Abstract
Plants cannot uptake the insoluble form of phosphate from soil. Phosphate-solubilizing microbes (PSMs) release gluconic acid (C6H12O7) that is synthesized by the interaction between co-factor pyrroloquinoline quinine (PQQ) and glucose dehydrogenase within themselves and hence convert the insoluble phosphate into a soluble form. Phylogenetic analyses based on individual sequences of PqqA–PqqE proteins involved in the PQQ biosynthetic pathway manifested clear clustering formation of the selected species according to their respective genera such asPantoea, Rouxiella, Rahnella, Kosakonia, Mixta, Cronobacter, andSerratia. In multiple sequence alignment (MSA), numerous semi-conserved sites were identified that indicate acquired mutation during evolution. The selectedpqqgenes that appeared within an operon system sustain a specified order viz.pqqABCDEfor both positive and negative strands. The nucleotide composition of the encoding genes displayed higher content of GCs at different positions of the codons and has also been properly reflected in relative synonymous codon usage (RSCU) values of the codons with few exceptions. The correspondence analysis (COA) based on RSCU proclaimed that thepqqBgenes prefer A/U-ending codons over G/C, while for thepqqEgene, G/C-ending codons are comparatively more preferable (except CGU). Mutational pressure contributes to shaping the codon usage pattern for the selectedpqqgenes evinced from the COAs, while the ENc and neutrality plot gives attestation of natural selection. The higher values of CAI indicate the gene adaptability and codon usage bias. These comprehensive computational studies can be beneficial for further research in molecular phylogenetics, genomics, and proteomics and to better understand the evolutionary dynamics of PQQ.
Highlights
Microbes present in the rhizosphere, the nutrient-rich region of the soil surrounding the plant’s roots, play important roles in the enhancement of plants’ nutrient uptake, metabolic activities, crop productivity, and tolerance to multiple biotic and abiotic stresses
An in silico approach was used to investigate the molecular evolution of the genes involved in the pyrroloquinoline quinine (PQQ) biosynthetic pathway among different species of Gammaproteobacteria
Phylogenetic analyses based on individual sequences of PqqA–PqqE proteins involved in the PQQ biosynthetic pathway depicted all the selected species getting clustered prominently according to their genera, such as Pantoea, Rouxiella, Rahnella, Kosakonia, Mixta, Cronobacter, and Serratia, suggesting their phylogenetic closeness
Summary
Microbes present in the rhizosphere, the nutrient-rich region of the soil surrounding the plant’s roots, play important roles in the enhancement of plants’ nutrient uptake, metabolic activities, crop productivity, and tolerance to multiple biotic and abiotic stresses. P plays an important role in carrying out metabolic processes such as photosynthesis, signal transduction, cell division, nutrient transport, and macromolecular biosynthesis, increasing the efficiency of nitrogen fixation in legumes and respiration in plants (Alaylar et al, 2019; Billah et al, 2019). It is a fundamental component of enzymes, coenzymes, proteins, phospholipids, nucleotides, and nucleic acids (Kafle et al, 2019; Kalayu, 2019; Alayler et al, 2020). Plants can utilize only a smidgen amount of these fertilizers and the remaining portion precipitates out into the soil as perennial complexes, resulting in numerous adverse effects on Mother Nature like environmental degradation by the emission of CO2, eutrophication (Youssef and Eissa, 2014; Bhattacharyya et al, 2020), soil fertility depletion (Gyaneshwar et al, 2002), consumption of non-renewable energy, etc
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