Project description:The Wood-Ljungdahl pathway in acetogens converts C1 compounds, such as CO2 and CO, into acetyl-CoA. Similarly, the glycine synthase pathway assimilates C1 compounds into glycine. Partial glycine synthase genes are widely conserved in the Wood-Ljungdahl pathway gene cluster but functional relationship between the pathways in autotrophic condition remains unknown. To comprehend, we assembled Clostridium drakei genome (5.7-Mbp) with intact glycine synthase pathway and constructed a genome-scale metabolic model, iSL836, predicting increased metabolic flux rates of the Wood-Ljungdahl pathway and the glycine synthase-reductase associated reactions under autotrophic conditions. Along with the observation of significant transcriptional activation of genes in the pathways, surprisingly, 13C-labeling experiments and enzyme activity assays confirmed the strain synthesizes glycine and converts into acetyl-phosphate. This study suggests the Wood-Ljungdahl and the glycine synthase-reductase pathways convert CO2 into acetyl-CoA and acetyl-phosphate, respectively. In our knowledge, this is the first report on co-utilization of the pathways under autotrophic growth in acetogen.

2019-08-01 | GSE118519 | GEO

Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis

Project description:Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin transcriptional activators, proteins harbouring a domain of unknown function (DUF2249), and a cyanoglobin. Additionally, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.

2024-04-22 | GSE245042 | GEO

Aerobic heterotrophic denitrification

Project description:Roothans et al., analyzed heterotrophic denitrification processes that can be an important source of nitrous oxide. We employed planktonic nitrification-inhibited denitrifying enrichment cultures under alternating oxic-anoxic conditions. The dynamic conditions resulted in a general presence of the denitrifying enzymes. Overall, we show that aerobic denitrification should not be neglected as an ecologically relevant process. Contact author: m.laureni@tudelft.nl

2024-07-17 | PXD042057 | Pride

Catma1-bou-bou mutant characterisation: Autotrophic growth acquisition in the ABOUTDESOUFFLE (bou) mutant

Project description:rs07-09_bou - catma1-bou - Autotrophic growth acquisition is abolished in the bou mutant in Arabidopsis thaliana. BOU encodes a putative mitochondrial acyl carnitine carrier. bou mutant is blocked at the cotyledon stage. Autotrophic growth of the bou mutant can be achieved with addition of sugar in the medium or in darkness. Moreover, BOU gene expression is activated by light and depends on plant developmental stage. We wish to determine what are the consequences of bou gene mutation at the transcriptome level. We wish to understand whether bou growth arrest is due to the modification of specific genes expression or to a general effect on metabolism at the transition from heterotrophic to autotrophic growth. - Seeds from a heterozygous plants were grown for either 5 or 8 days after germination on synthetic medium (MS/2) without sugar under continuous light. We harvested cotyledon-stage blocked plants (bou phenotype) from three independent Petri dishes and also green seedlings with true leaves and fully developed root (heterozygotes with a wild-type phenotype) . We also grew independently Col-O plants for 5 and 8 days to compare them with the bou mutants. Keywords: gene knock in (transgenic),normal vs disease comparison,time course

2009-02-05 | GSE10399 | GEO

seawater autotrophic microorganisms

Project description:seawater autotrophic microorganisms Raw sequence reads

| PRJNA418635 | ENA

soil autotrophic bacteria

Project description:soil autotrophic bacteria Raw sequence reads

| PRJNA599486 | ENA

soil autotrophic archaea

Project description:soil autotrophic archaea Raw sequence reads

| PRJNA599557 | ENA