Bio-prospecting the future in perspective of amidohydrolase L-glutaminase from marine habitats

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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“…The synthesis of 5-fluoro-N 4 -benzoylcytidine and 5-fluoro-N 4 -pivaloylcytidine was described previously [17]. The synthesis of 5-fluoro-N 4…”

Section: Chemicalsmentioning

confidence: 99%

“…These enzymes are widespread in animals, plants, and microorganisms, where they are involved in several metabolic pathways, most commonly in nucleotide metabolism [ 2 ]. Due to their high stereo- and regioselectivity, amidohydrolases have a wide range of bio-applications not only in chemical synthesis, but also in the food and cosmetic industry, and especially in pharmaceutics [ 3 , 4 ]. Amidohydrolases may also have useful applications in cancer therapy: anticancer activity has been observed for some of these enzymes [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

Bacterial amidohydrolases and modified 5-fluorocytidine compounds: Novel enzyme-prodrug pairs

Preitakaitė,

Barasa,

Aučynaitė

et al. 2023

PLoS ONE

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Gene-directed enzyme prodrug therapy is an emerging strategy for cancer treatment based on the delivery of a gene that encodes an enzyme that is able to convert a prodrug into a potent cytotoxin exclusively in target cancer cells. However, it is limited by the lack of suitable enzyme variants and a scarce choice of chemical bonds that could be activated. Therefore, this study is aimed to determine the capability of bacterial amidohydrolases YqfB and D8_RL to activate novel prodrugs and the effect such system has on the viability of eukaryotic cancer cells. We have established cancer cell lines that stably express the bacterial amidohydrolase genes and selected several N4-acylated cytidine derivatives as potential prodrugs. A significant decrease in the viability of HCT116 human colon cancer cell lines expressing either the YqfB or the D8_RL was observed after exposure to the novel prodrugs. The data we acquired suggests that bacterial YqfB and D8_RL amidohydrolases, together with the modified cytidine-based prodrugs, may serve as a promising enzyme-prodrug system for gene-directed enzyme prodrug therapy.

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“…This group includes numerous hydrolytic enzymes with a varied spectrum of substrates and reactions. The microbial obtained amidohydrolase possesses extensive biotechnological applications that include cosmetics, food, and therapeutics, especially as an anticancer/anti-proliferative agent (Durthi et al, 2020;Patel et al, 2021). This hydrolase group also contains amylases and 𝛼-amylase derived from B. licheniformis, B. amyloliquefaciens and B. stearothermophilus has been commercially used in fermentation, paper, and textiles industries (Pandey et al, 2000;Konsoula and Liakopoulou-Kyriakides, 2007).…”

Section: Proteins With Biotechnological Potentialsmentioning

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

Bio-prospecting the future in perspective of amidohydrolase L-glutaminase from marine habitats

Cited by 14 publications

References 91 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

Bacterial amidohydrolases and modified 5-fluorocytidine compounds: Novel enzyme-prodrug pairs

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

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