Patterns of genome-wide codon usage bias in tobacco, tomato and potato

In-silico identification of putatively functional intergenic small open reading frames in the cucumber genome and their predicted response to biotic and abiotic stresses

The availability of high-throughput sequencing technologies increased our understanding of different genomes. However, the genomes of all living organisms still have many unidentified coding sequences. The increased number of missing small open reading frames (sORFs) is due to the length threshold used in most gene identification tools, which is true in the genic and, more importantly and surprisingly, in the intergenic regions. Scanning the cucumber genome intergenic regions revealed 420 723 sORF. We excluded 3850 sORF with similarities to annotated cucumber proteins. To propose the functionality of the remaining 416 873 sORF, we calculated their codon adaptation index (CAI). We found 398 937 novel sORF (nsORF) with CAI ≥ 0.7 that were further used for downstream analysis. Searching against the Rfam database revealed 109 nsORFs similar to multiple RNA families. Using SignalP-5.0 and NLS, identified 11 592 signal peptides. Five predicted proteins interacting with Meloidogyne incognita and Powdery mildew proteins were selected using published transcriptome data of host-pathogen interactions. Gene ontology enrichment interpreted the function of those proteins, illustrating that nsORFs' expression could contribute to the cucumber's response to biotic and abiotic stresses. This research highlights the importance of previously overlooked nsORFs in the cucumber genome and provides novel insights into their potential functions.

Investigation of CaMV-host co-evolution through synonymous codon pattern

Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.

Production of functional recombinant roseltide rT1 antimicrobial peptide in tobacco plants

Plant-derived peptides represent a promising group of natural compounds with broad industrial and pharmaceutical applications. Low-efficiency production level is the major obstacle to the commercial production of such bioactive peptides. Today, recombinant techniques have been developed for fast and cost-effective production of high-quality peptides for various applications in the chemical and food industries. The roseltide rT1 is a plant peptide with different antimicrobial properties and therapeutic applications in the prevention and treatment of inflammatory lung diseases by inhibiting human neutrophil elastases. Here, we report the expression of functional recombinant roseltide rT1 peptide in tobacco plants. Transgenic plants were generated by the Agrobacterium-mediated transformation method followed by molecular analysis of transgenic plants to demonstrate successful integration and expression of recombinant rT1 peptide. Protein extracts of transgenic plants expressing a single-copy rT1 gene showed efficient antimicrobial properties as verified by growth inhibition of different bacterial strains. Our results illustrate that plant-derived recombinant rT1 peptide is a promising alternative for rapid and cost-effective production of this important antimicrobial peptide for application in therapeutic and food industries.

Codon Pattern and Context Analysis in Genes Triggering Alzheimer's Disease and Latent Tau Protein Aggregation Post-Anesthesia Exhibited Unique Molecular Patterns Associated with Functional Aspects

Background

Previous reports have demonstrated post-operative dementia and Alzheimer's disease (AD), and increased amyloid-β levels and tau hyperphosphorylation have been observed in animal models post-anesthesia.

Objective

After surgical interventions, loss in memory has been observed that has been found linked with genes modulated after anesthesia. Present study aimed to study molecular pattern present in genes modulated post anesthesia and involved in characters progressing towards AD.

Methods

In the present study, 17 transcript variants belonging to eight genes, which have been found to modulate post-anesthesia and contribute to AD progression, were envisaged for their compositional features, molecular patterns, and codon and codon context-associated studies.

Results

The sequences' composition was G/C rich, influencing dinucleotide preference, codon preference, codon usage, and codon context. The G/C nucleotides being highly occurring nucleotides, CpGdinucleotides were also preferred; however, CpG was highly disfavored at p3-1 at the codon junction. The nucleotide composition of Cytosine exhibited a unique feature, and unlike other nucleotides, it did not correlate with codon bias. Contrarily, it correlated with the sequence lengths. The sequences were leucine-rich, and multiple leucine repeats were present, exhibiting the functional role of neuroprotection from neuroinflammation post-anesthesia.

Conclusions

The analysis pave the way to elucidate unique molecular patterns in genes modulated during anesthetic treatment and might help ameliorate the ill effects of anesthetics in the future.

Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities

Introduction

Neurodegeneration and cancer present in comorbidities with inverse effects due to the expression of genes and pathways acting in opposition. Identifying and studying the genes simultaneously up or downregulated during morbidities helps curb both ailments together.

Methods

This study examines four genes. Three of these (Amyloid Beta Precursor Protein (APP), Cyclin D1 (CCND1), and Cyclin E2 (CCNE2) are upregulated, and one protein phosphatase 2 phosphatase activator (PTPA) is simultaneously downregulated in both disorders. We investigated molecular patterns, codon usage, codon usage bias, nucleotide bias in the third codon position, preferred codons, preferred codon pairs, rare codons, and codon context.

Results

Parity analysis revealed that T is preferred over A, and G is preferred over C in the third codon position, suggesting composition plays no role in nucleotide bias in both the upregulated and downregulated gene sets and that mutational forces are stronger in upregulated gene sets than in downregulated ones. Transcript length influenced the overall %A composition and codon bias, and the codon AGG exerted the strongest influence on codon usage in both the upregulated and downregulated gene sets. Codons ending in G/C were preferred for 16 amino acids, and glutamic acid-, aspartic acid-, leucine-, valine-, and phenylalanine-initiated codon pairs were preferred in all genes. Codons CTA (Leu), GTA (Val), CAA (Gln), and CGT (Arg) were underrepresented in all examined genes.

