PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach

Abstract

Fusarium oxysporum remains one of the leading causes of economic losses and poor crop yields; its detection is strained due to its presentation in various morphological and physiological forms. This research work sought to identify novel biomarkers for the detection of Fusarium oxysporum using in silico approaches. Experimentally validated anti-Fusarium oxysporum antimicrobial peptides (AMPs) were used to construct a profile against Fusarium oxysporum. The performance and physicochemical parameters of these peptides were predicted. The gene for the Fusarium oxysporum receptor protein PR-1-like Protein, Fpr1, was identified and translated. The resulting protein model from the translation was then validated. The anti-Fusarium oxysporum AMPs and Fusarium oxysporum receptor protein 3-D structures were characterized, and their docking interaction analyses were carried out. The HMMER in silico tool identified novel anti-Fusarium oxysporum antimicrobial peptides with good performance in terms of accuracy, sensitivity, and specificity. These AMPs also displayed good physicochemical properties and bound with greater affinity to Fusarium oxysporum protein receptor PR-1-like Protein. The tendency of these AMPs to precisely detect Fusarium oxysporum PR-1-like Protein, Fpr1, would justify their use for the identification of the fungus. This study would enhance and facilitate the identification of Fusarium oxysporum to reduce problems associated with poor crop yield, economic losses, and decreased nutritional values of plants to keep up with the growing population.

Keywords: algorithms; antimicrobial peptides; fungal; pesticides; proteins; receptors; resistance.

Figure 1

Flow chart of the HMMER command lines. The command line (i) in the flow chart above used “Clustalo” module of the HMMER software for the multiple alignment and GCG postscript output for the graphical printing of the AMPs. The command line hmmbuildin (ii) built the aligned sequences in (i) to enhance the construction of the profile by showing common motifs/signatures within the profile. The command line hmmsearchin (iii) evaluated the performance of the resulting constructed profile in (ii) by querying it on independent datasets. The command line (iv) allowed the identification of the anti-Fusarium oxysporum AMPs.

Figure 2

BIOVIA result for modeled PR-1-like Protein (Fpr1) of Fusarium oxysporum using the generated model from I-TASSER. Residues in most favored regions (upper first box on the left), residues in additional allowed regions (lower box on the left), and residues in generously allowed regions (upper box on the right).

Figure 3

3D structures of the anti-Fusarium oxysporum AMPs and Fusarium oxysporum PR-1-like protein, Fpr1, as determined by I-TASSER. 3D structures of anti-Fusarium oxysporum AMPs (a–l) represented in red and Fusarium oxysporum Fpr1 (m) represented in blue.

Figure 4

Docking interaction analysis of the anti-Fusarium oxysporum AMPs with Fusarium oxysporum PR-1 like protein, Fpr1. The blue color represents PR-1 like protein (Fpr1), the red is the AMPs.