Nucleotide Of Codon Research Articles

Evolution of codon and amino acid usage in bacterial protein toxins

Toxin proteins are secreted by most pathogens as an integral part of pathogenic mechanism(s). The toxins act by either damaging the host cell membrane (for example, pore-forming toxins and RTX toxins) or by modulation of important cellular pathways (for example, inhibition of protein translation by ribosome-inactivating proteins). The mechanism of action of these toxins provides the pathogen with strategies for adaptation in the unfavorable host environment. Though, secreted by different pathogenic species, the protein toxins seem to share common features that allow the protein to bind to specific molecules and enter the host cell. Earlier studies have suggested role of several events like horizontal gene transfer and insertion-deletion mutations in evolution of protein toxins. The present study involving 125 bacterial protein toxins secreted by 49 pathogenic bacteria focuses on the role and constraints of the bacterial genome on evolution of codon and amino acid usage in respective bacterial protein toxins. We compare the nucleotide composition, codon and dinucleotide usage trends between different classes of bacterial protein toxins and between individual toxins and the parent bacterial genome expressing the toxin(s)

Comparative analysis of mitochondrial genomes reveals family-specific architectures and molecular features in scorpions (Arthropoda: Arachnida: Scorpiones)

Scorpions are a group of arachnids with great evolutionary success that comprise more than 2,000 described species. Mitochondrial genomes have been little studied in this clade. We describe and compare different scorpion mitochondrial genomes and analyze their architecture and molecular characteristics. We assembled eight new scorpion mitochondrial genomes from transcriptomic datasets, annotated them, predicted the secondary structures of tRNAs, and compared the nucleotide composition, codon usage, and relative synonymous codon usage of 16 complete scorpion mitochondrial genomes. Lastly, we provided a phylogeny based on all mitochondrial protein coding genes. We characterized the mitogenomes in detail and reported particularities such as dissimilar synteny in the family Buthidae compared to other scorpions, unusual tRNA secondary structures, and unconventional start and stop codons in all scorpions. Our comparative analysis revealed that scorpion mitochondrial genomes exhibit different architectures and features depending on taxonomic identity. We highlight the parvorder Buthida, particularly the family Buthidae, as it invariably exhibited different mitogenome features such as synteny, codon usage, and AT-skew compared to the parvorder Iurida that included the rest of the scorpion families we analyzed in this study. Our results provide a better understanding of the evolution of mitogenome features and phylogenetic relationships in scorpions.

Identification of the novel HLA-DQA1*01:03:07 allele using next-generation sequencing.

The HLA-DQA1*01:03:07 allele differs from HLA-DQA1*01:03:01:01 allele by a single nucleotide in codon -8.

Identification of the novel HLA-DPA1*02:89 allele using next-generation sequencing.

The HLA-DPA1*02:89 allele differs from HLA-DPA1*02:02:02:01 allele by a single nucleotide in codon 224.

Artificial nucleotide codons for enzymatic DNA synthesis.

Herein, we report the high-yielding solid-phase synthesis of unmodified and chemically modified trinucleotide triphosphates (dN3TPs). These synthetic codons can be used for enzymatic DNA synthesis provided their scaffold is stabilized with phosphorothioate units. Enzymatic synthesis with three rather than one letter nucleotides will be useful to produce xenonucleic acids (XNAs) and for in vitro selection of modified functional nucleic acids.

Nucleotide augmentation for machine learning-guided protein engineering.

Machine learning-guided protein engineering is a rapidly advancing field. Despite major experimental and computational advances, collecting protein genotype (sequence) and phenotype (function) data remains time- and resource-intensive. As a result, the quality and quantity of training data are often a limiting factor in developing machine learning models. Data augmentation techniques have been successfully applied to the fields of computer vision and natural language processing; however, there is a lack of such augmentation techniques for biological sequence data. Towards this end, we develop nucleotide augmentation (NTA), which leverages natural nucleotide codon degeneracy to augment protein sequence data via synonymous codon substitution. As a proof of concept for protein engineering, we test several online and offline augmentation implementations to train machine learning models with benchmark datasets of protein genotype and phenotype, revealing performance gains on par and surpassing benchmark models using a fraction of the training data. NTA also enables substantial improvements for classification tasks under heavy class imbalance. The code used in this study is publicly available at https://github.com/minotm/NTA. Supplementary data are available at Bioinformatics Advances online.

