Questing functions and structures of hypothetical proteins from <i>Campylobacter jejuni</i>: a computer-aided approach

Gazi, Amran; Mahmud, Sultan; Fahim, Shah Mohammad; Islam, Rezaul; Das, Subhasish; Mahfuz, Mustafa; Ahmed, Tahmeed

doi:10.1042/bsr20193939

Cited by 8 publications

(4 citation statements)

References 90 publications

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“…To determine the interaction partners of the HPs, we performed a protein-protein interaction analysis [ 72 ]. In this study, protein WP_095290960.1, RNA polymerase sporulation sigma factor SigK showed a very strong interaction (score 0.930) with the sporulation stage IV protein A (SpoIVA) which is involved in sporulation [ 73 ].…”

Section: Resultsmentioning

confidence: 99%

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

Rahman

Heme²,

Parvez³

2022

PLoS ONE

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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.

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Section: Resultsmentioning

confidence: 99%

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

Rahman

Heme²,

Parvez³

2022

PLoS ONE

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“…Q8RGQ9 protein catalyzes ATP-dependent phosphorylation of 4-carbon acid sugars and nucleotides by binding them through N & C terminal domains respectively [61]. Q8RG53 and Q8RF83 contain a tetratricopeptide repeat and it has been identified that proteins with this repeat are involved in virulence related functions [6,62].…”

Section: Binding Proteinsmentioning

confidence: 99%

“…These previously uncharacterized proteins may yield interesting results and shed some light on functionality of a cell [5]. Many researchers have used this computer guided approach to functionally annotate the uncharacterized protein or HP from different organisms [6][7][8]. In the present study, we have attempted the functional annotation of uncharacterized proteins present in the genome of F. nucleatum strain ATCC 25586.…”

Section: Introductionmentioning

confidence: 99%

Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors

et al. 2023

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Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as “Uncharacterized.” Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

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“…To determine the interaction partners of the HPs, we performed a protein-protein interaction analysis (Gazi et al, 2020). In this study, protein WP_095290960.1, RNA polymerase sporulation sigma factor SigK showed a very strong interaction (score 0.930) with the sporulation stage IV protein A (spoIVA) which is involved in sporulation (Roels et al, 1992).…”

Section: Protein-protein Interactionsmentioning

confidence: 99%

Functional Annotation Of Hypothetical Proteins From The Bacillus Paralicheniformis Strain Bac84 Reveals Proteins with Biotechnological Potentials – an In Silico Approach

Rahman

Heme

Parvez

2022

Preprint

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A significant number of proteins in the genome of the Bacillus paralicheniformis strain Bac84 are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from its genome. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation and characterization. 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. Eight proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, antibiotic biosynthesis, 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.

show abstract

Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

Cited by 8 publications

References 90 publications

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

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

Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors

Functional Annotation Of Hypothetical Proteins From The Bacillus Paralicheniformis Strain Bac84 Reveals Proteins with Biotechnological Potentials – an In Silico Approach

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