Dataset Information

Proteome of NtrY defective mutant in Paracoccus denitrificans PD1222

ABSTRACT: Quantitative proteomic analysis of Paracoccus denitrificans PD1222 wild type and NtrY defective mutant in denitrifying conditions (anaerobiosis, nitrate as nitrogen source)

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Bacteria Paracoccus Denitrificans Pd1222

SUBMITTER: Alfonso Olaya Abril

LAB HEAD: María Dolores Roldán Ruiz

PROVIDER: PXD033855 | Pride | 2022-10-13

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	DIANNResultsDE2-first-pass.gg_matrix.tsv	Tabular
	DIANNResultsDE2-first-pass.pg_matrix.tsv	Tabular
	DIANNResultsDE2-first-pass.pr_matrix.tsv	Tabular
	DIANNResultsDE2-first-pass.stats.tsv	Tabular
	DIANNResultsDE2-first-pass.tsv	Tabular

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Publications

The NtrYX Two-Component System of <i>Paracoccus denitrificans</i> Is Required for the Maintenance of Cellular Iron Homeostasis and for a Complete Denitrification under Iron-Limited Conditions.

Olaya-Abril Alfonso A Luque-Almagro Víctor M VM Hidalgo-Carrillo Jesús J Chicano-Gálvez Eduardo E Urbano Francisco J FJ Moreno-Vivián Conrado C Richardson David J DJ Roldán María Dolores MD

International journal of molecular sciences 20220815 16

Denitrification consists of the sequential reduction of nitrate to nitrite, nitric oxide, nitrous oxide, and dinitrogen. Nitrous oxide escapes to the atmosphere, depending on copper availability and other environmental factors. Iron is also a key element because many proteins involved in denitrification contain iron-sulfur or heme centers. The NtrYX two-component regulatory system mediates the responses in a variety of metabolic processes, including denitrification. A quantitative proteomic anal ...[more]

PMID: 36012437

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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