Engineering Modified mRNA-Based Vaccine against Dengue Virus Using Computational and Reverse Vaccinology Approaches.

Dengue virus belonging to the family Flaviviridae and its four serotypes are responsible for dengue infections, which extend over 60 countries in tropical and subtropical areas of the world including Pakistan. During the ongoing dengue outbreak in Pakistan (2022), over 30,000 cases have been reported, and over 70 lives have been lost. The only commercialized vaccine against DENV, Dengvaxia, cannot be administered as a prophylactic measure to cure this infection due to various complications. Using machine learning and reverse vaccinology approaches, this study was designed to develop a tetravalent modified nucleotide mRNA vaccine using NS1, prM, and EIII sequences of dengue virus from Pakistani isolates. Based on high antigenicity, non-allergenicity, and toxicity profiling, B-cell epitope, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) putative vaccine targets were predicted. Molecular docking confirmed favorable interactions between T-cell epitopes and their respective HLA alleles, while normal mode analysis validated high-affinity interactions of vaccine proteins with immune receptors. In silico immune simulations confirmed adequate immune responses to eliminate the antigen and generate memory. Codon optimization, physicochemical features, nucleotide modifications, and suitable vector availability further ensured better antigen expression and adaptive immune responses. We predict that this vaccine construct may prove to be a good vaccinal candidate against dengue virus in vitro as well.

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy.

Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy.

Mitochondrial genomes of the land hermit crab Coenobita clypeatus (Anomura: Paguroidea) and the mole crab Emerita talpoida (Anomura: Hippoidea) with insights into phylogenetic relationships in the Anomura (Crustacea: Decapoda)

The infraorder Anomura is a species-rich clade of decapod crustaceans recognized by its remarkable disparity in terms of morphology, anatomy, ecology, physiology, and behavior. This study assembled and characterized the complete mitochondrial genomes of two anomuran species, the hermit crab Coenobita clypeatus and the mole crab Emerita talpoida. The AT-rich mitochondrial genomes of C. clypeatus and E. talpoida are 16,469 bp and 15,810 bp long, respectively, and are composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 1,390 bp and 553 bp long intergenic space is assumed to be the D-loop in C. clypeatus and E. talpoida, respectively. Mitochondrial synteny in C. clypeatus is identical to that reported in other congeneric hermit crabs while synteny in E. talpoida is identical to that described for the confamilial mole crab Stemonopa insignis. No major differences occur between the studied species and their respective congeneric / cofamilial species in terms of nucleotide composition and codon usage profiles of PCGs. Selective pressure analysis in PCGs, rarely conducted in anomuran crabs, indicate that all these mitochondrial PCGs experience purifying selection and that this purifying selection is stronger in some (i.e., cox family genes and cob) compared to other PCGs (e.g., atp8). Most of the tRNA genes exhibited a typical ‘cloverleaf’ secondary structure with few exceptions in the two studied species. In C. clypeatus, tRNA-Ser1 lacks the thymine pseudouracil cytosine (TΨC) loop while tRNA-Phe and tRNA-Tyr each exhibit a deletion of the dihydroxyuridine (DHU) loop but not the arm. In turn, in E. talpoida, tRNA-Phe and tRNA-Arg exhibit a deletion of the DHU loop but not the arm while tRNA-Ser1 lacks the TΨC arm. A phylogenomic analysis based on translated PCGs confirms the monophyly of the infraorder Anomura and retrieves most/all relationships at the superfamily and family level previously reported for anomurans. The analysis supports the monophyletic status of the families Albuneidae, Lithodidae, Coenobitidae, and Porcellanidae. In turn, the superfamily Paguroidea, and the families Paguridae and Diogenidae are polyphyletic.

Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae).

The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.

Identification of the novel HLA-DRB4*01:162N allele using next-generation sequencing.

The HLA-DRB4*01:162N allele differs from HLA-DRB4*01:03:01:01 allele by a single nucleotide in codon 131.

