402 | Pride
Project description:We compared changes, induced by the addition of 100 nM and 5 mM glucose in the proteome and metabolome complements in several strains of Synechococcus and Prochlorococcus, growing either under standard light conditions or darkness. Our results demonstrate that glucose is being metabolized by these cyanobacteria, using mainly the oxidative pentoses pathway, while no evidence was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the metabolic strategies for glucose utilization, both between genera, and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. Our results also suggest that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness.
2023-01-05 | PXD035481 | Pride
Project description:Nogales2012 - Genome-scale metabolic network
of Synechocystis sp. (iJN678)
This model is described in the article:
Detailing the optimality of
photosynthesis in cyanobacteria through systems biology
analysis.
Nogales J, Gudmundsson S, Knight EM,
Palsson BO, Thiele I.
Proc. Natl. Acad. Sci. U.S.A. 2012 Feb;
109(7): 2678-2683
Abstract:
Photosynthesis has recently gained considerable attention
for its potential role in the development of renewable energy
sources. Optimizing photosynthetic organisms for biomass or
biofuel production will therefore require a systems
understanding of photosynthetic processes. We reconstructed a
high-quality genome-scale metabolic network for Synechocystis
sp. PCC6803 that describes key photosynthetic processes in
mechanistic detail. We performed an exhaustive in silico
analysis of the reconstructed photosynthetic process under
different light and inorganic carbon (Ci) conditions as well as
under genetic perturbations. Our key results include the
following. (i) We identified two main states of the
photosynthetic apparatus: a Ci-limited state and a
light-limited state. (ii) We discovered nine alternative
electron flow pathways that assist the photosynthetic linear
electron flow in optimizing the photosynthesis performance.
(iii) A high degree of cooperativity between alternative
pathways was found to be critical for optimal autotrophic
metabolism. Although pathways with high photosynthetic yield
exist for optimizing growth under suboptimal light conditions,
pathways with low photosynthetic yield guarantee optimal growth
under excessive light or Ci limitation. (iv) Photorespiration
was found to be essential for the optimal photosynthetic
process, clarifying its role in high-light acclimation.
Finally, (v) an extremely high photosynthetic robustness drives
the optimal autotrophic metabolism at the expense of metabolic
versatility and robustness. The results and modeling approach
presented here may promote a better understanding of the
photosynthetic process. They can also guide bioengineering
projects toward optimal biofuel production in photosynthetic
organisms.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180046.
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 | MODEL1507180046 | BioModels