ИСТИНА

Precisely coordinated synthesis of ribosomal proteins is crucial for ribosome assembly. More than half of the ribosomal proteins in Escherichia coli are known to be controlled by distinct RNA regulatory elements situated in their own mRNA. In some cases such regulatory elements mimic the ribosomal RNA site where the regulated proteins may bind, hence providing a negative feedback from levels of ribosomal proteins. This mimicry mechanism may be effected by structurally different elements bound by orthologous proteins in distinct species. Because of that, existence of the structure potential, and not its exact form, is conserved. Hence, minimal free energy (MFE) based search tools may be more relevant than methods relying on the evolutionary conservation of RNA secondary structures. Here, we use a novel MFEbased comparative genomic approach to detect such nonhomologous RNA regulatory elements and identify new ribosomal protein binding to such structures.