Sequence Analysis of Hypothetical Proteins fromHelicobacter pylori26695 to Identify Potential Virulence Factors

Abstract

Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein.

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance

“…The sub-cellular localization of a protein plays an important role in the determination of its function, mainly because protein function is typically correlated to its location [ 45 , 62 ]. Therefore, the knowledge of a protein’s localization in the cellular space is helpful to unveil proteins with unknown function [ 22 , 75 , 76 ]. The sub-cellular localization can be inferred from the composition in amino acids due to evolutionary adaptation to different sub-cellular sites [ 75 , 77 ].…”

Genomics of Helicobacter pylori

“…After genome assembly, the annotation of genes is of paramount importance, and the H. pylori genome, similar to other bacteria, contains a high proportion of hypothetical proteins with unknown function. Naqvi et al . identified the predicted function of 104 hypothetical proteins of H. pylori that had characteristics similar to proteins of known functions, and 11 of them showed significant association to virulence and may constitute novel drug targets.…”

In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis

“…In recent years, several studies have focused on the annotation of proteins with unknown function, due to the importance of understanding the molecular mechanisms in different species, including pathogenic bacteria. The advance and availability of computational tools had a positive impact in the knowledge of the relationship between structure and function of proteins, also serving as a basis for the development of in vitro assays to the characterization of these proteins, which can reduce time and cost (Naqvi et al, 2016;Da Costa et al, 2018;Razali et al, 2019;Sen & Verma, 2020). Generally, the pipelines of functional annotation based on sequence search are combined with the use of other approaches in order to optimize the reliability of the computational predictions.…”