Background:
Riboswitches are structured elements that usually reside in the noncoding
regions of mRNAs, with which various ligands bind to control a wide variety of downstream gene
expressions. To date, more than twenty different classes of riboswitches have been characterized to
sense various metabolites, including purines and their derivatives, coenzymes, amino acids, and metal
ions, etc.
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Objective: This study aims to study the genome-wide analysis of the distribution of riboswitches and
function analyses of the corresponding downstream genes in prokaryotes.
Results:
In this study, we have completed a genome context analysis of 27 riboswitches to elucidate
their metabolic capacities of riboswitch-mediated gene regulation from the completely-sequenced 3,079
prokaryotic genomes. Furthermore, Cluster of Orthologous Groups of proteins (COG) annotation was
applied to predict and classify the possible functions of corresponding downstream genes of these
riboswitches. We found that they could all be successfully annotated and grouped into 20 different COG
functional categories, in which the two main clusters "coenzyme metabolism [H]" and "amino acid
transport and metabolism [E]" were the most significantly enriched.
Conclusion:
Riboswitches are found to be widespread in bacteria, among which three main classes of
TPP-, cobalamin- and SAM-riboswitch were the most widely distributed. We found a wide variety of
functions were associated with the corresponding downstream genes, suggesting that a wide extend of
regulatory roles were mediated by these riboswitches in prokaryotes.