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leuA-Halobacteria motif RNAs likely function as cis-regulatory elements, in view of their positions upstream of protein-coding genes. Specifically they are upstream of genes encoding 2-isopropylmalate synthase and related genes, which participate in the synthesis of branched-chain amino acids.
In bacteria, genes related to leucine are known to be regulated either by a short open reading frame known as the Leucine operon leader, or by T-boxes. In the leucine operon leader, a short ORF upstream of the regulated gene contains many leucine codons. When leucine levels are low, ribosomal stalling during the translation of these codons leads to a changed secondary structure that modifies gene expression. T-boxes measure cellular concentrations of leucine (or other amino acids) by binding uncharged leucine-tRNAs; low levels of leucine results in few tRNAs that are charged with leucine adducts. However, no specific evidence exists to suggest that leuA-Halobacteria motif RNAs function using these mechanisms. In addition, as of 2018, no mechanism is known for the regulation of leucine biosynthesis genes in archaea.
Consensus secondary structure and sequence conservation of leuA-Halobacteria RNA