Discussion

Using advanced gene editing tools such as CRISPR/Cas or any other gene augmentation technique, these recoded genes may be introduced into the human body to optimize gene expression levels to augment neurodegeneration and cancer therapeutic regimens simultaneously.

Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)

Codon usage bias (CUB) reveals the characteristics of species and can be utilized to understand their evolutionary relationship, increase the target genes' expression in the heterologous receptor plants, and further provide theoretic assistance for correlative study on molecular biology and genetic breeding. The chief aim of this work was to analyze the CUB in chloroplast (cp.) genes in nine Elaeagnus species to provide references for subsequent studies. The codons of Elaeagnus cp. genes preferred to end with A/T bases rather than with G/C bases. Most of the cp. genes were prone to mutation, while the rps7 genes were identical in sequences. Natural selection was inferred to have a powerful impact on the CUB in Elaeagnus cp. genomes, and their CUB was extremely strong. In addition, the optimal codons were identified in the nine cp. genomes based on the relative synonymous codon usage (RSCU) values, and the optimal codon numbers were between 15 and 19. The clustering analyses based on RSCU were contrasted with the maximum likelihood (ML)-based phylogenetic tree derived from coding sequences, suggesting that the t-distributed Stochastic Neighbor Embedding clustering method was more appropriate for evolutionary relationship analysis than the complete linkage method. Moreover, the ML-based phylogenetic tree based on the conservative matK genes and the whole cp. genomes had visible differences, indicating that the sequences of specific cp. genes were profoundly affected by their surroundings. Following the clustering analysis, Arabidopsis thaliana was considered the optimal heterologous expression receptor plant for the Elaeagnus cp. genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01289-6.

Comparison of Boraginales Plastomes: Insights into Codon Usage Bias, Adaptive Evolution, and Phylogenetic Relationships

The Boraginales (Boraginaceae a.l.) comprise more than 2450 species worldwide. However, little knowledge exists of the characteristics of the complete plastid genome. In this study, three new sequences representing the first pt genome of Heliotropiaceae and Cordiaceae were assembled and compared with other Boraginales species. The pt genome sizes of Cordia dichotoma, Heliotropium arborescens, and Tournefortia montana were 151,990 bp, 156,243 bp, and 155,891 bp, respectively. Multiple optimal codons were identified, which may provide meaningful information for enhancing the gene expression of Boraginales species. Furthermore, codon usage bias analyses revealed that natural selection and other factors may dominate codon usage patterns in the Boraginales species. The boundaries of the IR/LSC and IR/SSC regions were significantly different, and we also found a signal of obvious IR region expansion in the pt genome of Nonea vesicaria and Arnebia euchroma. Genes with high nucleic acid diversity (pi) values were also calculated, which may be used as potential DNA barcodes to investigate the phylogenetic relationships in Boraginales. psaI, rpl33, rpl36, and rps19 were found to be under positive selection, and these genes play an important role in our understanding of the adaptive evolution of the Boraginales species. Phylogenetic analyses implied that Boraginales can be divided into two groups. The existence of two subfamilies (Lithospermeae and Boragineae) in Boraginaceae is also strongly supported. Our study provides valuable information on pt genome evolution and phylogenetic relationships in the Boraginales species.

Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus

Soybean mosaic virus (SMV) has threatened the global yield of Leguminosae crops, but the mechanism of its infection, spread, and evolution remains unknown. A systemic analysis of 107 SMV strains was performed to explore the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SMV, which provides insight into its molecular evolution and elucidates its unknown host adaptation pattern. The overall nucleotide composition and correlation analysis revealed that the preferred synonymous codons mostly end with A/U. Clustering by RSCU value of each strain and phylogenetic tree analysis showed that the SMV isolates studied were divided into four clades, with a low overall extent of codon usage bias (CUB) in SMV. According to the ENC, PR2, neutrality plot, and correspondence analysis, natural selection of geographical diversity may play a critical role in the CUB. Higher adaptability was shown in Glycine with SMV and more pressure was received by clade III. These findings could not only provide valuable information about the overall codon usage pattern of the SMV genome, but could also aid in the clarification of the involved mechanisms that dominate the codon usage patterns and genetic evolution of the SMV genome.

Direct in vivo observation of the effect of codon usage bias on gene expression in Arabidopsis hybrids

Hybrids are the perfect materials to study cis regulatory elements because the two parental alleles are subjected to identical trans environments. There has been a debate on whether synonymous codon usage could affect gene expression. In vitro experiments found that luciferase genes with enhanced codon optimality showed elevated mRNA expression. However, the underlying mechanism is still unclear, and no direct evidence is observed to support this notion. By mapping the RNA-seq data of hybrids of Arabidopsis thaliana and Arabidopsis lyrata, we quantified the allele-specific reads and estimated the relative expression of orthologous genes. We focused on orthologous genes with dN = 0 and dS > 0, which means that they only differ in synonymous codon usage. We found that orthologous genes with higher codon optimality in A. thaliana tend to have higher expression levels of the A. thaliana allele. Codon usage bias could influence gene expression. This phenomenon is not only found in in vitro experiments but also supported by in vivo observations. Therefore, synonymous mutations could have a broad impact from multiple aspects and should not be automatically ignored in genomic studies. KEY MESSAGE: In Arabidopsis hybrids, alleles with higher codon optimality tend to have higher expression levels.