Codon Adaptation Research Articles

Comparison of N2O-reducing abilities and genome features of two nosZ-containing denitrifying bacteria, Pseudomonas veronii DM15 and Pseudomonas frederiksbergensis DM22.

The study systematically compared the N2O-reducing functional performances and the genomic features of two N2O-reducing isolates, aimed to screen out effective N2O-reducing bacteria with strong environmental adaption, and explore the possible regulation. Two N2O reducers, namely, Pseudomonas veronii DM15 (DM15) and Pseudomonas frederiksbergensis DM22 (DM22), isolated from paddy soil were selected. Their N2O-reducing abilities, and nosZ gene transcript abundance were determined under different temperatures (20°C, 30°C, 40°C) and oxygen concentrations (0%, 10%, 21%), and the whole genomes were sequenced by Illumina sequencing. The results showed that both DM15 and DM22 exhibited the strongest N2O reducing activity at 30°C and under anaerobic conditions. In comparison, DM15 generally exhibited significantly higher N2O reducing abilities and nosZ gene expression than DM22 under all tested conditions. In addition, DM15 possessed obviously higher expression potentials (codon adaptation index (CAI) value) of nos genes than DM22, and the nos cluster of the former contained a transcriptional regulator gene of dnr, while the latter did not. The results indicate that DM15 showed obviously stronger N2O-reducing abilities than DM22 under various conditions, which might be closely associated with its dnr transcriptional regulator, and thus promoting the higher transcriptional activities of nos genes. Although anaerobic conditions were the optimal conditions for N2O reduction in both strains, DM15 still reduced a certain amount of N2O even under aerobic conditions.

Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication.

Long-standing cyanobacterial harmful algal blooms (CyanoHABs) are known to result from synergistic interaction between elevated nutrients and superior ecophysiology of cyanobacteria. However, it remains to be determined whether CyanoHABs are a result of positive selection by eutrophic waters. To address this, we conducted molecular evolutionary analyses on the genomes of 9 bloom-forming cyanobacteria, combined with pangenomics and metatranscriptomics. The results showed no positive selection by water eutrophication. Instead, all homologous genes in the species are under strong purifying selection based on the ratio of divergence at nonsynonymous and synonymous sites (dN/dS) and phylogeny. The dN/dS < 0.85 (median = 0.3) for all homologous genes are similar between the genes in the pathways driving CyanoHABs and housekeeping functions. Phylogenetic support for non-positive selection comes from the mixed clustering of strains: strains of the same species from diverse geographic origins form the same clusters, while strains from the same origins form different clusters. Further support lies in the codon adaptation index (CAI) and single nucleotide polymorphism (SNP). The CAI ranged from 0.42 to 0.9 (mean = 0.75), which indicates high-level codon usage bias; the pathways for CyanoHABs and housekeeping functions showed a similar CAI. Interestingly, CAI was negatively correlated with gene expression in 3 metatranscriptomes. The numbers of SNPs were concentrated around 5 to 50. As the SNP number increases, the gene expression level decreases. These negative correlations agree with the population-level dN/dS and phylogeny in supporting purifying selection in bloom-forming cyanobacteria. In summary, superior ecophysiology appears to be acquired prior to water eutrophication. IMPORTANCE CyanoHABs are global environmental hazards, and their mechanisms of action are being intensively investigated. On an ecological scale, CyanoHABs are consequences of synergistic interactions between biological functions and elevated nutrients in eutrophic waters. On an evolutionary scale, one important question is how bloom-forming cyanobacteria acquire these superior biological functions. There are several possibilities, including adaptive evolution and horizontal gene transfer. Here, we explored the possibility of positive selection. We reasoned that there are two possible periods for cyanobacteria to acquire these functions: before the onset of water eutrophication or during water eutrophication. Either way, there should be molecular signatures in protein sequences for positive selection. Interestingly, we found no positive selection by water eutrophication, but strong purifying selection instead on nearly all the genes, suggesting these superior functions aiding CyanoHABs are acquired prior to water eutrophication.

Comparative Analysis on the Codon Usage Pattern of the Chloroplast Genomes in Malus Species.

