An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria
Ontology highlight
ABSTRACT:
ORGANISM(S): Synechococcus elongatus
PROVIDER: GSE227397 | GEO | 2023/08/08
REPOSITORIES: GEO
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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.
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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.
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Project description:Acclimation to low CO2 conditions in cyanobacteria involves the coordinated regulation of genes mainly encoding components of the carbon concentration mechanism (CCM). Making use of several independent microarray datasets a core set of CO2-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR and CmpR, whereas the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. Here we present results of transcript profiling of the wild type and a ΔcyabrB2 mutant of Synechocystis sp. PCC 6803 after shifts from high CO2 (5% in air, HC) to low CO2 (0.04%, LC). Evaluation of the transcriptomic data revealed that cyAbrB2 is involved in the regulation of several CCM-related genes such as sbtA/B, ndhF3/ndhD3/cupA and cmpABCD under LC conditions, but apparently acts supplementary to the main regulators. Under HC conditions, cyAbrB2 deletion changes the expression of photosystem II subunits, light-harvesting components, and Calvin-Benson-Bassham cycle enzymes.
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Project description:Ralstonia eutropha H16 is well-known to produce poly(3-hydroxybutyrate) [P(3HB)], a kind of polyhydroxyalkanoates attracted as bio-based biodegradable plastics, efficiently as an energy storage material under unbalanced growth conditions. To obtain further extended knowledge of PHA biosynthesis, this study employed quantitative transcriptome analysis based on deep sequencing of complementary DNA generated from RNA (RNA-seq) for R. eutropha H16. Total RNAs were extracted from R. eutropha cells in growth, PHA production, and stationary phases on fructose. rRNAs in the preparation were removed by repeated treatments with magnetic beads specific to bacterial rRNAs, and then the 36 bp sequences were determined by using Illumina high-throughput sequencer. The RNA-seq results supported induction of gene expression for transcription, translation, cell division, peptidoglycan biosynthesis, pilus and flagella assembly, energy conservation, and fatty acid biosynthesis in growth phase, and repression trends for genes involved in central metabolisms in PHA production phase. Interestingly, transcription of genes for Calvin-Benson-Bassham (CBB) cycle and several selected genes for ?-oxidation were significantly induced in PHA production phase even when the cells were grown on fructose. mRNA profiles of R. eutropha H16 grown on fructose at different phases were generated by deep sequencing, in duplicate, using Illumina GAIIx.
2014-06-07 | E-GEOD-47759 | biostudies-arrayexpress
Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.
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Project description:Bradyrhizobium diazoefficiens, the soybean N2-fixing symbiont, uses mannitol or arabinose as carbon and energy source, among other substances. In this bacterium, growth with mannitol led to higher biomass production, and inhibited the synthesis of its secondary (lateral) flagellar system, regarding growth with arabinose. A proteomic comparison of bacteria grown in mannitol or arabinose suggested that mannitol may be degraded by the Calvin-Benson-Bassham pathway, while arabinose seems degraded by the L-2-keto-3-deoxyarabonate pathway, both pathways sharing only the reactions from pyruvate to CO2. Despite these differences, the stoichiometric balances resulted in similar O2 consumption and ATP production per C-mole of substrate. The poly-3-hydroxybutyrate biosynthesis pathway was stimulated in mannitol, while in arabinose there was a consistent increase in enzymes for the synthesis of nicotinamide adenine dinucleotide from aspartate, suggesting a surplus of reducing power in mannitol. This may agree to previous reports showing higher O2 consumption rate in arabinose, which taking into account the similarity in O2 consumption balance, suggests higher maintenance energy demand in this carbon and energy source. Since lateral flagella are produced only in arabinose, we wondered whether their energy demand might explain this difference. Hence, we compared the O2 consumption rates in mannitol and arabinose of the wild-type and a lafR::Km mutant devoid of lateral flagella. We observed that, while there was a three-fold higher O2 consumption rate in the wild-type in arabinose with respect to mannitol, there was no difference in the mutant, suggesting that lateral flagella behave as parasitic structures in this medium.
2018-06-25 | PXD008263 | Pride
Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy. Two biological replicates of timecourses under four conditions: medium bubbled with air (control) or three experimental gases (low CO2; low O2; or low CO2 and low O2)
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Project description:Ralstonia eutropha H16 is well-known to produce poly(3-hydroxybutyrate) [P(3HB)], a kind of polyhydroxyalkanoates attracted as bio-based biodegradable plastics, efficiently as an energy storage material under unbalanced growth conditions. To obtain further extended knowledge of PHA biosynthesis, this study employed quantitative transcriptome analysis based on deep sequencing of complementary DNA generated from RNA (RNA-seq) for R. eutropha H16. Total RNAs were extracted from R. eutropha cells in growth, PHA production, and stationary phases on fructose. rRNAs in the preparation were removed by repeated treatments with magnetic beads specific to bacterial rRNAs, and then the 36 bp sequences were determined by using Illumina high-throughput sequencer. The RNA-seq results supported induction of gene expression for transcription, translation, cell division, peptidoglycan biosynthesis, pilus and flagella assembly, energy conservation, and fatty acid biosynthesis in growth phase, and repression trends for genes involved in central metabolisms in PHA production phase. Interestingly, transcription of genes for Calvin-Benson-Bassham (CBB) cycle and several selected genes for β-oxidation were significantly induced in PHA production phase even when the cells were grown on fructose.
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2019-01-17 | PXD007963 | Pride