Ontology highlight
ABSTRACT:
PROVIDER: PRJNA888460 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21876278_1.fastq.gz | Fastqsanger.gz | |||
| SRR21876278_2.fastq.gz | Fastqsanger.gz | |||
| SRR21876279_1.fastq.gz | Fastqsanger.gz | |||
| SRR21876279_2.fastq.gz | Fastqsanger.gz | |||
| SRR21876280_1.fastq.gz | Fastqsanger.gz |
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Project description:Beller, H. R., T. E. Letain, A. Chakicherla, S. R. Kane, T. C. Legler, and M. A. Coleman. 2006. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic vs. denitrifying conditions. Journal of Bacteriology 188:7005-7015. Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends. Keywords: bacterial metabolism
2006-10-06 | GSE5256 | GEO
Project description:Biological denitrification bacterial community YEM003
| PRJNA1051279 | ENA
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
Project description:Microbes in biofilms face the challenge of substrate limitation. In particular, cells in Pseudomonas aeruginosa biofilms growing in the laboratory or during host colonization often become limited for oxygen. Previously we found that phenazines, antibiotics produced by P. aeruginosa, balance the intracellular redox state for cells in biofilms. Here, we show that genes involved in denitrification are induced in phenazine-null (Δphz) mutant biofilms grown under an aerobic atmosphere, even in the absence of nitrate. This finding suggests that resident cells employ a bet-hedging strategy to anticipate the potential availability of nitrate and counterbalance their highly reduced redox state. Consistent with our previous characterization of aerobically-grown colonies supplemented with nitrate, we find that the pathway that is induced in Δphz colonies combines the nitrate reductase activity of the periplasmic enzyme Nap with downstream reduction of nitrite to nitrogen gas catalyzed by the enzymes Nir, Nor, and Nos. This regulatory relationship differs from the denitrification pathway that functions under anaerobic growth with nitrate as the terminal electron acceptor, which depends on the membrane-associated nitrate reductase Nar. We identify sequences in the promoter regions of the nap and nir operons that are required for the effects of phenazines on expression. We also show that specific phenazines have differential effects on nap gene expression. Finally, we provide evidence that individual steps of the denitrification pathway are catalyzed at different depths within aerobically grown biofilms, suggesting metabolic cross-feeding between community subpopulations. (corresponding publication)
2018-10-19 | PXD008924 | Pride