MRNA Vaccine Designing Using Chikungunya Virus E Glycoprotein through Immunoinformatics-Guided Approaches.

Chikungunya virus is an alphavirus transmitted by mosquitos that develops into chikungunya fever and joint pain in humans. This virus’ name originated from a Makonde term used to describe an illness that changes the joints and refers to the posture of afflicted patients who are affected by excruciating joint pain. There is currently no commercially available drug or vaccine for chikungunya virus infection and the treatment is performed by symptom reduction. Herein, we have developed a computationally constructed mRNA vaccine construct featuring envelope glycoprotein as the target molecule to aid in the treatment process. We have utilized the reverse vaccinology approach to determine epitopes that would generate adaptive immune reactions. The resulting T and B lymphocytes epitopes were screened by various immunoinformatic tools and a peptide vaccine construct was designed. It was validated by proceeding to docking and MD simulation studies. The following design was then back-translated in nucleotide sequence and codons were optimized according to the expression host system (H. sapiens). Various sequences, including 3′ and 5′ UTR regions, Kozak sequence, poly (A) tail, etc., were introduced into the sequence for the construction of the final mRNA vaccine construct. The secondary structure was generated for validation of the mRNA vaccine construct sequence. Additionally, in silico cloning was also performed to design a vector for proceeding towards in vitro experimentation. The proposed designed vaccine construct may proceed with experimental testing for further efficacy verification and the final development of a vaccine against chikungunya virus infection.

Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages.

Bovine viral diarrhea virus (BVDV), serving as an important pathogen for newborn calves, poses threat to reproductive and economic losses in the cattle industry. To survey the infection rate and genetic diversity of BVDV in newborn calves in northern China, a total of 676 sera samples of newborn calves were collected from four provinces between 2021 and 2022. All sera samples were individually detected for BVDV infection by RT-PCR and ELISA. Our results showed that the overall serological rate was 9.76% (66/676) and the average positive rate of BVDV RNA was 8.14% (55/676) in the newborn calves. Eight BVDV strains were successfully isolated from RT-PCR positive sera samples, and four isolates displayed the cytopathic effect (CPE). Based on phylogenetic tree at the genome level, the eight strains were classified into subgenotype 1c. Moreover, the BVDV isolates had a close genetic relationship with the GSTZ strain at either nucleotide or codon usage level. Interestingly, in comparison of synonymous codon usage patterns between the BVDV isolates with CPE and ones without CPE, there were four synonymous codons (UCG, CCC, GCA, and AAC) which displayed the significant differences (p < 0.05) at codon usage pattern, suggesting that synonymous codon usage bias might play a role in BVDV-1c biotypes. In addition, the usage of synonymous codons containing CpG dinucleotides was suppressed by the BVDV-1c isolates, reflecting one of strategies of immune evasion of BVDV to its host. Taken together, our study provided data for monitoring and vaccination strategies of BVDV for newborn calves in northern China.

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.

Codon Usage Bias Correlates With Gene Length in Neurodegeneration Associated Genes.

Codon usage analysis is a crucial part of molecular characterization and is used to determine the factors affecting the evolution of a gene. The length of a gene is an important parameter that affects the characteristics of the gene, such as codon usage, compositional parameters, and sometimes, its functions. In the present study, we investigated the association of various parameters related to codon usage with the length of genes. Gene expression is affected by nucleotide disproportion. In sixty genes related to neurodegenerative disorders, the G nucleotide was the most abundant and the T nucleotide was the least. The nucleotide T exhibited a significant association with the length of the gene at both the overall compositional level and the first and second codon positions. Codon usage bias (CUB) of these genes was affected by pyrimidine and keto skews. Gene length was found to be significantly correlated with codon bias in neurodegeneration associated genes. In gene segments with lengths below 1,200 bp and above 2,400 bp, CUB was positively associated with length. Relative synonymous CUB, which is another measure of CUB, showed that codons TTA, GTT, GTC, TCA, GGT, and GGA exhibited a positive association with length, whereas codons GTA, AGC, CGT, CGA, and GGG showed a negative association. GC-ending codons were preferred over AT-ending codons. Overall analysis indicated that the association between CUB and length varies depending on the segment size; however, CUB of 1,200–2,000 bp gene segments appeared not affected by gene length. In synopsis, analysis suggests that length of the genes correlates with various imperative molecular signatures including A/T nucleotide disproportion and codon choices. In the present study we additionally evaluated various molecular features and their correlation with different indices of codon usage, like the Codon Adaptation Index (CAI) and Relative Dynonymous Codon Usage (RSCU) of codons. We also considered the impact of gene fragment size on different molecular features in genes related to neurodegeneration. This analysis will aid our understanding of and in potentially modulating gene expression in cases of defective gene functioning in clinical settings.

