scholarly journals Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1281
Author(s):  
Wei Liu ◽  
Junhua Li ◽  
Hongli Du ◽  
Zhihua Ou
Keyword(s):  
Human Papillomavirus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Vaccine Development ◽  
Surface Protein ◽  
Glycosylation Site ◽  
Protein Glycosylation ◽  
Adaptation Mechanism ◽  
Human Papillomavirus Type 16 ◽  
Glycosylation Sites

Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1597 full genomes, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias (CUB) of HPV16 from different lineages and sublineages. Multiple lineage- or sublineage-conserved mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of different glycosylation sites from lineage A in both L1 and L2 capsid proteins, which might lead to their antigenic distances between the two lineages. CUB analysis showed that the HPV16 open reading frames (ORFs) preferred codons ending with A/T. The CUB of HPV16 ORFs was mainly affected by natural selection except for E1, E5 and L2. HPV16 only shared some of the preferred codons with humans, which might help reduce competition in translational resources. These findings increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells. In summary, this study might facilitate HPV classification and improve vaccine development and application.

scholarly journals Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of HPV16

2021 ◽  
Author(s):  
Zhihua Ou ◽  
Wei Liu ◽  
Junhua LI ◽  
Hongli Du
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Vaccine Development ◽  
Gc Content ◽  
Surface Protein ◽  
Nucleotide Composition ◽  
Glycosylation Site ◽  
Protein Glycosylation ◽  
Adaptation Mechanism ◽  
Site Distribution

Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1,597 full genomes of HPV16, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias of the eight open reading frames (ORFs) of HPV16 genomes from different lineages and sublineages. Multiple lineage- or subline-age-specific mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of unique potential glycosylation site in both L1 and L2 capsid protein, which might lead to their antigenic distances from other HPV16 lineages. Nucleotide composition of HPV16 showed that the overall AT content was higher than GC content at the 3rd codon position. Relatively high ENC values suggested that the HPV16 ORFs didn't have strong codon usage bias. Most of the HPV16 ORFs were mainly governed by natural selection pressure such as translational pressure, except for L2. HPV16 only shared some of the preferred codons with human, which might help reduce competition in translational resources. These findings may help increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells, which might facilitate HPV classification and improve vaccine development and application.

Codon usage bias and A+T content variation in human papillomavirus genomes

2003 ◽  
Vol 98 (2) ◽  
pp. 95-104 ◽  
Author(s):  
Kong-Nan Zhao ◽  
Wen Jun Liu ◽  
Ian H Frazer
Keyword(s):  
Human Papillomavirus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Content Variation

scholarly journals DeepNGlyPred: A Deep Neural Network-Based Approach for Human N-Linked Glycosylation Site Prediction

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7314
Author(s):  
Subash C. Pakhrin ◽  
Kiyoko F. Aoki-Kinoshita ◽  
Doina Caragea ◽  
Dukka B. KC
Keyword(s):  
Computational Prediction ◽  
Structural Features ◽  
Glycosylation Site ◽  
Protein Glycosylation ◽  
Evolutionary Information ◽  
Computational Technique ◽  
Post Translational Modification ◽  
Glycosylation Sites ◽  
Better Than

Protein N-linked glycosylation is a post-translational modification that plays an important role in a myriad of biological processes. Computational prediction approaches serve as complementary methods for the characterization of glycosylation sites. Most of the existing predictors for N-linked glycosylation utilize the information that the glycosylation site occurs at the N-X-[S/T] sequon, where X is any amino acid except proline. Not all N-X-[S/T] sequons are glycosylated, thus the N-X-[S/T] sequon is a necessary but not sufficient determinant for protein glycosylation. In that regard, computational prediction of N-linked glycosylation sites confined to N-X-[S/T] sequons is an important problem. Here, we report DeepNGlyPred a deep learning-based approach that encodes the positive and negative sequences in the human proteome dataset (extracted from N-GlycositeAtlas) using sequence-based features (gapped-dipeptide), predicted structural features, and evolutionary information. DeepNGlyPred produces SN, SP, MCC, and ACC of 88.62%, 73.92%, 0.60, and 79.41%, respectively on N-GlyDE independent test set, which is better than the compared approaches. These results demonstrate that DeepNGlyPred is a robust computational technique to predict N-Linked glycosylation sites confined to N-X-[S/T] sequon. DeepNGlyPred will be a useful resource for the glycobiology community.

