Functional Annotation and Classification of the Hypothetical Proteins of &amp;lt;i&amp;gt;Neisseria meningitides&amp;lt;/i&amp;gt; H44/76

Singh, Archana; Singal, Bharti; Nath, Onkar; Singh, Ishwar

doi:10.11648/j.bio.20150305.16

Cited by 6 publications

(8 citation statements)

References 51 publications

(54 reference statements)

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“…The utilization of in silico approaches to the functional prediction of HPs has been successfully used in several bacterial species, such as Vibrio cholerae , Neisseria gonorrhoeae , Clostridium difficile , and Staphylococcus aureus [ 22 , 33 – 35 ]. Due to the relevance of E .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of this bacterium, and the use of bioinformatics tools can assist in the biological understanding of this organism through functional annotation analysis. Thus, our study aimed to assign functions to proteins previously described as HPs, present in the genome of E. antarcticum B7. We used an extensive in silico workflow combining several bioinformatics tools for function annotation, sub-cellular localization and physicochemical characterization, three-dimensional structure determination, and protein-protein interactions. This genome contains 2772 genes, of which 765 CDS were annotated as HPs. The amino acid sequences of all HPs were submitted to our workflow and we successfully attributed function to 132 HPs. We identified 11 proteins that play important roles in the mechanisms of adaptation to adverse environments, such as flagellar biosynthesis, biofilm formation, carotenoids biosynthesis, and others. In addition, three predicted HPs are possibly related to arsenic tolerance. Through an in vitro assay, we verified that E. antarcticum B7 can grow at high concentrations of this metal. The approach used was important to precisely assign function to proteins from diverse classes and to infer relationships with proteins with functions already described in the literature. This approach aims to produce a better understanding of the mechanism by which this bacterium adapts to extreme environments and to the finding of targets with biotechnological interest.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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“…These molecules are labeled as hypothetical proteins (HP). 2 , 20 , 21 Nearly 30% to 40% genes of most bacterial genomes are classified as unknown or hypothetical. 22 These HPs are the translated nucleic acid sequences based on sequence similarity, but their biochemical and functional characterization evaluation is necessary for the experimental existence.…”

Section: Introductionmentioning

confidence: 99%

Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity

Dey

Shahrear

Zinnia

et al. 2022

Bioinform Biol Insights

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Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.

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“…Most of these hypothetical proteins are expected to play essential roles and their annotation can unveil novel functional pathways. The utilisation of in silico approaches to predict annotations of HPs has been successful in numerous bacterial species ( Singh et al, 2015 ; Varma et al, 2015 ; Prabhu et al, 2020 ). Additionally, there are still several challenges in annotating such proteins, given the scanty organelle information known and the pervasive nature of the subcellular location of these proteins.…”

Section: Introductionmentioning

confidence: 99%

In Silico Characterization of Uncharacterized Proteins From Multiple Strains of Clostridium Difficile

Abbasi¹,

Dharan²,

Mishra³

et al. 2022

Front. Genet.

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Clostridium difficile (C. difficile) is a multi-strain, spore-forming, Gram-positive, opportunistic enteropathogen bacteria, majorly associated with nosocomial infections, resulting in severe diarrhoea and colon inflammation. Several antibiotics including penicillin, tetracycline, and clindamycin have been employed to control C. difficile infection, but studies have suggested that injudicious use of antibiotics has led to the development of resistance in C. difficile strains. However, many proteins from its genome are still considered uncharacterized proteins that might serve crucial functions and assist in the biological understanding of the organism. In this study, we aimed to annotate and characterise the 6 C. difficile strains using in silico approaches. We first analysed the complete genome of 6 C. difficile strains using standardised approaches and analysed hypothetical proteins (HPs) employing various bioinformatics approaches coalescing, including identifying contigs, coding sequences, phage sequences, CRISPR-Cas9 systems, antimicrobial resistance determination, membrane helices, instability index, secretory nature, conserved domain, and vaccine target properties like comparative homology analysis, allergenicity, antigenicity determination along with structure prediction and binding-site analysis. This study provides crucial supporting information about the functional characterization of the HPs involved in the pathophysiology of the disease. Moreover, this information also aims to assist in mechanisms associated with bacterial pathogenesis and further design candidate inhibitors and bona fide pharmaceutical targets.

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Functional Annotation and Classification of the Hypothetical Proteins of <i>Neisseria meningitides</i> H44/76

Cited by 6 publications

References 51 publications

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

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

Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity

In Silico Characterization of Uncharacterized Proteins From Multiple Strains of Clostridium Difficile

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