In-silico characterization of GABAT protein found in gut-brain axis associated bacteria of healthy individuals and multiple sclerosis patients

Abstract

Background: Multiple sclerosis (MS) is a neurodegenerative disease characterized by inflammation and demyelination of neurons. There is evidence to suggest that level of a neurotransmitter gamma-aminobutyric acid (GABA), due to the degradation by γ-aminobutyric acid transaminase (GABAT), is reduced in certain areas of the brain in MS patients. MS is always accompanied by gut bacteria dysbiosis. In healthy individuals, Faecalibacterium sp. while in MS patients A. calcoaceticus, Clostridium sp. and S. typhimurium are found abundantly. Although all these microbes produce GABAT but only in MS patients this enzyme significantly degrades GABA.

Objective: Present study is an attempt to characterize the GABAT protein sequences of these bacteria.

Methodology: Sequences of GABAT protein were retrieved from Uniprot database. Sequences were analyzed by Protparam, Gneg-mPLoc, SOSUI, PFP-FunDSeqE, Pepwheel program, PROTEUS and Alphafold and SAVES servers, MEME suite and HDOCK server.

Results: In healthy individuals gastrointestinal tract (GIT) bacteria, GABAT protein was present in inner-membrane with α helix content (61 and 62%) and β sheet content (5%), 4-helical cytokines functional domains. It has greater number of B-cell epitopes and more complex 3D configuration as compared to MS patients GIT bacterial enzymes.

Conclusion: Present study might enable us to modify the GABAT encoding gene and enzyme through site-directed mutagenesis in pathogenic bacteria thus reducing their potential of causing MS.

Keywords: 4-aminobutyrate transaminase; Dysbiosis; Faecalibacterium; Gut-brain axis; Multiple sclerosis; Postbiotics; Uniprot.

Fig. 1

Graphical representation of present study (Ramachandran V. S., 2002). (A)Mechanism of action of GABAT in microbiota-gut-brain axis of healthy individuals and multiple sclerosis patients (B) Layout of methodology involved in present study

Fig. 2

Phylogenetic tree constructed using MEGA 11 software to analyze the evolutionary relationship among the present study bacteria with reference to GABAT protein.

Fig. 3

Three dimensional (3D) configuration of GABAT proteins of GIT bacteria of healthy individuals and MS patients and validation of these structures with the help of Ramachandran plots. (a1 and a2) Faecalibacterium sp. An58, (b1 and b2) Faecalibacterium sp. An121, (c1 and c2) Acinetobacter calcoaceticus I, (d1 and d2) Acinetobacter calcoaceticus II, (e1 and e2) Acinetobacter calcoaceticus III, (f1 and f2) Acinetobacter calcoaceticus IV, (g1 and g2) Acinetobacter calcoaceticus V, (h1 and h2) Acinetobacter calcoaceticus VI, (i1 and i2) Clostridium sp. I, (j1 and j2) Clostridium sp. II, (k1 and k2) Salmonella typhimurium.

Fig. 4

E-value and location of conserved protein motifs of GABAT proteins of GIT bacteria of healthy individuals and multiple sclerosis patients predicted using MEME suite.

Fig. 5

Docking analysis of GABAT proteins of GIT bacteria of multiple sclerosis patients with FDA approved drug isoniazid. (a) Acinetobacter calcoaceticus I, (b) Acinetobacter calcoaceticus II, (c) Acinetobacter calcoaceticus III, (d) Acinetobacter calcoaceticus IV, (e) Acinetobacter calcoaceticus V, (f) Acinetobacter calcoaceticus VI, (g) Clostridium sp. I, (h) Clostridium sp. II, (i) Salmonella typhimurium.