Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes

Wen, Qing-Feng; Liu, Shuo; Dong, Chuan; Guo, Haixia; Gao, Yi‐Zhou; Guo, Feng-Biao

doi:10.3389/fmicb.2019.01236

Cited by 35 publications

(25 citation statements)

References 26 publications

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“…Firstly, essential proteins, without which M. catarrhalis cannot survive, were detected using the Geptop 2.0 webserver with an essentiality cutoff of 0.24. This server detects essential proteins through comparing the orthology and phylogeny of query proteins against the datasets defined experimentally in the database of essential genes (DEG) [ 11 ]. Following that, the PSORTb v3.0.2 online server [ 12 ] was used to analyze the subcellular localization of the essential proteins.…”

Section: Methodsmentioning

confidence: 99%

In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics

et al. 2021

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Moraxella catarrhalis (M. catarrhalis) is a Gram-negative bacterium that can cause serious respiratory tract infections and middle ear infections in children and adults. M. catarrhalis has demonstrated an increasing rate of antibiotic resistance in the last few years, thus development of an effective vaccine is a major health priority. We report here a novel designed multitope vaccine based on the mapped epitopes of the vaccine candidates filtered out of the whole proteome of M. catarrhalis. After analysis of 1615 proteins using a reverse vaccinology approach, only two proteins (outer membrane protein assembly factor BamA and LPS assembly protein LptD) were nominated as potential vaccine candidates. These proteins were found to be essential, outer membrane, virulent and non-human homologs with appropriate molecular weight and high antigenicity score. For each protein, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell lymphocyte (BCL) epitopes were predicted and confirmed to be highly antigenic and cover conserved regions of the proteins. The mapped epitopes constituted the base of the designed multitope vaccine where suitable linkers were added to conjugate them. Additionally, beta defensin adjuvant and pan-HLA DR-binding epitope (PADRE) peptide were also incorporated into the construct to improve the stimulated immune response. The constructed multitope vaccine was analyzed for its physicochemical, structural and immunological characteristics and it was found to be antigenic, soluble, stable, non-allergenic and have a high affinity to its target receptor. Although the in silico analysis of the current study revealed that the designed multitope vaccine has the ability to trigger a specific immune response against M. catarrhalis, additional translational research is required to confirm the effectiveness of the designed vaccine.

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Section: Methodsmentioning

confidence: 99%

In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics

et al. 2021

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“…Geptop is a web server that provides a forum for identifying essential genes for bacterial organisms, comparing query protein orthology and phylogeny with the experimentally developed essential gene datasets (from the Database of Essential Genes DEG). Geptop can be utilized for any species of bacteria that has a sequenced genome [19].…”

Section: Retrieval Of Essential Proteinsmentioning

confidence: 99%

In Silico Subtractive Proteomics Approach for Identification of Potential Drug Targets in Staphylococcus saprophyticus

Shahid

Ashfaq

Saeed

et al. 2020

IJERPH

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Staphylococcus saprophyticus is a uropathogenic bacteria responsible for acute urinary tract infections (UTIs) mainly in young female patients. Patients suffering from urinary catheterization, pregnant patients, the elderly as well as those with nosocomial UTIs are at greater risk of the colonizing S. saprophyticus infection. The causative factors include benign prostatic hyperplasia, indwelling catheter, neurogenic bladder, pregnancy, and history of frequent UTIs. Recent findings have exhibited that S. saprophyticus is resistant to several antimicrobial agents. Moreover, there is a global concern regarding the increasing level of antimicrobial resistance, which leads to treatment failure and reduced effectiveness of broad-spectrum antimicrobials. Therefore, a novel approach is being utilized to combat resistant microbes since the past few years. Subtractive proteome analysis has been performed with the entire proteome of S. saprophyticus strain American Type Culture Collection (ATCC) 15305 using several bioinformatics servers and software. The proteins that were non-homologous to humans and bacteria were identified for metabolic pathway analysis. Only four cytoplasmic proteins were found possessing the potential of novel drug target candidates. The development of innovative therapeutic agents by targeting the inhibition of any essential proteins may disrupt the metabolic pathways specific to the pathogen, thus causing destruction as well as eradication of the pathogen from a particular host. The identified targets can facilitate in designing novel and potent drugs against S. saprophyticus strain ATCC 15305.

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“…For prokaryotes, prediction of essential genes is possible with a tool that uses sequence comparisons (20). Essential gene prediction for eukaryotes is more challenging as less genome wide experimental screens are available and the approaches are heterogeneous.…”

Section: Discussionmentioning

confidence: 99%

“…It is The copyright holder for this preprint this version posted April 15, 2021. ; https://doi.org/10.1101/2021.04. 15.439934 doi: bioRxiv preprint bacteria, the software Geptop 2.0 (20) calculates an essentiality score of an unknown gene based on information of 37 (bacterial) species and sequence similarity. For eukaryotes the task is more challenging, considering their complex multi-cellular architecture.…”

Section: Introductionmentioning

confidence: 99%

Identifying essential genes across eukaryotes by machine learning

Beder¹,

Aromolaran

Doenitz

et al. 2021

Preprint

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Identifying essential genes on a genome scale is resource intensive and has been performed for only a few eukaryotes. For less studied organisms essentiality might be predicted by gene homology. However, this approach cannot be applied to non-conserved genes. Additionally, divergent essentiality information is obtained from studying single cells or whole, multi-cellular organisms, and particularly when derived from human cell line screens and human population studies. We employed machine learning across six model eukaryotes and 60,381 genes, using 41,635 features derived from sequence, gene functions and network topology. Within a leave-one-organism-out cross-validation, the classifiers showed a high generalizability with an average accuracy close to 80% in the left-out species. As a case study, we applied the method to Tribolium castaneum and validated predictions experimentally yielding similar performance. Finally, using the classifier based on the studied model organisms enabled linking the essentiality information of human cell line screens and population studies.

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Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes

Cited by 35 publications

References 26 publications

In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics

In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics

In Silico Subtractive Proteomics Approach for Identification of Potential Drug Targets in Staphylococcus saprophyticus

Identifying essential genes across eukaryotes by machine learning

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