Codon usage bias of coding sequences has been usually used for exploring the evolutionary factors that affect the variation of genes. We took 20 chloroplast genomes of Malus species into account to explore the codon usage patterns, including the composition, relationship between GC3s and effective number of codons, the parity rule two analyses, the relative synonymous codon usage, the codon adaptation index, the frequency of optimal codons, the codon bias index, etc., of their coding genes. The relationship between GC3 and the ENC values showed that when the separate genes are concerned, the distribution of their GC3 contents is relatively concentrated and the distribution of the ENC values are from 35 to 61 or so. The neutrality plot showed that the correlation coefficient between GC12 and GC3 is 0.095, revealing the mutation factor played a weak role in codon pattern formation. Correspondence analysis results revealed that the codon usage patterns in the chloroplast genomes of Malus species are similar. All these results showed that all Malus chloroplast genomes are AT rich ones, the third bases of the codons are affected by the natural selection pressure, the first two nucleotide base of the codon are affected by mutation pressure. Some genes, such as the rsp7, psbA and ycf2 are of lower codon usage divergences, while the rps12, rps16 and ndhD are of higher codon usage divergences. Codon usage bias exists in the Malus genomes could be used for exploring the evolutionary characteristics in chloroplast genomes and for further study on evolutionary phenomenon in other species.

Analysis of Heat Shock Proteins Based on Amino Acids for the Tomato Genome.

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.

Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT.

Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.

Recombination in sarbecovirus lineage and mutations/insertions in spike protein are linked to the emergence and adaptation of SARS-CoV-2.

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan city, China in December 2019 and thereafter its spillover across the world has created a global pandemic and public health crisis. Right after, there has been intense interest in understanding how the SARS-CoV-2 originated and evolved. This paper also aims to shed light on the origin and evolution of SARS-CoV- 2. A consensus result based on whole genome phylogeny, gene tree analysis, and genetic similarity study revealed that SARS-CoV-2 evolved from Bat-CoV-RaTG13. Furthermore, recombination analysis indicated that probable origin of SARS-CoV-2 is the results of ancestral intra-species recombination events between bat coronaviruses belonging to Sarbecovirus sub-genus. Multiple sequence alignment (MSA) revealed the insertion of four amino acid residues "PRRA" (Proline-Arginine-Arginine-Alanine) to the S1/S2 site in the spike protein of SARS-CoV-2, and structural modeling of spike protein of bat-CoV-RaTG13 also shows a high number of mutations at one of the receptor binding domains (RBD). Acquisition of the furin cleavage sites ("PRRA") along with high number of mutations at one of its RBD is probably responsible for the adaptation of SARS-CoV-2 into human systems. Furthermore, the codon adaptation index (CAI) was used to quantify the magnitude of adaptive efficacy of SARS-CoV-2 in human host in comparison with SARS-CoV. The CAI result showed a relatively less adaptive efficacy of the newly emerged SARS-CoV-2 to the human systems, which might be an indication of its mild clinical severity and progression compared to SARS-CoVs.

Comparative analysis of codon usage of mitochondrial genomes provides evolutionary insights into reptiles

Current available information on reptile genomes provides great potential for the study of unique adaptations from a genomic perspective. We compared differences in base composition and codon usage patterns across 400 reptile mitochondrial genomes assessing AT and GC skew, GC frequency, codon usage, effective number of codons, and codon adaptation index. We identified poor GC content in reptile mitochondrial genomes, with a predominant bias toward Adenine. We determined a compositional asymmetry between different taxonomic groups, which are inversely correlated to the rates of rearrangements in the mitogenome. We found that the most common codons in reptile mitochondrion are CTA (L), ATA (M) and ACA (T), which relates with have been found in birds, meaning that these patterns are shared across sauropsid mitogenomes. Codon usage bias clustering and effective codon number analyses revelated compositional asymmetry based on RSCU as well as that reptile mitogenomes are translationally efficient and are under selection pressure. Codon adaptation index revealed highest values in turtles indicating higher translational efficiency of mitochondrial genes among all reptiles, which could be related to metabolic adaptations (i.e., tolerance to anoxic conditions). This was also seen in other groups such as crocodiles (i.e., acclimation to cold) and snakes (phylogenetic origin of toxin-secreting oral glands and the evolutionary redesign of cytochrome c oxidase complex genes). We discuss our findings in the context of potential adaptations and evolutionary implications that these genomic differences provide to reptiles.

