Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria

ABSTRACT: An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria

PROVIDER: PRJNA944967 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23869300_1.fastq.gz	Fastqsanger.gz
	SRR23869300_2.fastq.gz	Fastqsanger.gz
	SRR23869301_1.fastq.gz	Fastqsanger.gz
	SRR23869301_2.fastq.gz	Fastqsanger.gz
	SRR23869302_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria

Project description:Regulation of CO2 fixation in cyanobacteria is important both for the organism and the global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP sensing mechanism, which upon ATP drops, allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham (CBB) cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light-dark transitions. In high-density cultures, the xpk strain showed a 60% increase in carbon fixation, and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.

2023-08-08 | GSE227397 | GEO

An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria.

Project description:Regulation of CO2 fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light-dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.

| S-EPMC10365998 | biostudies-literature

TrxA-mediated regulation of protein synthesis contributes to the maintenance of carbon and nitrogen balance in cyanobacteria.

Project description:Thioredoxins play an essential role in regulating enzyme activity upon response to environmental changes, especially in photosynthetic organisms. These are crucial for the regulation of metabolism in cyanobacteria, but the key central processes redox-regulated remain to be determined. Physiological, metabolic and transcriptomic characterization of a conditional mutant of the essential trxA gene in Synechocystis (STXA2) revealed that reduced TrxA levels alter cell morphology and enter in a dormant-like state. TrxA depletion in the STXA2 strain inhibited protein synthesis and led to changes in amino acid pools and nitrogen/carbon reserve polymers, accompanied by oxidation of the Elongation Factor EF-Tu. Transcriptomic analysis of TrxA depletion in STXA2 showed a robust transcriptional response. Genes that responded negatively were grouped in a large cluster and were directly related to photosynthesis, ATP synthesis and CO2 fixation, while genes that responded positively were grouped in different clusters and related to respiratory electron transport, carotenoids synthesis, amino acid metabolism and protein degradation, among others. Regulation of cyanobacterial metabolism is complex and fine-tuned, our results link TrxA to the switch from anabolic to maintenance metabolism in cyanobacteria, regulating carbon and nitrogen balance.

2023-09-24 | GSE243518 | GEO

Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts

Project description:Biological carbon fixation is foundational to the biosphere. Most autotrophs are thought to possess one carbon fixation pathway. The hydrothermal vent tubeworm Riftia pachyptila’s chemoautotrophic symbionts, however, possess two functional pathways: the Calvin Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. Little is known about how Riftia’s symbionts and related organisms coordinate the functioning of these two pathways. Here we investigated net carbon fixation rates, transcriptional/metabolic responses, and transcriptional co-expression patterns of Riftia pachyptila’s endosymbionts by incubating tubeworms at environmental pressures, temperature, and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes, suggesting distinctive yet complementary roles in metabolic function. Net carbon fixation rates were also exemplary, and accordingly we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.

2024-03-28 | GSE249345 | GEO

In serach of the pH limit of growth in halo-alkaliphilic cyanobacteria

Project description:We cultivated two halo-alkaliphilic cyanobacteria consortia in chemostats at pH 10.2-11.4. One consortium was dominated by Ca. Sodalinema alkaliphilum, the other by a species of Nodosilinea. These two cyanobacteria dominate natural communities in Canadian and Asian alkaline soda lakes. We show that increasing the pH decreased biomass yield. This decrease was caused, in part, by a dramatic increase in carbon transfer to heterotrophs. At pH 11.4, cyanobacterial growth became limited by bicarbonate uptake, which was mainly ATP-dependent. In parallel, the higher the pH, the more sensitive cyanobacteria became to light, resulting in photoinhibition and upregulation of DNA repair systems.

2024-10-17 | PXD052563 | Pride

Co-existence of CBB cycle and rTCA carbon fixation pathway in thermophilic Actinomycetota Carbonactinospora thermoautotrophica StC and correlation with the CO2-concentrating microcompartment

Project description:Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation. The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.

2024-04-09 | GSE263135 | GEO

Carbon limitation of heterotrophic N2 fixation

Project description:Carbon limitation of heterotrophic dinitrogen fixation in the coastal Eastern Mediterranean Sea

| PRJEB8799 | ENA

Dark carbon fixation in stratified boreal lakes water column

Project description:Dark carbon fixation in stratified boreal lakes water column

| PRJEB76863 | ENA

Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids

Project description:we determine genome-wide binding profiles of a maize CCA1 homolog, ZmCCA1b, in maize inbreds and F1 hybrids at different times of the day. ZmCCA1b is characterized as a central clock regulator gene with evolutionarily conserved molecular and circadian functions and nonadditively expressed in F1 hybrid seedlings. ZmCCA1b binds to over 4,300 target genes in the maize genomes, of which annotation confirms energy metabolic pathways as the main output. We report that an altered temporal binding activity of ZmCCA1b in the hybrid seedlings, which increases expression of carbon fixation genes, increases carbon fixation rates and biomass, demonstrating a novel example of how circadian-regulatory networks directly contribute to growth vigor in maize hybrids. These results collectively offer new insights into clock-mediated regulation of growth vigor in hybrid plants and crops.

2016-06-30 | GSE67655 | GEO

Transcriptional cycle suited to daytime N2 fixation in the unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A)

Project description:Investigation of whole genome gene expression level changes in two strains of the cyanobacteria Atelocyanobacterium thalasaa (UCYN-A) from environmental samples. The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2017. Unicellular cyanobacterial symbiosis facilitates aerobic nitrogen fixation. Science (to be submitted).

2018-12-05 | GSE100124 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data