Roadmap to the study of gene and protein phylogeny and evolution-A practical guide

Characterization and organization of telomeric-linked helicase (tlh) gene families in Fusarium oxysporum

Telomere-linked RecQ helicase (tlh) genes have been reported in several fungi and a choanoflagellate in the regions adjacent to the terminal telomere repeats. In this study, we explored the Telomere-linked RecQ helicase (tlh) genes in four strains of Fusarium oxysporum, offering new insights into their genomic structure, functional motifs, and impact on chromosomal ends. We conducted a comprehensive analysis, comparing the tlh genes of F. oxysporum with those previously identified in other organisms and uncovering significant similarities. Through comparative genomics, we identified conserved protein motifs across these genes, including a TLH domain, C2H2, and RecQ helicase motifs. Our phylogenetic analysis positions the F. oxysporum tlh genes in a cluster with other known tlhs, suggesting a shared evolutionary origin. Mutation analysis revealed a relatively low level of deleterious mutations in tlh gene paralogs, with a notable proportion of full-size structures maintained across strains. Analysis of subtelomeric sequences indicates that a region with almost identical sequences flanks the majority of chromosome ends, termed tlh-containing region (TLHcr), across these strains. The presence of TLHcrs at chromosome ends, either as single entities or in arrays, underscores their potential role in telomere function and genome stability. Our findings provide a detailed examination of tlh genes in four strains of F. oxysporum, laying the groundwork for future studies on their biological significance and evolutionary history in fungal genomes.

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP riboswitch sites and consequent dual posttranscriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome data sets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1.

Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept

It is demonstrated, for the first time, that a mass spectrometry approach (known as phylonumerics) can be successfully implemented for structural phylogenetics investigations to chart the evolution of a protein's structure and function. Illustrated for the compact globular protein myoglobin, peptide masses produced from the proteolytic digestion of the protein across animal species generate trees congruent to the sequence tree counterparts. Single point mutations calculated during the same mass tree building step can be followed along interconnected branches of the tree and represent a viable structural metric. A mass tree built for 15 diverse animal species, easily resolve the birds from mammal species, and the ruminant mammals from the remainder of the animals. Mutations within helix-spanning peptide segments alter both the mass and structure of the protein in these segments. Greater evolution is found in the B-helix over the A, E, F, G and H helices. A further mass tree study, of six more closely related primate species, resolves gorilla from the other primates based on a P22S mutation within the B-helix. The remaining five primates are resolved into two groups based on whether they contain a glycine or serine at position 23 in the same helix. The orangutan is resolved from the gibbon and siamang by its G-helix C110S mutation, while homo sapiens are resolved from chimpanzee based on the Q116H mutation. All are associated with structural perturbations in such helices. These structure altering mutations can be tracked along interconnecting branches of a mass tree, to follow the protein's structure and evolution, and ultimately the evolution of the species in which the proteins are expressed. Those that have the greatest impact on a protein's structure, its function, and ultimately the evolution of the species, can be selectively tracked or monitored.

Protein homeostasis imprinting across evolution

Protein homeostasis (a.k.a. proteostasis) is associated with the primary functions of life, and therefore with evolution. However, it is unclear how cellular proteostasis machines have evolved to adjust protein biogenesis needs to environmental constraints. Herein, we describe a novel computational approach, based on semantic network analysis, to evaluate proteostasis plasticity during evolution. We show that the molecular components of the proteostasis network (PN) are reliable metrics to deconvolute the life forms into Archaea, Bacteria and Eukarya and to assess the evolution rates among species. Semantic graphs were used as new criteria to evaluate PN complexity in 93 Eukarya, 250 Bacteria and 62 Archaea, thus representing a novel strategy for taxonomic classification, which provided information about species divergence. Kingdom-specific PN components were identified, suggesting that PN complexity may correlate with evolution. We found that the gains that occurred throughout PN evolution revealed a dichotomy within both the PN conserved modules and within kingdom-specific modules. Additionally, many of these components contribute to the evolutionary imprinting of other conserved mechanisms. Finally, the current study suggests a new way to exploit the genomic annotation of biomedical ontologies, deriving new knowledge from the semantic comparison of different biological systems.

Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea

Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins.