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 datasets 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 post-transcriptional 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 datasets 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.

In silico investigation of riboswitches in fungi: structural and dynamical insights into TPP riboswitches in Aspergillus oryzae.

Riboswitches are RNA sensors affecting post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch plays a crucial role in regulating genes involved in synthesizing or transporting thiamine and phosphorylated derivatives in bacteria, archaea, plants, and fungi. Although TPP riboswitch is reasonably well known in bacteria, there is a gap in the knowledge of the fungal TPP riboswitches structure and dynamics, involving mainly sequence variation and TPP interaction with the aptamers. On the other hand, the increase of fungal infections and antifungal resistance raises the need for new antifungal therapies. In this work, we used computational approaches to build three-dimensional models for the three TPP riboswitches identified in Aspergillus oryzae, in which we studied their structure, dynamics, and binding free energy change (ΔGbind) with TPP. Interaction patterns between the TPP and the surrounding nucleotides were conserved among the three models, evidencing high structural conservation. Furthermore, we show that the TPP riboswitch from the A. oryzae NMT1 gene behaves similarly to the E. coli thiA gene concerning the ΔGbind. In contrast, mutations in the fungal TPP riboswitches from THI4 and the nucleoside transporter genes led to structural differences, affecting the binding-site volume, hydrogen bond occupancy, and ΔGbind. Besides, the number of water molecules surrounding TPP influenced the ΔGbind considerably. Notably, our ΔGbind estimation agreed with previous experimental data, reinforcing the relationship between sequence conservation and TPP interaction.