Dataset Information

Effect of pH on the proteome of Paracoccus denitrificans PD1222 under denitrifying conditions

ABSTRACT: The work is based on the quantitative proteomic analysis free of marking samples of the gram negative denitrification bacteria Paracoccus denitrificans grown at different pH.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Paracoccus Denitrificans Pd1222

TISSUE(S): Prokaryotic Cell

SUBMITTER: Alfonso Olaya Abril

LAB HEAD: María Dolores Roldán Ruiz

PROVIDER: PXD013138 | Pride | 2021-09-08

REPOSITORIES: Pride

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Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans 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 Dolores MD

Scientific reports 20210826 1

Denitrification is a respiratory process by which nitrate is reduced to dinitrogen. Incomplete denitrification results in the emission of the greenhouse gas nitrous oxide and this is potentiated in acidic soils, which display reduced denitrification rates and high N<sub>2</sub>O/N<sub>2</sub> ratios compared to alkaline soils. In this work, impact of pH on the proteome of the soil denitrifying bacterium Paracoccus denitrificans PD1222 was analysed with nitrate as sole energy and nitrogen source ...[more]

PMID: 34446760

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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

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	pH6.5_1.raw	Raw
	pH6.5_2.raw	Raw
	pH6.5_3.raw	Raw
	pH7.0_1.raw	Raw
	pH7.0_2.raw	Raw