scholarly journals N-glycosylation Site Analysis Reveals Sex-related Differences in Protein N-glycosylation in the Rice Brown Planthopper (Nilaparvata lugens)

2020 ◽  
Vol 19 (3) ◽  
pp. 529-539 ◽  
Author(s):  
Freja Scheys ◽  
Els J. M. Van Damme ◽  
Jarne Pauwels ◽  
An Staes ◽  
Kris Gevaert ◽  
...  
Keyword(s):  
Pest Control ◽  
Control Strategies ◽  
Brown Planthopper ◽  
Original Data ◽  
Nilaparvata Lugens ◽  
Glycosylation Site ◽  
Protein Glycosylation ◽  
Biological Pest Control ◽  
Glycosylation Sites ◽  
Wide Range

Glycosylation is a common modification of proteins and critical for a wide range of biological processes. Differences in protein glycosylation between sexes have already been observed in humans, nematodes and trematodes, and have recently also been reported in the rice pest insect Nilaparvata lugens. Although protein N-glycosylation in insects is nowadays of high interest because of its potential for exploitation in pest control strategies, the functionality of differential N-glycosylation between sexes is yet unknown. In this study, therefore, the occurrence and role of sex-related protein N-glycosylation in insects were examined. A comprehensive investigation of the N-glycosylation sites from the adult stages of N. lugens was conducted, allowing a qualitative and quantitative comparison between sexes at the glycopeptide level. N-glycopeptide enrichment via lectin capturing using the high mannose/paucimannose-binding lectin Concanavalin A, or the Rhizoctonia solani agglutinin which interacts with complex N-glycans, resulted in the identification of over 1300 N-glycosylation sites derived from over 600 glycoproteins. Comparison of these N-glycopeptides revealed striking differences in protein N-glycosylation between sexes. Male- and female-specific N-glycosylation sites were identified, and some of these sex-specific N-glycosylation sites were shown to be derived from proteins with a putative role in insect reproduction. In addition, differential glycan composition between males and females was observed for proteins shared across sexes. Both lectin blotting experiments as well as transcript expression analyses with complete insects and insect tissues confirmed the observed differences in N-glycosylation of proteins between sexes. In conclusion, this study provides further evidence for protein N-glycosylation to be sex-related in insects. Furthermore, original data on N-glycosylation sites of N. lugens adults are presented, providing novel insights into planthopper's biology and information for future biological pest control strategies.

scholarly journals Prediction of O-glycosylation Sites Using Random Forest and GA-Tuned PSO Technique

2015 ◽  
Vol 9 ◽  
pp. BBI.S26864 ◽  
Author(s):  
Hebatallah Hassan ◽  
Amr Badr ◽  
M. B. Abdelhalim
Keyword(s):  
Genetic Algorithm ◽  
Random Forest ◽  
Classification Accuracy ◽  
Characteristic Curve ◽  
Pso Algorithm ◽  
Glycosylation Site ◽  
Protein Glycosylation ◽  
Parameters Optimization ◽  
Minority Class ◽  
Glycosylation Sites

O-glycosylation is one of the main types of the mammalian protein glycosylation; it occurs on the particular site of serine (S) or threonine (T). Several O-glycosylation site predictors have been developed. However, a need to get even better prediction tools remains. One challenge in training the classifiers is that the available datasets are highly imbalanced, which makes the classification accuracy for the minority class to become unsatisfactory. In our previous work, we have proposed a new classification approach, which is based on particle swarm optimization (PSO) and random forest (RF); this approach has considered the imbalanced dataset problem. The PSO parameters setting in the training process impacts the classification accuracy. Thus, in this paper, we perform parameters optimization for the PSO algorithm, based on genetic algorithm, in order to increase the classification accuracy. Our proposed genetic algorithm-based approach has shown better performance in terms of area under the receiver operating characteristic curve against existing predictors. In addition, we implemented a glycosylation predictor tool based on that approach, and we demonstrated that this tool could successfully identify candidate glycosylation sites in case study protein.

scholarly journals Involvement of oligomerization, N-glycosylation and sialylation in the clearance of cholinesterases from the circulation

