Comprehensive profiling of codon usage signatures and codon context variations in the genus Ustilago

Codon usage bias of secretory protein in Fusarium oxysporum f. sp. cubense tropical race 4

Banana Fusarium oxysporum f. sp. cubense tropical race 4 (Foc-TR4) is a highly destructive pathogen that infects nearly all major banana cultivars and has a tendency to spread further. Secreted proteins play a crucial role in the process of Fusarium wilt infection in bananas. In this study, we analyzed the codon usage bias (CUB) of the Foc-TR4 classical secretory protein genome for the first time and observed a strong bias toward codons ending with C. We found that 572 out of the 14,543 amino acid sequences in the Foc-TR4 genome exhibited characteristics of classical secretory proteins. The CUB was largely influenced by selection optimization pressure, as indicated by the ENC value and neutral plot analysis. Among the identified codons, such as UCC and CCC, 11 were found to be optimal for Foc-TR4 gene expression. Codons with higher GC content and a C base in the third position showed greater selectivity. The CUB in the secretory proteins encoded by Foc-TR4 provides insights into their evolutionary patterns, contributing to the development and screening of novel and effective antifungal drugs.

Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi

Zinc binuclear cluster proteins (ZBC; Zn(II)₂Cys₆) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host-pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)₂Cys₆ coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)₂Cys₆ genes. The perseverance of GC-rich codons of Zn(II)₂Cys₆ in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host-pathogen interactions through genome editing and functional genomics tools.

Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses

Background

Hepatitis E virus (HEV) is a member of the family Hepeviridae and causes acute HEV infections resulting in thousands of deaths worldwide. The zoonotic nature of HEV in addition to its tendency from human to human transmission has led scientists across the globe to work on its different aspects. HEV also accounts for about 30% mortality rates in case of pregnant women. The genome of HEV is organized into three open reading frames (ORFs): ORF1 ORF2 and ORF3. A reading frame encoded protein ORF4 has recently been discovered which is exclusive to GT 1 isolates of HEV. The ORF4 is suggested to play crucial role in pregnancy-associated pathology and enhanced replication. Though studies have documented the ORF4’s importance, the genetic features of ORF4 protein genes in terms of compositional patterns have not been elucidated. As codon usage performs critical role in establishment of the host–pathogen relationship, therefore, the present study reports the codon usage analysis (based on nucleotide sequences of HEV ORF4 available in the public database) in three hosts along with the factors influencing the codon usage patterns of the protein genes of ORF4 of HEV.

Results

The nucleotide composition analysis indicated that ORF4 protein genes showed overrepresentation of C nucleotide and while A nucleotide was the least-represented, with random distribution of G and T(U) nucleotides. The relative synonymous codon usage (RSCU) analysis revealed biasness toward C/G-ended codons (over U/A) in all three natural HEV-hosts (human, rat and ferret). It was observed that all the ORF4 genes were richly endowed with GC content. Further, our results showed the occurrence of both coincidence and antagonistic codon usage patterns among HEV-hosts. The findings further emphasized that both mutational and selection forces influenced the codon usage patterns of ORF4 protein genes.

Conclusions

To the best of our knowledge, this is first bioinformatics study evaluating codon usage patterns in HEV ORF4 protein genes. The findings from this study are expected to increase our understanding toward significant factors involved in evolutionary changes of ORF4.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43088-022-00244-w.

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata

Meloidogyne incognita (Root-knot nematode) and Alternaria alternata (fungus) were among the dominant parasites of the medicinal plant Withania somnifera. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation is lacking. The present study elucidates evolutionary and codon usage bias analysis of W. somnifera (host plant), M. incognita (root-knot nematode) and A. alternata (fungal parasite). The results of the present study revealed a weak codon usage bias prevalent in all the three organisms. Based on the nucleotide analysis, genome of W. somnifera and M. incognita was found to be A-T biased while A. alternata had GC biased genome. We found high similarity of CUB pattern between host and its nematode pathogen as compared to the fungal pathogen. Inclusively, both the evolutionary forces influenced the CUB in host and its associated pathogens. However, neutrality plot indicated the pervasiveness of natural selection on CUB of the host and its pathogens. Correspondence analysis revealed the dominant effect of mutation on CUB of W. somnifera and M. incognita while natural selection was the main force affecting CUB of A. alternata. Taken together the present study would provide some prolific insight into the role of codon usage bias in the adaptability of pathogens to the host’s environment for establishing parasitic relationship.

Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens

Codon usage bias influences the genetic features prevalent in genomes of all the organisms. It also plays a crucial role in establishing the host-pathogen relationship. The present study elucidates the role of codon usage pattern regarding the predilection of fungal pathogens Aspergillus flavus, Aspergillus niger, Fusarium oxysporum and Colletotrichum gloeosporioides towards host plant Zingiber officinale. We found a similar trend of codon usage pattern operative in plant and fungal pathogens. This concurrence might be attributed for the colonization of fungal pathogens in Z. officinale. The transcriptome of both plant and pathogens showed bias towards GC-ending codons. Natural selection and mutational pressure seem to be accountable for shaping the codon usage pattern of host and pathogen. We also identified some distinctive preferred codons in A. flavus, F. oxysporum and Z. officinale that could be regarded as signature codons for the identification of these organisms. Knowledge of favored, avoided and unique codons will help to devise strategies for reducing spice losses due to fungal pathogens.

Evaluation of multi-color genetically encoded Ca2+ indicators in filamentous fungi

Genetically encoded Ca²⁺ indicators (GECIs) enable long-term monitoring of cellular and subcellular dynamics of this second messenger in response to environmental and developmental cues without relying on exogenous dyes. Continued development and optimization in GECIs, combined with advances in gene manipulation, offer new opportunities for investigating the mechanism of Ca²⁺ signaling in fungi, ranging from documenting Ca²⁺ signatures under diverse conditions and genetic backgrounds to evaluating how changes in Ca²⁺ signature impact calcium-binding proteins and subsequent cellular changes. Here, we attempted to express multi-color (green, yellow, blue, cyan, and red) circularly permuted fluorescent protein (FP)-based Ca²⁺ indicators driven by multiple fungal promoters in Fusarium oxysporum, F. graminearum, and Neurospora crassa. Several variants were successfully expressed, with GCaMP5G driven by the Magnaporthe oryzae ribosomal protein 27 and F. verticillioides elongation factor-1α gene promoters being optimal for F. graminearum and F. oxysporum, respectively. Transformants expressing GCaMP5G were compared with those expressing YC3.60, a ratiometric Cameleon Ca²⁺ indicator. Wild-type and three Ca²⁺ signaling mutants of F. graminearum expressing GCaMP5G exhibited improved signal-to-noise and increased temporal and spatial resolution and are also more amenable to studies involving multiple FPs compared to strains expressing YC3.60.

Codon usage signatures in the genus Cryptococcus: A complex interplay of gene expression, translational selection and compositional bias

The fungal genus Cryptococcus comprises of several diverse species. The pathogens forming Cryptococcus neoformans/ Cryptococcus gatti species complex are of immense clinical significance owing to the high frequency of infections and deaths globally. Three closely related non-pathogenic species namely, Cryptococcus amylolentus, Cryptococcus wingfieldii and Cryptococcus depauperatus are the non-pathogenic ancestral species from which pathogenic lineages have diverged. In the current study, a comprehensive analysis of factors influencing the codon and amino acid usage bias in six pathogenic and three non-pathogenic species was performed. Our results revealed that though compositional bias played a crucial role, translational selection and gene expression were the key determinants of codon usage variations. Analysis of relative dinucleotide abundance and codon context signatures revealed strict avoidance of TpA dinucleotide across genomes. Multivariate statistical analysis based on codon usage data resulted in discrete clustering of pathogens and non-pathogens which correlated with previous reports on their phylogenetic distribution.