Hepatitis B virus (HBV) codon adapts well to the gene expression profile of liver cancer: an evolutionary explanation for HBV's oncogenic role.

Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins. Highly expressed genes in hosts have a codon bias related to tRNA abundance, the primary RNA translation rate determinant. We calculated the relative synonymous codon usage (RSCU) of three hepatitis viruses (HAV, HBV, and HCV), SARS-CoV-2, 30 human tissues, and hepatocellular carcinoma (HCC). After comparing RSCU between viruses and human tissues, we calculated the codon adaptation index (CAI) of viral and human genes. HBV and HCV showed the highest correlations with HCC and the normal liver, while SARS-CoV-2 had the strongest association with lungs. In addition, based on HCC RSCU, the CAI of HBV and HCV genes was the highest. HBV and HCV preferentially adapt to the tRNA pool in HCC, facilitating viral RNA translation. After an initial trigger, rapid HBV/HCV translation and replication may change normal liver cells into HCC cells. Our findings reveal a novel perspective on virus-mediated oncogenesis.

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus.

Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.

Immunoinformatic-based design of immune-boosting multiepitope subunit vaccines against monkeypox virus and validation through molecular dynamics and immune simulation.

Monkeypox virus is the causative agent of monkeypox disease, belonging to an orthopoxvirus genus, with a disease pattern similar to that of smallpox. The number of monkeypox cases have robustly increased recently in several countries around the world, potentially causing an international threat. Therefore, serious measures are indispensable to be taken to mitigate the spread of the disease and hence, under these circumstances, vaccination is the best choice to neutralize the monkeypox virus. In the current study, we used immunoinformatic approaches to target the L1R, B5R, and A33R proteins of the monkeypox virus to screen for immunogenic cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes to construct multiepitope subunit vaccines. Various online tools predicted the best epitope from immunogenic targets (L1R, B5R, and A33R) of monkeypox virus. The predicted epitopes were joined together by different linkers and subjected to 3D structure prediction. Molecular dynamics simulation analysis confirmed the proper folding of the modeled proteins. The strong binding of the constructed vaccines with human TLR-2 was verified by the molecular docking and determination of dissociation constant values. The GC content and codon adaptation index (CAI) values confirmed the high expression of the constructed vaccines in the pET-28a (+) expression vector. The immune response simulation data delineated that the injected vaccines robustly activated the immune system, triggering the production of high titers of IgG and IgM antibodies. In conclusion, this study provided a solid base of concept to develop dynamic and effective vaccines that contain several monkeypox virus-derived highly antigenic and nonallergenic peptides to control the current pandemic of monkeypox virus.

Analysis of nested alternate open reading frames and their encoded proteins.

Transcriptional and post-transcriptional mechanisms diversify the proteome beyond gene number, while maintaining a sequence relationship between original and altered proteins. A new mechanism breaks this paradigm, generating novel proteins by translating alternative open reading frames (Alt-ORFs) within canonical host mRNAs. Uniquely, ‘alt-proteins’ lack sequence homology with host ORF-derived proteins. We show global amino acid frequencies, and consequent biochemical characteristics of Alt-ORFs nested within host ORFs (nAlt-ORFs), are genetically-driven, and predicted by summation of frequencies of hundreds of encompassing host codon-pairs. Analysis of 101 human nAlt-ORFs of length ≥150 codons confirms the theoretical predictions, revealing an extraordinarily high median isoelectric point (pI) of 11.68, due to anomalous charged amino acid levels. Also, nAlt-ORF proteins exhibit a >2-fold preference for reading frame 2 versus 3, predicted mitochondrial and nuclear localization, and elevated codon adaptation index indicative of natural selection. Our results provide a theoretical and conceptual framework for exploration of these largely unannotated, but potentially significant, alternative ORFs and their encoded proteins.