Complete mitochondrial genome of Kentrochrysalis streckeri (Lepidoptera: Sphingidae) and phylogenetic analysis

In this study, we sequenced the complete mitogenome of Kentrochrysalis streckeri (Staudinger, 1880). The complete mitogenome sequence of K. streckeri is circular, 15,253 bp in size and contains 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). Nucleotide composition was A + T biased, and all the PCGs exhibited a positive AT-skew, which was reflected in the nucleotide composition, codon, and amino acid usage. Most PCGs start with ATG or ATT and stop with TAA. However, COX1 gene starts with CGA and three genes (COX1, COX2, NAD5) use the incomplete stop codon T. Phylogenetic analyses showed that the relationship (K. streckeri+((Manduca sexta+Sphinx morio)+(Psilogramma increta+(Psilogramma menephron+Notonagemia analis scribae)))).

Identification of the novel HLA-B*56:01:18 allele using next-generation sequencing.

The HLA-B*56:01:18 allele differs from HLA-B*56:01:01:01 allele by a single nucleotide in codon 326.3.

Identification of the novel HLA-A*26:01:75 allele using next-generation sequencing.

The HLA-A*26:01:75 allele differs from HLA-A*26:01:01:01 allele by a single nucleotide in codon -10.3.

Mutation of rpsL Gene in Streptomycin-Resistant Pseudomonas syringae pv. actinidiae Biovar 3 Strains Isolated from Korea

Pseudomonas syringae pv. actinidiae (Psa) is the causal agent responsible for the bacterial canker disease of kiwifruit plants. Psa strains are divided into five different biovars based on genetic and biochemical characteristics. Among them, biovar 2 and 3 strains of Psa were isolated and have been causing widespread damages in Korea. One of the most effective ways to control Psa is to use an antibiotic such as streptomycin. However, Psa strains resistant to this antibiotic were isolated in Korea, and an earlier study revealed that the resistance in the biovar 2 is associated with strA-strB genes. This study aimed to determine the molecular resistance mechanism of Psa biovar 3 strains to streptomycin. Sequencing the rpsL gene encoding ribosomal protein S12 from three streptomycin-resistant strains screened in the laboratory revealed that a spontaneous mutation occurred either at codon 43 or 88. Meanwhile, in four streptomycin-resistant strains of Psa biovar 3 isolated from two kiwifruit orchards, a single nucleotide in codon 43 of the rpsL, which is AAA in streptomycin-sensitive strain, was substituted for AGA causing an amino acid change from lysine to arginine. The resistant mechanism in all biovar 3 strains obtained in Korea was identified as a mutation of the rpsL gene.

Bias at the third nucleotide of codon pairs in virus and host genomes

Genomes of different sizes and complexity can be compared using common features. Most genomes contain open reading frames, and most genomes use the same genetic code. Redundancy in the genetic code means that different biases in the third nucleotide position of a codon exist in different genomes. However, the nucleotide composition of viruses can be quite different from host nucleotide composition making it difficult to assess the relevance of these biases. Here we show that grouping codons of a codon-pair according to the GC content of the first two nucleotide positions of each codon reveals patterns in nucleotide usage at the third position of the 1st codon. Differences between the observed and expected biases occur predominantly when the first two nucleotides of the 2nd codon are both S (strong, G or C) or both W (weak, A or T), not a mixture of strong and weak. The data indicates that some codon pairs are preferred because of the strength of the interactions between the codon and anticodon, the adjacent tRNAs and the ribosome. Using base-pairing strength and third position bias facilitates the comparison of genomes of different size and nucleotide composition and reveals patterns not previously described.