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Comparative transcriptomics illustrates the unique N2-fixation strategies in thermophilic Methanococcales

ABSTRACT: The unique N2-fixation strategies in thermophilic Methanococcales

PROVIDER: PRJEB53446 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR9919970_1.fastq.gz	Fastqsanger.gz
	ERR9919970_2.fastq.gz	Fastqsanger.gz
	ERR9919980_1.fastq.gz	Fastqsanger.gz
	ERR9919980_2.fastq.gz	Fastqsanger.gz

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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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RNA-Seq provides new insights into the nitrogen response of Azoarcus olearius BH72 during N2-fixation beyond the nitrogen fixation process

Project description:Azoarcus olearius BH72 is a diazotrophic endophyte carrying out biological nitrogen fixation (BNF) and supplying nitrogen to its host plant. Our previous microarray approach provided insights in the transcriptome of strain BH72 under N2-fixation in comparison to ammonium-grown conditions, which already indicated induction of genes not related to the BNF process. Due to the known limitations of the technique, we might have missed additional differentially regulated genes (DEGs). Thus we used directional RNA-Seq to better comprehend the transcriptional landscape under these growth conditions. RNA-Seq detected almost 24 % of the annotated genes to be regulated, twice the amount identified by microarray. In addition to confirming entire regulated operons containing known DEGs, the new approach detected induction of genes involved in carbon metabolism and flagellar and twitching motility. On the other hand, genes encoding for proteins involved in translation and vitamin biosynthesis were detected to be suppressed. Nonetheless, strain BH72 appears not to be content with N2-fixation but is primed for alternative economic N-sources, such as nitrate, urea or amino acids: we detected strong induction of machineries for uptake and assimilation.

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Project description:This project investigates the proteomic remodeling associated with N2 fixation and NH4+ assimilation in Zymomona mobilis. Previous work has elucidated the metabolic and proteomic response of Zymomona mobilis during steady state N2 fixation. These experiments examine the proteomic profile during the dynamic shift of N2 and NH4+.

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RNA-Seq provides new insights into the nitrogen response of Azoarcus olearius BH72 during N2-fixation beyond the nitrogen fixation process

Project description:RNA-Seq provides new insights into the nitrogen response of Azoarcus olearius BH72 during N2-fixation beyond the nitrogen fixation process

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Project description:The global significance of marine non-cyanobacterial diazotrophs, notably heterotrophic bacterial diazotrophs (HBDs), has become increasingly clear. Understanding N2 fixation rates for these largely uncultured organisms poses a challenge due to uncertain growth requirements and complex nitrogenase regulation. We identified Candidatus Thalassolituus haligoni as an Oceanospirillales member, closely related to other significant γ-proteobacterial HBDs. Pangenome analysis reinforces this classification, indicating the isolate belongs to the same species as the uncultured metagenome-assembled genome Arc-Gamma-03. Analysis of the nifH gene in amplicon sequencing libraries reveals the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic and Arctic Oceans. Through combined proteomic analysis and N2 fixation rate measurements, we confirmed the isolate’s capacity for nitrate independent N2 fixation, although a clear understanding of nitrogenase regulation remains unclear. Overall, our study highlights the significance of Cand. T. haligoni as the first globally distributed, cultured model species within the understudied group of Oceanospirillales, and γ-HBDs in general.

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Carbon limitation of heterotrophic N2 fixation

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

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