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

Abstract

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 (ΔG bind ) 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 ΔG bind . 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 ΔG bind . Besides, the number of water molecules surrounding TPP influenced the ΔG bind considerably. Notably, our ΔG bind estimation agreed with previous experimental data, reinforcing the relationship between sequence conservation and TPP interaction.

Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy

“…[238] The TPP riboswitch is present in fungi and plays a role in the generation and regulation of methionine derivatives in such organisms. Vargas-Junior et al [239] used a computer technique to investigate the structural and dynamic properties of the TPP riboswitch in fungi in order to provide medicinal and biotechnological avenues for addressing the problem of fungal antibiotic resistance.…”

“…In 2007, a regulatory mechanism for the TPP riboswitch in higher plants was proposed by Bocobza et al., indicating that the TPP riboswitch is controlled in the thiamin biosynthesis pathway by variable splicing in the 3”UTR region. [ 70 ] Recent studies have identified the presence of novel TPP riboswitches in various species, including Lactobacillus , [ 71 ] diatoms, [ 72 ] and Aspergillus niger , [ 73 ] which are all widely employed in food production, classification of intestinal bacteria, and the development of antimicrobial drugs.…”

“…Vargas‐Junior et al. [ 239 ] used a computer technique to investigate the structural and dynamic properties of the TPP riboswitch in fungi in order to provide medicinal and biotechnological avenues for addressing the problem of fungal antibiotic resistance.…”

Key players in regulatory RNA realm of bacteria

“…To date, six riboswitch classes have been identified that sense the levels of coenzyme S -adenosylhomocysteine (SAH) and/or S -adenosylmethionine SAM [ [122] , [123] , [124] ]. In addition to SAM riboswitches, several other riboswitch classes have also been identified as sensors for RNA-derived coenzymes such as Thiamin pyrophosphate (TPP) [ 125 ], flavin mononucleotide (FMN), adenosylcobalamin (AdoCbl), and tetrahydrofolate (THF) [ 119 , 121 , 123 , 126 ]. Members of THF riboswitch class were termed as “folE motif” RNAs.…”