Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination.

Md Muzahid Ahmed Ezaj,Mst Tania Khatun,Md Sajedul Haque,Golam Rosul Rizvi,Laila Khaleda,S M Abdul Nayeem,Md Shakil Ahmed Khan,Kazi Rejvee Ahmed,Shifath Bin Syed,Mohammad Al-Forkan,Jinn-Moon Yang

doi:10.1371/journal.pone.0252295

Abstract

Stenotrophomonas maltophilia is a multidrug-resistant bacterium with no precise clinical treatment. This bacterium can be a vital cause for death and different organ failures in immune-compromised, immune-competent, and long-time hospitalized patients. Extensive quorum sensing capability has become a challenge to develop new drugs against this pathogen. Moreover, the organism possesses about 789 proteins which function, structure, and pathogenesis remain obscured. In this piece of work, we tried to enlighten the aforementioned sectors using highly reliable bioinformatics tools validated by the scientific community. At first, the whole proteome sequence of the organism was retrieved and stored. Then we separated the hypothetical proteins and searched for the conserved domain with a high confidence level and multi-server validation, which resulted in 24 such proteins. Furthermore, all of their physical and chemical characterizations were performed, such as theoretical isoelectric point, molecular weight, GRAVY value, and many more. Besides, the subcellular localization, protein-protein interactions, functional motifs, 3D structures, antigenicity, and virulence factors were also evaluated. As an extension of this work, ’RTFAMSSER’ and ’PAAPQPSAS’ were predicted as potential T and B cell epitopes, respectively. We hope our findings will help in better understating the pathogenesis and smoothen the way to the cure.

Highlights

Stenotrophomonas maltophilia is a major emerging nosocomial pathogen [1] and is most commonly found in cystic fibrosis (CF) patients worldwide [2]
S. maltophilia is generally found in plant roots, animals, and soils [13,14,15,16,17,18,19], dialysate sample and hemodialysis water [20], cannulae, nebulizer, dental units, prosthetic devices [21,22,23,24,25,26], ICU (Intensive Care Unit) [27] and airborne transmission can occur from the infected CF patients [28]
We found the grand average of hydropathy (GRAVY) values of our concerned proteins ranging from -0.958 to -0.044, which points towards the hydrophilic properties of the proteins and helps in predicting the localization

Summary

Introduction

Stenotrophomonas maltophilia is a major emerging nosocomial pathogen [1] and is most commonly found in cystic fibrosis (CF) patients worldwide [2]. S. maltophilia is generally found in plant roots, animals, and soils [13,14,15,16,17,18,19], dialysate sample and hemodialysis water [20], cannulae, nebulizer, dental units, prosthetic devices [21,22,23,24,25,26], ICU (Intensive Care Unit) [27] and airborne transmission can occur from the infected CF patients [28] This pathogen causes a broad spectrum of infections including respiratory tract infections (RTIs), COPD (Chronic Obstructive Pulmonary Disease), pneumonia, biliary sepsis, bacteremia, bone and joint, soft tissues, and urinary tract infections, eye infections, endocarditis, endophthalmitis, meningitis [28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43]. We will predict the best epitope-based subunit vaccine candidate and different B and T cell epitopes

Materials and methods

B Cell Epitope Prediction

Result and discussion

Findings

WTKGSDDGL 7 RTFAMSSER

Conclusions