In Silico evaluation and identification of fungi capable of producing endo-inulinase enzyme

Jayaram Chikkerur; Ashis Kumar Samanta; Arindam Dhali; Atul Purushottam Kolte; Sohini Roy; Pratheepa Maria

doi:10.1371/journal.pone.0200607

In Silico evaluation and identification of fungi capable of producing endo-inulinase enzyme

PLoS One. 2018 Jul 12;13(7):e0200607. doi: 10.1371/journal.pone.0200607. eCollection 2018.

Authors

Jayaram Chikkerur^{1

2}, Ashis Kumar Samanta¹, Arindam Dhali³, Atul Purushottam Kolte¹, Sohini Roy^{1

2}, Pratheepa Maria⁴

Affiliations

¹ Animal Nutrition Division, ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, Karnataka, India.
² Department of Microbiology, School of Sciences, Jain University, Bengaluru, Karnataka, India.
³ Bioenergetics and Environmental Sciences Division, ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, Karnataka, India.
⁴ Division of Genomic Resources, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, Karnataka, India.

Abstract

The enzyme endo-inulinase hydrolyzes inulin to short chain fructooligosaccharides (FOS) that are potential prebiotics with many health promoting benefits. Although the raw materials for inulin production are inexpensive and readily available, commercial production of FOS from inulin is limited due to inadequate availability of the enzyme source. This study aimed to identify the fungi capable of producing endo-inulinase based on the in silico analysis of proteins retrieved from non-redundant protein sequence database. The endo-inulinase of Aspergillus ficuum was used as reference sequence. The amino acid sequences with >90% sequence coverage, belonging to different fungi were retrieved from the database and used for constructing three-dimensional (3D) protein models using SWISS-MODEL and Bagheerath H. The 3D models of comparable quality as that of the reference endo-inulinase were selected based on QMEAN Z score. The selected models were evaluated and validated for different structural and functional qualities using Pro-Q, ProSA, PSN-QA, VERIFY-3D, PROCHECK, PROTSAV metaserver, STRAP, molecular docking, and molecular dynamic simulation analyses. A total of 230 proteins belonging to 53 fungal species exhibited sequence coverage >90%. Sixty one protein sequences with >60% sequence identity were modeled as endo-inulinase with higher QMEAN Z Score. The evaluations and validations of these 61 selected models for different structural and functional qualities revealed that 60 models belonging to 22 fungal species exhibited native like structure and unique motifs and residues as that of the reference endo-inulinase. Further, these models also exhibited similar kind of interaction between the active site around the conserved glutamate residue and substrate as that of the reference endo-inulinase. In conclusion, based on the current study, 22 fungal species could be identified as endo-inulinase producer. Nevertheless, further biological assessment of their capability for producing endo-inulinase is imminent if they are to be used for commercial endo-inulinase production for application in FOS industry.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aspergillus / enzymology*
Computer Simulation*
Fungal Proteins / chemistry*
Glycoside Hydrolases / chemistry*
Molecular Docking Simulation*
Molecular Dynamics Simulation*

Substances

Fungal Proteins
Glycoside Hydrolases

Grants and funding

The authors gratefully acknowledge the Council of Scientific and Industrial Research (CSIR); (Sanctioned File No. 09/1158(0002)2K17), Ministry of Science and Technology, Government of India for the senior research fellowship. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.