Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222

Abstract

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 Paracoccus denitrificans 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 respiratory nitrate, nitrite, nitric oxide, and nitrous oxide reductases, was increased. However, the periplasmic and assimilatory nitrate reductases decreased. Synthesis of transporters for alcohols, D-methionine, sulfate and copper, most of the enzymes involved in the tricarboxylic acid cycle, and proteins involved in other metabolic processes like lysine catabolism, fatty acids degradation and acetyl-CoA synthesis, was increased during denitrification in P. denitrificans PD1222. As consequence, an enhanced production of the central metabolite acetyl-CoA was observed. After establishing the key features of the denitrification proteome, its changes by the influence of a competitive electron acceptor, oxygen, or competitive nitrogen source, ammonium, were evaluated.

Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344

“…Finally, the quantification of the protein concentration in the samples was carried out by the method of Bradford (1976). The samples were analyzed in the Central Service for Research Support (SCAI) of the University of Córdoba, as previously described (Olaya-Abril et al, 2018). Following an analysis by using MaxQuant (Cox and Mann, 2008), which uses the free available software Perseus (version 1.5.6.0) 2 , a differential analysis was carried out.…”

“…Proteins identified from only one peptide and/or in only one replicate were discarded. Proteins identified in at least two replicates per each condition were used for differential pairwise comparison analysis if they were positive after considering a two-way Student-test (Olaya-Abril et al, 2018). Proteins were considered differentially expressed when the fold change was ≥2 with a p value <0.05.…”

“…RNA isolation, cDNA synthesis and cDNA quantitation was carried out from the wild-type and dapA1 − cells grown with the cyanide-containing jewelry residue (2 mM free cyanide) as nitrogen source, as previously described (Olaya-Abril et al, 2018). Target cDNAs were amplified in three independent PCR reactions using specific primers ( Supplementary Table S4).…”

Systems biology approaches towards predictive microbial ecology

“…In‐depth understanding of denitrification and nitrification pathways is mainly based on pure culture studies in the laboratory with model organisms, such as the denitrifier Paracoccus denitrificans. Through dozens of studies that employ a range of techniques (e.g., transcriptomics, proteomics, enzyme kinetics, gas flux analysis), its denitrification phenotype, including biochemical pathways and regulatory networks involved, has been well‐characterized (Bakken et al, ; Qu et al, ; Giannopoulos et al, ; Olaya‐Abril et al, ; Bergaust et al, ). For example, higher N 2 O production is associated with low pH conditions, an observation that is consistent with field observations (SImek & Cooper, ).…”

Paracoccus bengalensis is a later heterotypic synonym of Paracoccus versutu

“…Members of this genus exhibit excellent metabolic diversity and flexibility, which could contribute to adequately responding and adapting to environmental changes [1]. The two well-studied examples are the species P. denitrificans and Paracoccus pantotrophus characterized by fixing carbon dioxide [3], utilizing methanol and methylamine as the sole carbon source for growth [4], degrading n-alkanes and aromatic hydrocarbons [5], reducing nitrate to gaseous nitrogen [3], and oxidizing reduced inorganic sulfur compounds [6], thereby showing promising potential in bioremediation. Chemotaxonomically, strains of this genus are characterized by ubiquinone-10 (Q-10) as the major respiratory quinone, C 18 : 1 ω7c as the predominant fatty acid and a wide range of DNA G+C contents from 64 to 70 mol% [7].…”