Evolutionary and compositional analysis of streptokinase including its interaction with plasminogen: An in silico approach

Due to the accumulation of cholesterol in arterial wall, clot-forming cascade activated in the blood capillaries lead to conditions like myocardial ischemia and heart failure. These clots are dissolved by the enzyme streptokinase (SK), produced by Streptococcus sp., a normal flora in the human body. In the present study, codon-dependent evolution of twenty-three SK from Streptococcus sp. bacteria, isolated from distinct geographical origins were analyzed. Besides, domain variation, compositional analysis, effective number of codons (ENc) plot, codon adaptation index (CAI), and effect of polymorphism on SK interaction with its substrate plasminogen (Plg) were analyzed. Codon usage bias varied within a tiny range. Studies also reveal that AT ending codons are preferred over GC ending codons. Analyses of the other parameters reveal that the mutational pressure is one of the main factors to shape codon usage biasness. Interfacing and polar contact forming amino acid residues of SK with Plg is identical for all Streptococcus dysgalactiae but not for all Streptococcus pyogenes. Changes of those interfacing amino acid sites exhibit a substantial effect on polar interaction between SK and Plg. The present in silico studies are expected to shed further light to characterize and moreover, to understand the various contributing factors to influence SK adaptation that will be fulfilling to develop efficient thrombolytic therapeutics.

Host adaptation of codon usage in SARS-CoV-2 from mammals indicates potential natural selection and viral fitness.

SARS-CoV-2 infection, which is the cause of the COVID-19 pandemic, has expanded across various animal hosts, and the virus can be transmitted particularly efficiently in minks. It is still not clear how SARS-CoV-2 is selected and evolves in its hosts, or how mutations affect viral fitness. In this report, sequences of SARS-CoV-2 isolated from human and animal hosts were analyzed, and the binding energy and capacity of the spike protein to bind human ACE2 and the mink receptor were compared. Codon adaptation index (CAI) analysis indicated the optimization of viral codons in some animals such as bats and minks, and a neutrality plot demonstrated that natural selection had a greater influence on some SARS-CoV-2 sequences than mutational pressure. Molecular dynamics simulation results showed that the mutations Y453F and N501T in mink SARS-CoV-2 could enhance the binding of the viral spike to the mink receptor, indicating the involvement of these mutations in natural selection and viral fitness. Receptor binding analysis revealed that the mink SARS-CoV-2 spike interacted more strongly with the mink receptor than the human receptor. Tracking the variations and codon bias of SARS-CoV-2 is helpful for understanding the fitness of the virus in virus transmission, pathogenesis, and immune evasion.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00705-022-05612-6.

Componential usage patterns in dengue 4 viruses reveal their better evolutionary adaptation to humans.

There have been at least four types of dengue outbreaks in the past few years. The evolutionary characteristics of dengue viruses have aroused great concerns. The evolutionary characteristics of dengue 4 viruses are studied in the present study based on their base usage patterns and codon usage patterns. The effective number of codons and relative synonymous codon usage (RSCU) values of four types of dengue viruses were counted or calculated. The Kullback–Leibler (K–L) divergences of relative synonymous codon usage from dengue viruses to humans and the Kullback–Leibler divergences of amino acid usage patterns from dengue viruses to humans were calculated to explore the adaptation levels of dengue viruses. The results suggested that: (1) codon adaptation in dengue 4 viruses occurred through an evolutionary process from 1956 to 2021, (2) overall relative synonymous codon usage values of dengue 4 viruses showed more similarities to humans than those of other subtypes of dengue viruses, and (3) the smaller Kullback–Leibler divergence of amino acid usage and relative synonymous codon usage from dengue viruses to humans indicated that the dengue 4 viruses adapted to human hosts better. All results indicated that both mutation pressure and natural selection pressure contributed to the codon usage pattern of dengue 4 viruses more obvious than to other subtypes of dengue viruses and that the dengue 4 viruses adapted to human hosts better than other types of dengue viruses during their evolutionary process.

