Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses

Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.

The Insights of Genomic Synteny and Codon Usage Preference on Genera Demarcation of Iridoviridae Family

The members of the family Iridoviridae are large, double-stranded DNA viruses that infect various hosts, including both vertebrates and invertebrates. Although great progress has been made in genomic and phylogenetic analyses, the adequacy of the existing criteria for classification within the Iridoviridae family remains unknown. In this study, we redetermined 23 Iridoviridae core genes by re-annotation, core-pan analysis and local BLASTN search. The phylogenetic tree based on the 23 re-annotated core genes (Maximum Likelihood, ML-Tree) and amino acid sequences (composition vector, CV-Tree) were found to be consistent with previous reports. Furthermore, the information provided by synteny analysis and codon usage preference (relative synonymous codon usage, correspondence analysis, ENC-plot and Neutrality plot) also supports the phylogenetic relationship. Collectively, our results will be conducive to understanding the genera demarcation within the Iridoviridae family based on genomic synteny and component (codon usage preference) and contribute to the existing taxonomy methods for the Iridoviridae family.

Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2

Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.

Synonymous SNPs of viral genes facilitate virus to escape host antiviral RNAi immunity

Synonymous single nucleotide polymorphisms (SNPs) are involved in codon usage preference or mRNA splicing. Up to date, however, the role of synonymous SNPs in immunity remains unclear. To address this issue, the SNPs of white spot syndrome virus (WSSV) were characterized in shrimp in the present study. Our results indicated that there existed synonymous SNPs in the mRNAs of wsv151 and wsv226, two viral genes of WSSV. In the presence of SNP siRNA, wild-type siRNA, wild-type mRNA and SNP mRNA of wsv151 or wsv226, RNAi was significantly suppressed, showing that the synonymous SNPs of wsv151 and wsv226 played negative roles in host siRNA pathway due to mismatch of siRNA with its target. In insect cells, the mismatch, caused by synonymous SNPs of wsv151 or wsv226, between siRNA and its target inhibited the host RNAi. Furthermore, the data revealed that the co-injection of SNP siRNA and wild-type siRNA of wsv151 or wsv226 into WSSV-infected shrimp led to a significant increase of WSSV copies compared with that of SNP siRNA alone or wild-type siRNA alone, indicating that the synonymous SNPs of viral genes could be a strategy of virus escaping host siRNA pathway in shrimp in vivo. Therefore, our study provided novel insights into the underlying mechanism of virus escaping host antiviral RNAi immunity by synonymous SNPs of viral genes.

Expression and Hydroxylamine Cleavage of Thymosin Alpha 1 Concatemer

Human thymosin alpha 1 (Tα1) is an important peptide in the development and senescence of immunological competence in human, and many studies have reported the expression of this peptide. In this study, we designed and synthesized theTα1gene according to theE. colicodon usage preference and constructed a 6×Tα1 concatemer. The latter was inserted into anE. coliexpression vector pET-22b (+), and transformed intoE. coliBL21 (DE3). After induction with IPTG, the concatemer protein was successfully expressed inE. colithen cleaved by hydroxylamine to release the Tα1 monomer. Gly-SDS-PAGE and mass spectrometry confirmed that the recombinant protein was cleaved as intended. The bioactivity of the Tα1 monomer was analyzed by lymphocyte proliferation and by mitochondrial activity in two different tumor cell lines. This study provides a description of the preparation of a bioactive Tα1, which may prove useful in future biomedical research.

Usage Patterns of Codons Versus Complementary Codons Among Cellular Organisms and Organelles

Genetic code is one of the most important biological languages in communications between DNA and protein, so peoples have been paying a great attention to the usage bias of synonymous codons. Based on Grosjean and Ikemura's "optimum combination of codon-anticodon complex" and "translation efficiency" hypotheses, in this paper, we put forward that a biased codon usage is identical to its corresponding complementary codon usage preference. To testify the hypothesis and reveal usage patterns between codons and corresponding complementary codons among different cellular organisms and organelles, the usage data of both codons and corresponding complementary ones from 28 cellular organisms and 20 organelles were analyzed. The results showed that: (1) there is a significantly positive correlation between codons and their complementary ones in most cellular organisms, chloroplasts and mitochondria; (2) all 32 single pairs codon versus complementary codon shared the likely usage correlation patterns, with the significantly positive, unrelated and significantly negative pair number of 18, 12 and 2 within 28 cellular organisms as well as 11, 17 and 4 within 20 organelles respectively, and some usage patterns of 32 single pairs codon versus complementary codon of cellular organisms are highly consistency with two kinds of organelles, which strongly implied that their codon usage has undergone the similar evolutionary selection in their wobbling and modification; (3) the codon-frequency tree agreed fairly well with the traditional one. These results demonstrated the validity of our hypothesis, and indicated the usefulness of correlation between codon and complementary codon in elucidating molecular evolutionary mechanisms.