Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus

Wang, Sheng-Fan; Su, Ming Wei; Tseng, Sung-Pin; Li, Ming Chun; Tsao, Che-Wei; Huang, Szu Wei; Chu, Woei Chyn; Liu, Wu Tse; Chen, Yi Ming Arthur; Huang, Jason C.

doi:10.1016/j.jmii.2014.08.011

Cited by 7 publications

(6 citation statements)

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“…Studies have shown that the higher the gene expression level is, the stronger is the preferred use of codon [1][2][3]6,15,16,49,[55][56][57][58][59][60]. In our study, the codon usage bias results of all cotton species were shown in S1 Table. The correlation between the parameters of 4 cotton species and 4 subgenomes had the same rule, except the correlation between G3s and C3s.…”

Section: Correlation Analysis Between Codon Usage Bias Indicesmentioning

confidence: 74%

“…The RSCU value is the ratio between the actual observed values of the codon and the theoretical expectations. It reflects the relative usage preference for the specific composition of codons encoding the same amino acid [49]. If RSCU = 1, codon usage is unbiased; if RSCU > 1, specific codon frequency is higher than other synonymous codons, otherwise, the frequency is low [49].…”

Section: Enc-plot (Enc Versus Gc3smentioning

confidence: 99%

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Genome-wide analysis of codon usage bias in four sequenced cotton species

et al. 2018

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Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

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Section: Correlation Analysis Between Codon Usage Bias Indicesmentioning

confidence: 74%

Section: Enc-plot (Enc Versus Gc3smentioning

confidence: 99%

Genome-wide analysis of codon usage bias in four sequenced cotton species

et al. 2018

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“…Influenza HA is a highly glycosylated protein [32][33][34]. Cellular lectin receptors may recognize the glycans on HA of influenza A virus, allowing for the binding of the virus to the cells and permitting internalization.…”

Section: Introductionmentioning

confidence: 99%

Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection

Yang,

Huang,

Wang

et al. 2021

IJMS

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DC-SIGN, a C-type lectin mainly expressed in dendritic cells (DCs), has been reported to mediate several viral infections. We previously reported that DC-SIGN mediated H5N1 influenza A virus (AIVs) infection, however, the important DC-SIGN interaction with N-glycosylation sites remain unknown. This study aims to identify the optimal DC-SIGN interacting N-glycosylation sites in HA proteins of H5N1-AIVs. Results from NetNGlyc program analyzed the H5 hemagglutinin sequences of isolates during 2004–2020, revealing that seven and two conserved N-glycosylation sites were detected in HA1 and HA2 domain, respectively. A lentivirus pseudotyped A/Vietnam/1203/04 H5N1 envelope (H5N1-PVs) was generated which displayed an abundance of HA5 proteins on the virions via immuno-electron microscope observation. Further, H5N1-PVs or reverse-genetics (H5N1-RG) strains carrying a serial N-glycosylated mutation was generated by site-directed mutagenesis assay. Human recombinant DC-SIGN (rDC-SIGN) coated ELISA showed that H5N1-PVs bound to DC-SIGN, however, mutation on the N27Q, N39Q, and N181Q significantly reduced this binding (p < 0.05). Infectivity and capture assay demonstrated that N27Q and N39Q mutations significantly ameliorated DC-SIGN mediated H5N1 infection. Furthermore, combined mutations (N27Q&N39Q) significantly waned the interaction on either H5N1-PVs or -RG infection in cis and in trans (p < 0.01). This study concludes that N27 and N39 are two essential N-glycosylation contributing to DC-SIGN mediating H5N1 infection.

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“…The relative synonymous codon usage (RSCU) value which is measured by the ratio between the actual observed values of the codon and the theoretical expectations was also calculated. RSCU reflects the relative usage preference for the specific codons encoding the same amino acid [92]. If RSCU value equals to 1, codon usage is supposed to be unbiased but if RSCU>1, specific codon frequency is higher than other synonymous codons and codon usage is considered to be biased [93].…”

Section: Methodsmentioning

confidence: 99%

Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination

Pal

Saha

2019

PLoS ONE

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The deluge of sequence information in the recent times provide us with an excellent opportunity to compare organisms on a large genomic scale. In this study we have tried to decipher the variation in the gene organization and structuring of a vital bacterial gene called ftsZ which codes for an integral component of the bacterial cell division, the FtsZ protein. FtsZ is homologous to tubulin protein and has been found to be ubiquitous in eubacteria. FtsZ is showing increasing promise as a target for antibacterial drug discovery. Our study of ftsZ protein from 143 different bacterial species spanning a wider range of morphological and physiological type demonstrates that the ftsZ gene of about ninety three percent of the organisms show relatively biased codon usage profile and significant GC deviation from their genomic GC content. Comparative codon usage analysis of ftsZ and a core housekeeping gene rpoB demonstrated that codon usage pattern of ftsZ CDS is shaped by natural selection to a large extent and mimics that of a housekeeping gene. We have also detected a tendency among the different organisms to utilize a core set of codons in structuring the ftsZ coding sequence. We observed that the compositional frequency of the amino acid serine in the FtsZ protein appears to be a indicator of the bacterial lifestyle. Our meticulous analysis of the ftsZ gene linked with the corresponding FtsZ protein show that there is a bias towards the use of specific synonymous codons particularly in the helix and strand regions of the multi-domain FtsZ protein. Overall our findings suggest that in an indispensable and vital protein such as FtsZ, there is an inherent tendency to maintain form for optimized performance in spite of the extrinsic variability in coding features.

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Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus

Abstract: This study proposes a new and effective way to gain a better understanding of the features of the S-OIV genome and evolutionary processes based on the codon usage pattern. It is useful to trace influenza viral origins and cross-species virus transmission.

Cited by 7 publications

References 41 publications

Genome-wide analysis of codon usage bias in four sequenced cotton species

Genome-wide analysis of codon usage bias in four sequenced cotton species

Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection

Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination

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