Many-objective approach based on problem-aware mutation operators for protein encoding

One of the research pathways in synthetic biology is protein encoding, which aims to improve and increase protein expression. The production of heterologous proteins is important in different fields, such as medicine, environmental biology, and agriculture. Protein encoding is a difficult task and can be defined as a many-objective optimization problem, where four objectives must be optimized concurrently: codon adaptation, guanine-cytosine content, difference between sequences, and avoidance of hairpin loops. These objectives are why we propose and describe a many-objective approach based on the non-dominated sorting genetic algorithm-III (NSGA-III) for protein encoding. The proposed algorithm was designed to work with novel mutation operators that are problem-aware and consider the different optimization objectives. The results of the proposed algorithm were compared to those of different tools that were reported by other authors to determine its efficiency. Comparisons were made using several quality metrics and with statistical analyses. The average improvements in hypervolume and set coverage were between 5.34% and 55.75%, and 53.01% and 100%, respectively. Based on the statistical analyses, the proposed algorithm was found to produce statistically significant improvements compared to other algorithms, thus highlighting the relevance of the proposed approach for protein encoding.

An integrative reverse vaccinology, immunoinformatic, docking and simulation approaches towards designing of multi-epitopes based vaccine against monkeypox virus

Monkeypox is a viral zoonotic disease that is caused by the monkeypox virus (MPXV) and is mainly transmitted to human through close contact with an infected person, animal, or fomites which is contaminated by the virus. In the present research work, reverse vaccinology and several other bioinformatics and immunoinformatics tools were utilized to design multi-epitopes-based vaccine against MPXV by exploring three probable antigenic extracellular proteins: cupin domain-containing protein, ABC transporter ATP-binding protein and DUF192 domain-containing protein. Both cellular and humoral immunity induction were the main concerning qualities of the vaccine construct, hence from selected proteins both B and T-cells epitopes were predicted. Antigenicity, allergenicity, toxicity, and water solubility of the predicted epitopes were assessed and only probable antigenic, non-allergic, non-toxic and good water-soluble epitopes were used in the multi-epitopes vaccine construct. The developed vaccine was found to be potentially effective against MPXV and to be highly immunogenic, cytokine-producing, antigenic, non-toxic, non-allergenic, and stable. Additionally, to increase stability and expression efficiency in the host E. coli, disulfide engineering, codon adaptation, and in silico cloning were employed. Molecular docking and other biophysical approaches were utilized to evaluate the binding mode and dynamic behavior of the vaccine construct with TLR-2, TLR-4, and TLR-8. The outcomes of the immune simulation demonstrated that both B and T cells responded more strongly to the vaccination component. The detailed in silico analysis concludes that the proposed vaccine will induce a strong immune response against MPXV infection, making it a promising target for additional experimental trials. Communicated by Ramaswamy H. Sarma

Genome dynamics, codon usage patterns and influencing factors in Aeromonas hydrophila phages

In the present study, genome characteristics and codon usage patterns of 44 Aeromonas hydrophila phages were studied. Phage genomes varied from 30.8 to 262.0 kb with mean±SD and median values of 111.3 ± 81.4 kb and 79.4 kb, respectively. Though the great variation in phage GC contents (35.1–62.2%) was observed, GC contents of all phages (except two phages) were significantly less than the GC content (62.4 ± 5.6%) of the host. The effective number of codons (ENC) values of phage genes ranged from 27.7 to 61 with a mean±SD value of 47.4 ± 6.8. Out of a total 5773 phage genes, 207 (3.6%), 3,528 (61.1%) and 2,012 (34.9%) genes had strong (ENC < 35), moderate (35 < ENC < 50) and low (ENC ≥ 50) codon usage bias, respectively. During relative synonymous codon usage (RSCU) analysis, shared usage of preferred codons was also observed between the phages and host. During codon adaptation index (CAI) analysis, 1028 (17.8%) phage genes showed significant adaptation towards the host. Among these genes, 797 (78.0%) genes encoded hypothetical proteins or proteins of unknown function; whereas 118 (12%) genes encoded the phage structural and packaging proteins. Segregation of ENC, RSCU and CAI analysis results based on genome size also indicated that codon usage bias was more prominent in phages with small genomes. Correlation, neutrality and GC3 versus ENC analyzes indicated a more dominant role of natural selection in shaping the codon usage patterns of A. hydrophila phages. The findings of the current study could be useful from evolutionary and host-pathogen interaction perspectives leading to efficient utilization of phages for therapeutic and other applications.

