Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

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 as Pantoea, Rouxiella, Rahnella, Kosakonia, Mixta, Cronobacter, and Serratia. In multiple sequence alignment (MSA), numerous semi-conserved sites were identified that indicate acquired mutation during evolution. The selected pqq genes that appeared within an operon system sustain a specified order viz. pqqABCDE for 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 the pqqB genes prefer A/U-ending codons over G/C, while for the pqqE gene, G/C-ending codons are comparatively more preferable (except CGU). Mutational pressure contributes to shaping the codon usage pattern for the selected pqq genes 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.

Development of a Multicomponent Microbiological Soil Inoculant and Its Performance in Sweet Potato Cultivation

“…The genus Pseudomonas is well known for IAA production [60][61][62] and several strains were also tested on Sedum alfredii and Arabidopsis thaliana with promising results [63,64]. The genome sequence of the P. resinovorans strain SZMC 25872 [28] contains the tryptophane side chain oxidase (tso) and the aldehyde dehydrogenase (AldA) genes enabling IAA production [65], as well as the genes pqqB, pqqC and pqqE of the pyrroloquinoline quinine biosynthetic pathway, which are contributing to phosphate solubilization [66].…”

Designing Synergistic Biostimulants Formulation Containing Autochthonous Phosphate-Solubilizing Bacteria for Sustainable Wheat Production

“…The pqqC and pqqE genes of strain SSR were amplified and known as most essential genes of PQQ operon. The biosynthesis of PQQ is only accomplished when the complex of gene products, i.e., pqq A, B, D, and F gets attached to pqqC at the C-terminal and with pqqE at the N-terminal (Bhanja et al, 2021 ). The amplification of these essential genes is the significant contribution and can provide novel insights into understanding the PQQ biosynthesis pathway in Ochrobactrum sp.…”

“…At present, the research on the genes of PSB related to P i solubilization is mainly focused on pyrroloquinoline quinone–glucose dehydrogenase (gcd) and six redox–coenzyme pyrroloquinoline quinone genes pqq A, B, C, D, E, F , and G (Bhanja et al, 2021 ). By contrast, the organic phosphates are hydrolyzed by acid phosphatases, alkaline phosphatases, and phytases (inositol phosphate phosphatases) that are encoded by phosphatase ( pho ) genes (Sarr et al, 2020 ).…”

Virtual screening and docking analysis of novel ligands for selective enhancement of tea (Camellia sinensis) flavonoids

“…GC content ( Bhanja et al, 2021 ) , Relative synonymous codon usage (RSCU) values ( Sharp and Li, 1987 , Mondal et al, 2016 ), GC3s ( Bhanja et al, 2021 ), effective number of codons (ENcs) values ( Wright, 1990 ), GRAVY score, and aromaticity score were considered for compositional analysis ( Kyte and Doolittle, 1982 ) and were generated using CodonW 1.4.4 and in house PERL script. These are well-known measures of codon bias and provide useful information regarding the existence of mutational pressures acting on the genes.…”

“…These are well-known measures of codon bias and provide useful information regarding the existence of mutational pressures acting on the genes. The start and stop codons were excluded from the calculation to reduce the influence of amino acid composition on codon usage ( Bhanja et al, 2021 ).…”