Metabolic and Evolutionary Insights in the Transformation of Diphenylamine by a Pseudomonas putida Strain Unravelled by Genomic, Proteomic, and Transcription Analysis

The role of oxidative stress in genome destabilization and adaptive evolution of bacteria

The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.

Surfactant-Assisted Synthesis of Praseodymium Orthovanadate Nanofiber-Supported NiFe-Layered Double Hydroxide Bifunctional Catalyst: The Electrochemical Detection and Degradation of Diphenylamine

Physiological storage disorders are caused by ineffective post-harvest handling of horticultural crops, particularly fruits. To address these post-harvest concerns, diphenylamine (DPAH^•+) is widely used as a preservative to prevent fruit degradation and surface scald during storage around the world. Humans are negatively affected by the use of high concentrations of DPAH^•+ because of the various health complications related to its exposure. As a result, accurate detection and quantification of DPAH^•+ residues in treated fruits are critical. Rare earth metal orthovanadates, which have excellent physical and chemical properties, are potential materials for electrochemical sensors in this area. Herein, we present a simple and direct ultrasonication technique for the surfactant-assisted synthesis of praseodymium orthovanadate (PrVO₄ or PrV) loaded on nickel iron layered double hydroxide (NiFe-LDH) synthesized with deep eutectic solvent assistance, as well as its application as an effective catalyst in the detection and degradation of DPAH^•+ in fruits and water samples. The current work presents supreme electrochemical features of a PrV@NiFe-LDH-modified screen-printed carbon electrode (SPCE) where cetyltrimethylammonium bromide (CTAB) surfactant-driven fabrication of PrV directs the formation of highly qualified engineered structures and the deep eutectic solvent based green synthesis of NiFe-LDH creates hierarchical lamellar structures following the principles of green chemistry. PrV and NiFe-LDH combine to produce a synergistic effect that improves the number of active sites, charge transfer kinetics, and electronic conductivity. Differential pulse voltammetry analysis of PrV@NiFe-LDH/SPCE reveals a dynamic working range (0.005-226.26 μM), increased sensitivity (133.13 μA μM^-1 cm^-2), enhanced photocatalytic activity, and low detection limit (0.001 μM), which are considered significant when compared with the former reported electrodes in the literature for the determination of DPAḢ⁺ for its real-time applications.

Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis

The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.

Bioinoculant capability enhancement through metabolomics and systems biology approaches

Bioinoculants are eco-friendly microorganisms, and their products are utilized for improving the potential of soil and fulfill the nutrients requirement for the host plant. The agricultural yield has increased due to the use of bioinoculants over chemical-based fertilizers, and thus it generates interest in understanding the innovation process by various methods. By gene-editing tool, the desired gene product can be changed for engineered microbial inoculants. We have also described various modern biotechnological tools like constraint-based modeling, OptKnock, flux balance analysis and modeling of the biological network for enhancing the bioinoculant capability. These fluxes give the fascinating perception of the metabolic network in the absence of comprehensive kinetic information. These tools also help in the stimulation of the metabolic networks by incorporation of enzyme-encoding genes. The present review explains the use of systems biology and gene-editing tools for improving the capability of bioinoculants. Moreover, this review also emphasizes on the challenges and future perspective of systems biology and its multidisciplinary facets.