Evolutionary dynamics of codon usages for peste des petits ruminants virus.

Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.

Decoding molecular factors shaping human angiotensin converting enzyme 2 receptor usage by spike glycoprotein in lineage B beta-coronaviruses

Acquiring the human ACE2 receptor usage trait enables the coronaviruses to spill over to humans. However, the origin of the ACE2 usage trait in coronaviruses is poorly understood. Using a multi-disciplinary approach combining evolutionary bioinformatics and molecular dynamics simulation, we decode the principal driving force behind human ACE2 receptor recognition in coronaviruses. Genomic content, evolutionary divergence, and codon usage bias analysis reveal that SARS-CoV2 is evolutionarily divergent from other human ACE2-user CoVs, indicating that SARS-CoV2 originates from a different lineage. Sequence analysis shows that all the human ACE2-user CoVs contain two insertions in the receptor-binding motif (RBM) that directly interact with ACE2. However, the insertion sequences in SARS-CoV2 are divergent from other ACE2-user CoVs, implicating their different recombination origins. The potential of mean force calculations reveals that the high binding affinity of SARS-CoV2 RBD to human ACE2 is primarily attributed to its ability to form a higher number of hydrogen bonds than the other ACE2-user CoVs. The adaptive branch-site random effects likelihood method identifies positive selection bias across the ACE2 user CoVs lineages. Recombination and selection forces shape the spike evolution in human ACE2-using beta-CoVs to optimize the interfacial hydrogen bonds between RBD and ACE2. However, these evolutionary forces work within the constraints of nucleotide composition, ensuring optimum codon adaptation of the spike (S) gene within the host cell.

In silico design of a multi-epitope vaccine against HPV16/18

BackgroundCervical cancer is the fourth most common cancer affecting women and is caused by human Papillomavirus (HPV) infections that are sexually transmitted. There are currently commercially available prophylactic vaccines that have been shown to protect vaccinated individuals against HPV infections, however, these vaccines have no therapeutic effects for those who are previously infected with the virus. The current study’s aim was to use immunoinformatics to develop a multi-epitope vaccine with therapeutic potential against cervical cancer.ResultsIn this study, T-cell epitopes from E5 and E7 proteins of HPV16/18 were predicted. These epitopes were evaluated and chosen based on their antigenicity, allergenicity, toxicity, and induction of IFN-γ production (only in helper T lymphocytes). Then, the selected epitopes were sequentially linked by appropriate linkers. In addition, a C-terminal fragment of Mycobacterium tuberculosis heat shock protein 70 (HSP70) was used as an adjuvant for the vaccine construct. The physicochemical parameters of the vaccine construct were acceptable. Furthermore, the vaccine was soluble, highly antigenic, and non-allergenic. The vaccine’s 3D model was predicted, and the structural improvement after refinement was confirmed using the Ramachandran plot and ProSA-web. The vaccine’s B-cell epitopes were predicted. Molecular docking analysis showed that the vaccine's refined 3D model had a strong interaction with the Toll-like receptor 4. The structural stability of the vaccine construct was confirmed by molecular dynamics simulation. Codon adaptation was performed in order to achieve efficient vaccine expression in Escherichia coli strain K12 (E. coli). Subsequently, in silico cloning of the multi-epitope vaccine was conducted into pET-28a ( +) expression vector.ConclusionsAccording to the results of bioinformatics analyses, the multi-epitope vaccine is structurally stable, as well as a non-allergic and non-toxic antigen. However, in vitro and in vivo studies are needed to validate the vaccine’s efficacy and safety. If satisfactory results are obtained from in vitro and in vivo studies, the vaccine designed in this study may be effective as a therapeutic vaccine against cervical cancer.