Dataset Information

Quantitative proteomic analysis by Liquid Chromatography-Mass Spectrometry/Mass Spectrometry of Paracoccus denitrificans PD1222 under denitrifying conditions

ABSTRACT: In this work, the denitrification process carried out by Paracoccus denitrificans PD1222 has been followed up by a quantitative proteomic analysis.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Paracoccus Denitrificans Pd1222

TISSUE(S): Prokaryotic Cell

SUBMITTER: Alfonso Olaya Abril

LAB HEAD: María Dolores Roldán Ruiz

PROVIDER: PXD006821 | Pride | 2018-06-14

REPOSITORIES: Pride

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Publications

Exploring the Denitrification Proteome of <i>Paracoccus denitrificans</i> PD1222.

Olaya-Abril Alfonso A Hidalgo-Carrillo Jesús J Luque-Almagro Víctor M VM Fuentes-Almagro Carlos C Urbano Francisco J FJ Moreno-Vivián Conrado C Richardson David J DJ Roldán María D MD

Frontiers in microbiology 20180529

Denitrification is a respiratory process that produces nitrous oxide as an intermediate, which may escape to the atmosphere before its reduction to dinitrogen through the nitrous oxide reductase NosZ. In this work, the denitrification process carried out by <i>Paracoccus denitrificans</i> PD1222 has been explored through a quantitative proteomic analysis. Under anaerobic conditions, with nitrate as sole nitrogen source, the synthesis of all the enzymes involved in denitrification, the respirator ...[more]

PMID: 29896187

Similar Datasets

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

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