1995 ◽  
Vol 311 (3) ◽  
pp. 959-967 ◽  
Author(s):  
C Kronman ◽  
B Velan ◽  
D Marcus ◽  
A Ordentlich ◽  
S Reuveny ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Half Life ◽  
Sharp Decrease ◽  
Life Time ◽  
Absolute Number ◽  
Glycosylation Site ◽  
Protein Glycosylation ◽  
Wild Type ◽  
Attachment Sites ◽  
Glycosylation Sites

The possible role of post-translational modifications such as subunit oligomerization, protein glycosylation and oligosaccharide processing on the circulatory life-time of proteins was studied using recombinant human acetylcholinesterase (rHuAChE). Different preparations of rHuAChE containing various amounts of tetramers, dimers and monomers are cleared at similar rates from the circulation, suggesting that oligomerization does not play an important role in determining the rate of clearance. An engineered rHuAChE mutant containing only one N-glycosylation site was cleared from the circulation more rapidly than the wild-type triglycosylated enzyme. On the other hand, hyperglycosylated mutants containing either four or five occupied N-glycosylation sites, analagous to those present on the slowly cleared fetal bovine serum acetylcholinesterase (FBS-AChE), were also cleared more rapidly from the bloodstream than the wild-type species. Furthermore, the two different tetraglycosylated mutants were cleared at different rates while the pentaglycosylated mutant exhibited the most rapid clearance profile. These results imply that though the number of N-glycosylation sites plays a role in the circulatory life-time of the enzyme, the number of N-glycan units in itself does not determine the rate of clearance. When saturating amounts of asialofetuin were administered together with rHuAChE, the circulatory half-life of the enzyme was dramatically increased (from 80 min to 19 h) and was found to be similar to that displayed by plasma-derived cholinesterases while desialylation of these enzymes caused a sharp decrease in the circulatory half-life to approximately 3-5 min. Determination of the average number of sialic acid residues per enzyme subunit of the five different N-glycosylation species generated, revealed that the rate of clearance is not a function of the absolute number of appended sialic acid moieties but rather of the number of unoccupied sialic acid attachment sites per enzyme molecule. Specifically, we demonstrate an inverse-linear relationship between the number of vacant sialic acid attachment sites and the values of the enzyme residence time within the bloodstream.

scholarly journals Linking inherent O-Linked Protein Glycosylation of YghJ to Increased Antigen Potential

2021 ◽  
Vol 11 ◽  
Author(s):  
Mette Thorsing ◽  
Thøger Jensen Krogh ◽  
Lars Vitved ◽  
Arkadiusz Nawrocki ◽  
Rikke Jakobsen ◽  
...  
Keyword(s):  
Low Income ◽  
Vaccine Development ◽  
Preventive Intervention ◽  
Protein Glycosylation ◽  
Enterotoxigenic Escherichia Coli ◽  
Protein Variant ◽  
Middle Income ◽  
Antibiotic Resistant ◽  
Glycosylation Sites ◽  
A Minor

Enterotoxigenic Escherichia coli (ETEC) is a WHO priority pathogen and vaccine target which causes infections in low-income and middle-income countries, travelers visiting endemic regions. The global urgent demand for an effective preventive intervention has become more pressing as ETEC strains have become increasingly multiple antibiotic resistant. However, the vaccine development pipeline has been slow to address this urgent need. To date, vaccine development has focused mainly on canonical antigens such as colonization factors and expressed toxins but due to genomic plasticity of this enteric pathogen, it has proven difficult to develop effective vaccines. In this study, we investigated the highly conserved non-canonical vaccine candidate YghJ/SsLE. Using the mass spectrometry-based method BEMAP, we demonstrate that YghJ is hyperglycosylated in ETEC and identify 54 O-linked Set/Thr residues within the 1519 amino acid primary sequence. The glycosylation sites are evenly distributed throughout the sequence and do not appear to affect the folding of the overall protein structure. Although the glycosylation sites only constitute a minor subpopulation of the available epitopes, we observed a notable difference in the immunogenicity of the glycosylated YghJ and the non-glycosylated protein variant. We can demonstrate by ELISA that serum from patients enrolled in an ETEC H10407 controlled infection study are significantly more reactive with glycosylated YghJ compared to the non-glycosylated variant. This study provides an important link between O-linked glycosylation and the relative immunogenicity of bacterial proteins and further highlights the importance of this observation in considering ETEC proteins for inclusion in future broad coverage subunit vaccine candidates.

Sign in / Sign up

Export Citation Format

Share Document