In silico characterization of nifH gene of Rhizobium sp. TN04 isolated from the rhizosphere of non-leguminous potato plants

Abstract

The reliance on nitrogen (N) fertilizers in global crop production has led to significant environmental concerns and economic burdens due to their excessive usage. In order to effectively address this problem, a comprehensive understanding of biological N-fixation (BNF), governed by the Nif genes is essential. In legumes, the role of Rhizobium in BNF is well-established. However, limited studies are available regarding the function and structure of nif genes in non-leguminous plants using in silico modeling. Therefore, the present study was conducted to predict the structural and functional analysis of nifH gene from a Rhizobium strain isolated from potato plant. Various bioinformatics tools (ExPasy ProtParam, PSIPRED, MEMSAT-SVM, CATH classification, COFACTOR, COACH and STRING) were used to predict the primary, secondary and 3D structure of nifH protein. Results showed that TN04 has stable structure and hydrophobic nature similar to Rhizobium sp. S1SS148 and R. rosettiformans. Amino acid composition showed presence of different resides with glycine being most prevalent. Secondary structure analysis proved its stability due to the presence of coils, helices, and sheets. The nifH protein model derived from TN04 using I-TASSER displayed excellent structural characteristics, as confirmed by ERRAT. Functional annotations highlighted enzyme similarities and specific ligand-binding sites associated with nitrogenase activity. CATH categorization revealed the presence of a P-loop NTPase domain known to bind nucleotides, which can affect the activity of nitrogenase. In addition, the investigation of protein-protein interactions using STRING suggested potential interactions between nifH protein of TN04 and several nif proteins, hinting at its possible involvement in N-fixation. The results of these studies shed light on possible N-fixation mechanisms in Rhizobium sp. TN04 in non-legumes. Based on these predictions, the results suggest the possible pathways for implementation of sustainable agricultural methods. However, further studies are necessary to validate these findings and investigate the role of Rhizobium sp. TN04 in N-fixation in non-leguminous plants, thus, enhancing understanding in this domain.