In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments

Abstract

Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins’ functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins’ potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.

Unveiling the mysteries: Functional insights into hypothetical proteins from Bacteroides fragilis 638R

“…We conducted a thorough analysis of the 60 HPs utilizing Pfam, InterPro, SUPERFAMILY, SCANPROSITE, SMART, and CATH. The analysis aimed to assign functions to HPs and determine if they exhibited similar functions according to three or more of the aforementioned programs [ 37 , 38 ]. The results showed that 19 HPs had similar functions based on the analysis of multiple programs.…”

Genomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

“…Notably, most of these variable core genes encoded hypothetical proteins, with the remainder mostly linked to membrane proteins. These genes have often shown variations in response to specific conditions in bacteria (Ijaq et al, 2022; Rahman et al, 2022; Silhavy et al, 2010). This suggests that the observed higher variability in these core genes could indicate constant adjusting of their functionality in response to different conditions.…”

Bacterial hypothetical proteins may be of functional interest

“…Some research groups have demonstrated the value of investigating genes coding for hypothetical proteins. For example, Rahman et al identified genes involved in the adaptation of Bacillus paralicheniformis and other genes of potential biotechnological interest among the genes coding for hypothetical proteins (Rahman et al, 2022). In 2020, Araujo et al characterized genes coding for hypothetical proteins that could be involved in the pathogenesis of the bacterium Corynebacterium pseudotuberculosis (Araujo et al, 2020).…”