Exploring diversity in avian immune defence: Insights from cathelicidin clusters

Cathelicidins are a family of proteins from which a class of Host Defence Peptides (HDPs) is derived. They are components of the innate immune system of most vertebrates, including birds. Despite their promising activities, the genomic organisation and interspecies diversity of avian cathelicidins has been less studied than in other animal groups. In this research, we investigated the cathelicidin cluster in 72 avian species from 26 different orders by mining the avian genome assemblies available in NCBI database, using bioinformatics tools to analyse the cluster composition, gene structure and phylogenetic relationships. Cathelicidin clusters were found principally on chromosomes 1 and 2, usually located at the ends of the chromosomes, except in Falconiformes and Psittaciformes. The Galloanserae cluster diverged from the rest of avian groups by having cath1 in the Galliformes and a putative pseudogene of cathB1 in Anseriformes. In contrast, the remaining avian species displayed a predominantly cathelicidin cluster comprising cathB1, cath3, and cath2. However, Passeriformes lacked cath3 while Falconiformes exhibited the pseudogenisation of cath3. In addition, we found kelch like family member 18 and transforming growth factor beta 4 (zinc finger protein 777 in Passeriformes) as flanking genes. We identified 190 putative cathelicidins genes, of which 103 were undescribed, that displayed a high percentage of identity across cathelicidin type. Phylogenetic analysis revealed that cathelicidin genes are highly conserved supporting the hypothesis that cathelicidins play a crucial role in avian immunity. This work highlights the use of bioinformatic tools to improve our understanding of avian cathelicidins and the evolution of this important family protein.

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.

Analysis for codon usage bias in membrane anchor of nonstructural protein 5A from BVDV

The nonstructural protein 5A (NS5A) of the bovine viral diarrhea virus (BVDV) is a monotopic membrane protein. This protein can anchor to the cell membrane by an in-plane amphipathic ⍺-helix, which participates in the viral replication complex. In this study, the effects of synonymous codon usage pattern of NS5A and the overall transfer RNA (tRNA) abundance in cells on the formation of the in-plane membrane anchor of NS5A were analyzed, based on NS5A coding sequences of different BVDV genotypes. BVDV NS5A coding sequences represent the most potential for BVDV genotyping. Moreover, the nucleotide usage of BVDV NS5A dominates the genotype-specific pattern of synonymous codon usage. There is an obvious relationship between synonymous codon usage bias and the spatial conformation of the in-plane membrane anchor. Furthermore, the overall tRNA abundance profiling displays that codon positions with a high level of tRNA abundance are more than ones with a low level of tRNA abundance in the in-plane membrane anchor, implying that high translation speed probably acts on the spatial conformation of in-plane membrane anchor of BVDV NS5A. These results give a new opinion on the effect of codon usage bias in the formation of the in-plane membrane anchor of BVDV NS5A.

Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino acid choice of microbial communities at the habitat level is not clearly understood. Therefore, in this study, we analyzed codon and amino acid usage patterns of a large number of environmental samples collected from diverse ecological niches. Our results suggested that samples derived from similar environmental niches, in general, show overall similar codon and amino acid distribution as compared to samples from other habitats. To substantiate the relative impact of the environment, we considered several factors, such as their similarity in GC content, or in functional or taxonomic abundance. Our analysis demonstrated that none of these factors can fully explain the trends that we observed at the codon or amino acid level implying a direct environmental influence on them. Further, our analysis demonstrated different levels of selection on codon bias in different microbial communities with the highest bias in host-associated environments such as the digestive system or oral samples and the lowest level of selection in soil and water samples. Considering a large number of metagenomic samples here we showed that microorganisms collected from similar environmental backgrounds exhibit similar patterns of codon and amino acid usage irrespective of the location or time from where the samples were collected. Thus our study suggested a direct impact of the environment on codon and amino usage of microorganisms that cannot be explained considering the influence of other factors.

An Analysis of Algebraic Codes over Lattice Valued Intuitionistic Fuzzy Type-3 R -Submodules

In the last few decades, the algebraic coding theory found widespread applications in various disciplines due to its rich fascinating mathematical structure. Linear codes, the basic codes in coding theory, are significant in data transmission. In this article, the authors' aim is to enlighten the reader about the role of linear codes in a fuzzy environment. Thus, the reader will be aware of linear codes over lattice valued intuitionistic fuzzy type-3 (LIF-3) R-submodule and α-intuitionistic fuzzy (α-IF) submodule. The proof that the level set of LIF-3 is contained in the level set of α-IF is given, and it is exclusively employed to define linear codes over α-IF submodule. Further, α-IF cyclic codes are presented along with their fundamental properties. Finally, an application based on genetic code is presented, and it is found that the technique of defining codes over α-IF submodule is entirely applicable in this scenario. More specifically, a mapping from the ℤ₆₄ module to a lattice L (comprising 64 codons) is considered, and α-IF codes are defined along with the respective degrees.

Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.

A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell

The genetic code sets the correspondence between the sequence of a given nucleotide triplet in an mRNA molecule, called a codon, and the amino acid that is added to the growing polypeptide chain during protein synthesis. With four bases (A, G, U, and C), there are 64 possible triplet codons: 61 sense codons (encoding amino acids) and 3 nonsense codons (so-called, stop codons that define termination of translation). In most organisms, there are 20 common/standard amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids (with the exception of Met and Trp) are being encoded by more than one (synonymous) codon. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in mRNA suggested that the specific codon choice might have functional implications beyond coding for amino acid. Observation of nonequivalent use of codons in mRNAs implied a possibility of the existence of auxiliary information in the genetic code. Indeed, it has been found that genetic code contains several layers of such additional information and that synonymous codons are strategically placed within mRNAs to ensure a particular translation kinetics facilitating and fine-tuning co-translational protein folding in the cell via step-wise/sequential structuring of distinct regions of the polypeptide chain emerging from the ribosome at different points in time. This review summarizes key findings in the field that have identified the role of synonymous codons and their usage in protein folding in the cell.

Tailored biosynthesis of gibberellin plant hormones in yeast

The application of small amounts of natural plant growth hormones, such as gibberellins (GAs), can increase the productivity and quality of many vegetable and fruit crops. However, gibberellin growth hormones usage is limited by the high cost of their production, which is currently based on fermentation of a natural fungal producer Fusarium fujikuroi that produces a mix of several GAs. We explored the potential of the oleaginous yeast Yarrowia lipolytica to produce specific profiles of GAs. Firstly, the production of the GA-precursor ent-kaurenoic acid (KA) at 3.75 mg/L was achieved by expression of biosynthetic enzymes from the plant Arabidopsis thaliana and upregulation of the mevalonate (MVA) pathway.

We then built a GA₄-producing strain by extending the GA-biosynthetic pathway and upregulating the MVA-pathway further, resulting in 17.29 mg/L GA₄. Additional expression of the F. fujikoroi GA-biosynthetic enzymes resulted in the production of GA₇ (trace amounts) and GA₃ (2.93 mg/L). Lastly, through protein engineering and the expression of additional KA-biosynthetic genes, we increased the GA₃-production 4.4-fold resulting in 12.81 mg/L. The developed system presents a promising resource for the recombinant production of specific gibberellins, identifying bottlenecks in GA biosynthesis, and discovering new GA biosynthetic genes.

Classification

Biological Sciences, Applied Biological Sciences.

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A complete biosynthetic pathway towards gibberellins was reconstructed in a microbial host

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The pathway towards ent-kaurenoic acid consisted of Arabidopsis thaliana enzymes

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The pathway from ent-kaurenoic acid to gibberellins GA₃, GA₄ and GA₇ consisted of Fusarium fujikuroi enzymes

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Y. lipolytica expressed 14 heterologous genes for gibberellins biosynthesis and had 5 genome edits for improved mevalonate flux

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The strains produced up to 12 mg/L of GA₃ and up to 17 mg/L GA₄ in small-scale cultivations

A code within the genetic code: codon usage regulates co-translational protein folding

The genetic code is degenerate, and most amino acids are encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons, is a universal feature of all genomes examined. Synonymous codon mutations were previously thought to be silent; however, a growing body evidence now shows that codon usage regulates protein structure and gene expression through effects on co-translational protein folding, translation efficiency and accuracy, mRNA stability, and transcription. Codon usage regulates the speed of translation elongation, resulting in non-uniform ribosome decoding rates on mRNAs during translation that is adapted to co-translational protein folding process. Biochemical and genetic evidence demonstrate that codon usage plays an important role in regulating protein folding and function in both prokaryotic and eukaryotic organisms. Certain protein structural types are more sensitive than others to the effects of codon usage on protein folding, and predicted intrinsically disordered domains are more prone to misfolding caused by codon usage changes than other domain types. Bioinformatic analyses revealed that gene codon usage correlates with different protein structures in diverse organisms, indicating the existence of a codon usage code for co-translational protein folding. This review focuses on recent literature on the role and mechanism of codon usage in regulating translation kinetics and co-translational protein folding.